python-pysam →
0.15.3+ds-5 →
armhf → 2020-01-10 21:16:42
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| python-pysam 0.15.3+ds-5 (armhf) Fri, 10 Jan 2020 18:52:17 +0000 |
+==============================================================================+
Package: python-pysam
Version: 0.15.3+ds-5
Source Version: 0.15.3+ds-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-f6c866c0-22ef-4f8d-9f89-dd2c160fca07' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 27s (887 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-pysam.git
Please use:
git clone https://salsa.debian.org/med-team/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1740 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (dsc) [2561 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (tar) [1364 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.3+ds-5 (diff) [373 kB]
Fetched 1740 kB in 1s (3172 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-ZyQ2PT/python-pysam-0.15.3+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-ZyQ2PT' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-hdVePH/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-hdVePH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hdVePH/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2918 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hdVePH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12242 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
Filtered Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-hdVePH/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Sources [600 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Packages [666 B]
Fetched 2599 B in 1s (3303 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-hdVePH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install python-pysam build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libhts3 libicu63
libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2
libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev
libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support po-debconf python python-all python-all-dev
python-atomicwrites python-attr python-configparser python-contextlib2
python-dev python-funcsigs python-importlib-metadata python-minimal
python-more-itertools python-packaging python-pathlib2 python-pkg-resources
python-pluggy python-py python-pyparsing python-pytest python-scandir
python-setuptools python-six python-wcwidth python-zipp python2 python2-dev
python2-minimal python2.7 python2.7-dev python2.7-minimal python3
python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev
python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pytest
python3-setuptools python3-six python3-wcwidth python3-zipp python3.7
python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal
samtools sensible-utils tabix zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib
texlive-latex-recommended wamerican | wordlist whois vacation cython-doc
dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
python-attr-doc python-funcsigs-doc subversion python-pytest-xdist
python-pyparsing-doc python-mock python-setuptools-doc python2-doc
python2.7-doc binfmt-support python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc python3.8-venv python3.8-doc
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs javascript-common krb5-locales libgpm2
publicsuffix libltdl-dev libmail-sendmail-perl cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libhts3 libicu63
libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1
libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2
libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev
libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db mime-support po-debconf python python-all python-all-dev
python-atomicwrites python-attr python-configparser python-contextlib2
python-dev python-funcsigs python-importlib-metadata python-minimal
python-more-itertools python-packaging python-pathlib2 python-pkg-resources
python-pluggy python-py python-pyparsing python-pytest python-scandir
python-setuptools python-six python-wcwidth python-zipp python2 python2-dev
python2-minimal python2.7 python2.7-dev python2.7-minimal python3
python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev
python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal
python3-more-itertools python3-packaging python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pytest
python3-setuptools python3-six python3-wcwidth python3-zipp python3.7
python3.7-dev python3.7-minimal python3.8 python3.8-dev python3.8-minimal
samtools sbuild-build-depends-python-pysam-dummy sensible-utils tabix
zlib1g-dev
0 upgraded, 146 newly installed, 0 to remove and 0 not upgraded.
Need to get 165 MB of archives.
After this operation, 359 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hdVePH/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [956 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-1 [29.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.17-1 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.17-1 [1107 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.17-2 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.17-2 [21.1 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
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Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.17-1 [1823 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.17-1 [309 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.17-2 [20.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.17-2 [20.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.17-2 [41.7 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.17-2 [22.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1 [1527 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
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Get:33 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
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Get:35 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
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Get:45 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
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Get:48 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
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Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
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Get:55 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-2 [327 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf bcftools armhf 1.10.2-2 [520 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf cython armhf 0.29.14-0.1 [1355 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf cython3 armhf 0.29.14-0.1 [1375 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
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Get:64 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
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Get:68 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2 [25.3 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-2 [4784 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-12 [275 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 1.8.5-4 [96.7 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7 armhf 2.7.17-1 [883 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-dev armhf 2.7.17-1 [26.5 MB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libpython2-dev armhf 2.7.17-2 [21.0 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpython-dev armhf 2.7.17-2 [21.0 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libpython-all-dev armhf 2.7.17-2 [1068 B]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7 armhf 3.7.6-1 [1253 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-dev armhf 3.7.6-1 [40.2 MB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.7.5-3 [20.3 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.1-2 [1597 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8 armhf 3.8.1-2 [1361 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-dev armhf 3.8.1-2 [46.0 MB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libpython3-all-dev armhf 3.7.5-3 [1072 B]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python-all armhf 2.7.17-2 [1048 B]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python2.7-dev armhf 2.7.17-1 [284 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf python2-dev armhf 2.7.17-2 [1224 B]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf python-dev armhf 2.7.17-2 [1196 B]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf python-all-dev armhf 2.7.17-2 [1072 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf python-atomicwrites all 1.1.5-2 [6808 B]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf python-configparser all 3.5.0b2-3 [62.6 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python-contextlib2 all 0.5.5-3 [12.6 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python-funcsigs all 1.0.2-4 [13.7 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf python-six all 1.13.0-1 [16.2 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf python-scandir armhf 1.10.0-2 [17.2 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf python-pathlib2 all 2.3.5-1 [19.6 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf python-more-itertools all 4.2.0-1 [42.3 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python-zipp all 0.6.0-1 [5768 B]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python-importlib-metadata all 0.23-2 [9296 B]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf python-pyparsing all 2.4.2-1 [106 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf python-packaging all 19.1-2 [23.8 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf python-pkg-resources all 41.2.0-1 [183 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf python-pluggy all 0.13.0-2 [21.8 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf python-py all 1.8.0-1 [86.5 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf python-wcwidth all 0.1.7+dfsg1-6 [15.4 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf python-pytest all 4.6.7-1 [266 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf python-setuptools all 41.2.0-1 [384 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.1-2 [406 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf python3-all armhf 3.7.5-3 [1060 B]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf python3.7-dev armhf 3.7.6-1 [518 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.7.5-3 [1260 B]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf python3.8-dev armhf 3.8.1-2 [519 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.7.5-3 [1076 B]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf python3-atomicwrites all 1.1.5-2 [6892 B]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 18.2.0-1 [37.3 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.13.0-1 [16.2 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf python3-more-itertools all 4.2.0-1 [42.2 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf python3-zipp all 0.6.0-1 [5856 B]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf python3-importlib-metadata all 0.23-2 [9356 B]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.2-1 [106 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 19.1-2 [23.9 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.2.0-1 [154 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf python3-pluggy all 0.13.0-2 [21.9 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf python3-py all 1.8.0-1 [86.5 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf python3-wcwidth all 0.1.7+dfsg1-6 [15.5 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf python3-pytest all 4.6.7-1 [266 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 41.2.0-1 [307 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-7 [399 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf tabix armhf 1.10.2-2 [317 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.29-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 bcftools_1.10.2-2 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 cython_0.29.14-0.1 cython3_0.29.14-0.1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdeflate0_1.5-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-2 libhts2_1.9-12 libhts3_1.10.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjs-jquery_3.3.1~dfsg-3 libjs-sphinxdoc_1.8.5-4 libjs-underscore_1.9.1~dfsg-1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpsl5_0.20.2-2 libpython-all-dev_2.7.17-2 libpython-dev_2.7.17-2 libpython-stdlib_2.7.17-2 libpython2-dev_2.7.17-2 libpython2-stdlib_2.7.17-2 libpython2.7_2.7.17-1 libpython2.7-dev_2.7.17-1 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libpython3-all-dev_3.7.5-3 libpython3-dev_3.7.5-3 libpython3-stdlib_3.7.5-3 libpython3.7_3.7.6-1 libpython3.7-dev_3.7.6-1 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libpython3.8_3.8.1-2 libpython3.8-dev_3.8.1-2 libpython3.8-minimal_3.8.1-2 libpython3.8-stdlib_3.8.1-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python_2.7.17-2 python-all_2.7.17-2 python-all-dev_2.7.17-2 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-configparser_3.5.0b2-3 python-contextlib2_0.5.5-3 python-dev_2.7.17-2 python-funcsigs_1.0.2-4 python-importlib-metadata_0.23-2 python-minimal_2.7.17-2 python-more-itertools_4.2.0-1 python-packaging_19.1-2 python-pathlib2_2.3.5-1 python-pkg-resources_41.2.0-1 python-pluggy_0.13.0-2 python-py_1.8.0-1 python-pyparsing_2.4.2-1 python-pytest_4.6.7-1 python-scandir_1.10.0-2 python-setuptools_41.2.0-1 python-six_1.13.0-1 python-wcwidth_0.1.7+dfsg1-6 python-zipp_0.6.0-1 python2_2.7.17-2 python2-dev_2.7.17-2 python2-minimal_2.7.17-2 python2.7_2.7.17-1 python2.7-dev_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-3 python3-all_3.7.5-3 python3-all-dev_3.7.5-3 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.5-3 python3-distutils_3.8.0-1 python3-importlib-metadata_0.23-2 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3-more-itertools_4.2.0-1 python3-packaging_19.1-2 python3-pkg-resources_41.2.0-1 python3-pluggy_0.13.0-2 python3-py_1.8.0-1 python3-pyparsing_2.4.2-1 python3-pytest_4.6.7-1 python3-setuptools_41.2.0-1 python3-six_1.13.0-1 python3-wcwidth_0.1.7+dfsg1-6 python3-zipp_0.6.0-1 python3.7_3.7.6-1 python3.7-dev_3.7.6-1 python3.7-minimal_3.7.6-1 python3.8_3.8.1-2 python3.8-dev_3.8.1-2 python3.8-minimal_3.8.1-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.9-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tabix_1.10.2-2 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jan 6 17:28:20 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.3+ds-5.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.15.3+ds
dpkg-source: info: unpacking python-pysam_0.15.3+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.15.3+ds-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying hts1.10
dpkg-source: info: applying samtools_v1.10_full
dpkg-source: info: applying bcftools_v1.10_full
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-f6c866c0-22ef-4f8d-9f89-dd2c160fca07
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.15.3+ds-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*.bam" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "pysam_uncompressed.bam" -delete
rm -rf tests/pysam_test_work \
tests/example_htslib.gtf.gz.tbi \
tests/log.txt \
tests/test.bam \
tests/_compile_test.c \
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
pysam/cbcf.c \
tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
tests/pysam_data/ex1.fa.gz \
tests/pysam_data/ex1.fa.gz.gzi \
tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh clean --with python2,python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:217: python3.8 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.8' does not exist -- can't clean it
I: pybuild base:217: python3.7 setup.py clean
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
rm -f \
pysam/config.py \
pysam/config.h \
pysam/lib*.c \
samtools/config.h \
bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.8 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.7 setup.py config
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libchtslib.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcsamtools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbcftools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcutils.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcalignmentfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2530:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2535:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2540:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcsamfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcalignedsegment.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libctabix.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcfaidx.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcbgzf.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libctabixproxies.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam/libcvcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
creating build/temp.linux-armhf-2.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcsamtools.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/coverage.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-armhf-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘init_data’,
inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:1062:5:
bcftools/vcfcall.c.pysam.c:655:39: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
655 | args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/vcf.h:41,
from bcftools/vcfcall.c.pysam.c:34:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
| ^~~~~~
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcbcftools.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/cols.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
29326 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
| ~^~~~~~~~~~~~~~~~~~~
| |
| bam_pileup1_t ** {aka struct <anonymous> **}
In file included from pysam/htslib_util.h:4,
from pysam/libcalignmentfile.c:604:
/usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
| ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27579:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
27579 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:13704:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
13704 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14210:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
14210 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
| ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
| ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
pysam/libcbcf.c:65177:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
65177 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
pysam/libcbcf.c:64905:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
64905 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
pysam/libcbcf.c:69936:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
69936 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample’:
pysam/libcbcf.c:34751:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result]
34751 | (void)(bcf_hdr_sync(__pyx_v_self->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
pysam/libcbcf.c:34444:11: warning: ignoring return value of ‘bcf_hrec_add_key’, declared with attribute warn_unused_result [-Wunused-result]
34444 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_16, ((int)__pyx_t_17));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:34480:11: warning: ignoring return value of ‘bcf_hrec_set_val’, declared with attribute warn_unused_result [-Wunused-result]
34480 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_17), __pyx_v_quoted);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:34593:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result]
34593 | (void)(bcf_hdr_sync(__pyx_v_self->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line’:
pysam/libcbcf.c:34055:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result]
34055 | (void)(bcf_hdr_sync(__pyx_v_self->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record’:
pysam/libcbcf.c:33923:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result]
33923 | (void)(bcf_hdr_sync(__pyx_v_self->ptr));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LRS30k/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3.8 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.8
creating build/temp.linux-armhf-3.8/pysam
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-armhf-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-armhf-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libchtslib.o build/temp.linux-armhf-3.8/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.8/samtools
creating build/temp.linux-armhf-3.8/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcsamtools.o build/temp.linux-armhf-3.8/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.8/samtools/sample.c.pysam.o build/temp.linux-armhf-3.8/samtools/samtools.pysam.o build/temp.linux-armhf-3.8/samtools/bam.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.8/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.8/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.8/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.8/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.8/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.8/samtools/coverage.c.pysam.o build/temp.linux-armhf-3.8/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.8/samtools/dict.c.pysam.o build/temp.linux-armhf-3.8/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.8/samtools/padding.c.pysam.o build/temp.linux-armhf-3.8/samtools/phase.c.pysam.o build/temp.linux-armhf-3.8/samtools/sam.c.pysam.o build/temp.linux-armhf-3.8/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.8/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.8/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.8/samtools/stats.c.pysam.o build/temp.linux-armhf-3.8/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.8/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.8/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.8/bcftools
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/vcf.h:41,
from bcftools/vcfmerge.c.pysam.c:34:
/usr/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here
541 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcbcftools.o build/temp.linux-armhf-3.8/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.8/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.8/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.8/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.8/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.8/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.8/bcftools/em.c.pysam.o build/temp.linux-armhf-3.8/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.8/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.8/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.8/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.8/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.8/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.8/bcftools/cols.c.pysam.o build/temp.linux-armhf-3.8/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.8/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.8/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.8/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.8/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.8/bcftools/main.c.pysam.o build/temp.linux-armhf-3.8/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.8/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.8/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.8/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.8/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.8/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.8/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.8/bcftools/version.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcutils.c -o build/temp.linux-armhf-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
511 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
pysam/libcutils.c:5885:7: note: ‘__pyx_v_retval’ was declared here
5885 | int __pyx_v_retval;
| ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/pysam_util.c -o build/temp.linux-armhf-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcutils.o build/temp.linux-armhf-3.8/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcsamtools.cpython-38-arm-linux-gnueabihf -lcbcftools.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.8/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
29326 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
| ~^~~~~~~~~~~~~~~~~~~
| |
| bam_pileup1_t ** {aka struct <anonymous> **}
In file included from pysam/htslib_util.h:4,
from pysam/libcalignmentfile.c:604:
/usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
| ~~~~~~~~~~~~~~~~~~~~~~^~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libctabix.c -o build/temp.linux-armhf-3.8/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
| ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
| ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcbcf.c -o build/temp.linux-armhf-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.8 -c pysam/libcvcf.c -o build/temp.linux-armhf-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’:
pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.8/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-arm-linux-gnueabihf -lcutils.cpython-38-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3 setup.py build
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.7
creating build/temp.linux-armhf-3.7/pysam
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libchtslib.o build/temp.linux-armhf-3.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.7/samtools
creating build/temp.linux-armhf-3.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamtools.o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/coverage.c.pysam.o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.7/bcftools
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’:
bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/vcf.h:41,
from bcftools/vcfmerge.c.pysam.c:34:
/usr/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here
541 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcftools.o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/cols.c.pysam.o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-armhf-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
511 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
pysam/libcutils.c:5885:7: note: ‘__pyx_v_retval’ was declared here
5885 | int __pyx_v_retval;
| ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcutils.o build/temp.linux-armhf-3.7/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcsamtools.cpython-37m-arm-linux-gnueabihf -lcbcftools.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
29326 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
| ~^~~~~~~~~~~~~~~~~~~
| |
| bam_pileup1_t ** {aka struct <anonymous> **}
In file included from pysam/htslib_util.h:4,
from pysam/libcalignmentfile.c:604:
/usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
| ~~~~~~~~~~~~~~~~~~~~~~^~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-armhf-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
8643 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
| ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13709 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13741 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
| ^~~~~~~~
pysam/libctabix.c:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
| ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.3+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’:
pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view -bS with_md.sam > with_md.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS ex_spliced.sam > ex_spliced.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS test_query_position.sam > test_query_position.bam
touch tmp.list
samtools view -bt tmp.list -o example_unmapped_reads_no_sq.bam example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view -bS ex6.sam > ex6.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index example_dash_in_chr.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index example_reverse_complement.bam
samtools index ex4.bam
samtools index ex_spliced.bam
samtools index ex9_nofail.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz # create tbi index
bcftools index example_vcf40.vcf.gz # create csi index
bgzip < example_vcf43.vcf > example_vcf43.vcf.gz
tabix -p vcf example_vcf43.vcf.gz # create tbi index
bcftools index example_vcf43.vcf.gz # create csi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf gnomad_fixed.vcf.gz # create tbi index
bcftools index gnomad_fixed.vcf.gz # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz # create tbi index
bcftools index gnomad.vcf.gz # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz # create tbi index
bcftools index missing_genotypes.vcf.gz # create csi index
bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz
tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index
bcftools index example_vcf43_with_utf8.vcf.gz # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz # create tbi index
bcftools index example_vcf42.vcf.gz # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index
bcftools index example_vcf42_only_header.vcf.gz # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index example_vcf43.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf
bcftools index example_vcf43_with_utf8.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
export PYBUILD_TEST_ARGS='|| true' ; dh_auto_test
I: pybuild base:217: cd /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest || true
============================= test session starts ==============================
platform linux2 -- Python 2.7.17, pytest-4.6.7, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python2.7
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.15.3+ds, inifile: setup.cfg
collecting ... collected 933 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp___enter___GfaHIKnegative_integers.bam'
PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0vC1BV'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0vC1BV
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_VUfz1R'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_VUfz1R
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_8S6U6g
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_8Tcr_b'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_8Tcr_b
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wcBsRZ'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wcBsRZ
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_HXCFlS
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_atmpqFtmp_ex2.bam'
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_qyjCdHtmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_nAtDCGtmp_multi.bam'
PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_x1ee6Etmp_largecigar.bam'
PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
FAILED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_F2sY6w.bcf'
PASSED
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED
tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED
tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED
tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView [E::fai_load3_core] Failed to open FASTA index ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai: Network is unreachable
PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available [E::fai_load3_core] Failed to open FASTA index ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai: Network is unreachable
PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED
=================================== FAILURES ===================================
_________ TestSetTagGetTag.test_set_tag_with_automated_type_detection __________
self = <AlignedSegment_test.TestSetTagGetTag testMethod=test_set_tag_with_automated_type_detection>
def test_set_tag_with_automated_type_detection(self):
self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
self.check_tag('TT', -(1 << 7) - 1,
value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15) - 1,
value_type=None, alt_value_type="i")
> self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")
tests/AlignedSegment_test.py:1213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/AlignedSegment_test.py:1164: in check_tag
a.set_tag(tag, value, value_type=value_type)
pysam/libcalignedsegment.pyx:2226: in pysam.libcalignedsegment.AlignedSegment.set_tag
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: can't guess type or invalid type code specified: -2147483648 None
pysam/libcalignedsegment.pyx:2305: ValueError
_________ TestSetTagsGetTag.test_set_tag_with_automated_type_detection _________
self = <AlignedSegment_test.TestSetTagsGetTag testMethod=test_set_tag_with_automated_type_detection>
def test_set_tag_with_automated_type_detection(self):
self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
self.check_tag('TT', -(1 << 7) - 1,
value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
self.check_tag('TT', -(1 << 15) - 1,
value_type=None, alt_value_type="i")
> self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")
tests/AlignedSegment_test.py:1213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/AlignedSegment_test.py:1242: in check_tag
a.set_tags([(tag, value, value_type)])
pysam/libcalignedsegment.pyx:2571: in pysam.libcalignedsegment.AlignedSegment.set_tags
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E ValueError: could not deduce typecode for value -2147483648
pysam/libcalignedsegment.pyx:418: ValueError
________________________ TestIO.testEmptyWithHeaderBAM _________________________
self = <AlignmentFile_test.TestIO testMethod=testEmptyWithHeaderBAM>
def testEmptyWithHeaderBAM(self):
self.assertRaises(
ValueError,
pysam.Samfile,
os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
> "rb")
tests/AlignmentFile_test.py:802:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E IOError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: IOError
________________ TestEmptyHeader.test_bam_without_seq_in_header ________________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_in_header>
def test_bam_without_seq_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
tests/AlignmentFile_test.py:1409:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E IOError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: IOError
________ TestEmptyHeader.test_bam_without_seq_with_null_bytes_in_header ________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_with_null_bytes_in_header>
def test_bam_without_seq_with_null_bytes_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header_null_bytes.bam"))
tests/AlignmentFile_test.py:1414:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E IOError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: IOError
___________________ TestHeaderWithProgramOptions.testHeader ____________________
self = <AlignmentFile_test.TestHeaderWithProgramOptions testMethod=testHeader>
def testHeader(self):
s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
> 'rg_with_tab.bam'))
tests/AlignmentFile_test.py:1448:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E IOError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: IOError
_____________________ TestSettingRecordValues.testGenotype _____________________
self = <VariantFile_test.TestSettingRecordValues testMethod=testGenotype>
def testGenotype(self):
with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
record = next(inf)
sample = record.samples["NA00001"]
print(sample["GT"])
self.assertEqual(sample["GT"], (0, 0))
> sample["GT"] = sample["GT"]
tests/VariantFile_test.py:595:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcbcf.pyx:3455: in pysam.libcbcf.VariantRecordSample.__setitem__
???
pysam/libcbcf.pyx:859: in pysam.libcbcf.bcf_format_set_value
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: invalid value for Integer format
pysam/libcbcf.pyx:592: TypeError
=============================== warnings summary ===============================
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1472: UserWarning: no BGZF EOF marker; file may be truncated
ignore_truncation=True)
-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 7 failed, 909 passed, 17 skipped, 2 warnings in 480.69 seconds ========
I: pybuild base:217: cd /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build; python3.8 -m pytest || true
============================= test session starts ==============================
platform linux -- Python 3.8.1, pytest-4.6.7, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python3.8
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.15.3+ds, inifile: setup.cfg
collecting ... collected 937 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp___enter___gctpdtlqnegative_integers.bam'
PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_kus21n1_'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_kus21n1_
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mq4k3ne6'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mq4k3ne6
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_684t60z6
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_l0hsak14'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_l0hsak14
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_90_s4ph4'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_90_s4ph4
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e53mbrio
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_ex1tbo7qtmp_ex2.bam'
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_f_z0wvfvtmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_pdd_zehftmp_multi.bam'
PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_z59cvs0gtmp_largecigar.bam'
PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_um_qua4y.bcf'
PASSED
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED
tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED
tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED
tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestUnicode::testFromTabix PASSED
tests/tabix_test.py::TestUnicode::testFromVCF PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED
=================================== FAILURES ===================================
________________________ TestIO.testEmptyWithHeaderBAM _________________________
self = <AlignmentFile_test.TestIO testMethod=testEmptyWithHeaderBAM>
def testEmptyWithHeaderBAM(self):
> self.assertRaises(
ValueError,
pysam.Samfile,
os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
"rb")
tests/AlignmentFile_test.py:798:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
________________ TestEmptyHeader.test_bam_without_seq_in_header ________________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_in_header>
def test_bam_without_seq_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
tests/AlignmentFile_test.py:1409:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
________ TestEmptyHeader.test_bam_without_seq_with_null_bytes_in_header ________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_with_null_bytes_in_header>
def test_bam_without_seq_with_null_bytes_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header_null_bytes.bam"))
tests/AlignmentFile_test.py:1414:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
___________________ TestHeaderWithProgramOptions.testHeader ____________________
self = <AlignmentFile_test.TestHeaderWithProgramOptions testMethod=testHeader>
def testHeader(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
'rg_with_tab.bam'))
tests/AlignmentFile_test.py:1447:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/_compile_test.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py:1471: UserWarning: no BGZF EOF marker; file may be truncated
s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'),
-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 4 failed, 923 passed, 10 skipped, 2 warnings in 470.43 seconds ========
I: pybuild base:217: cd /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build; python3.7 -m pytest || true
============================= test session starts ==============================
platform linux -- Python 3.7.6, pytest-4.6.7, py-1.8.0, pluggy-0.13.0 -- /usr/bin/python3.7
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.15.3+ds, inifile: setup.cfg
collecting ... collected 937 items
tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp___enter___2icti45wnegative_integers.bam'
PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_qs7pp90r'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_qs7pp90r
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ndgdhds0'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ndgdhds0
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_k46y5s67
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_auzgdktk'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_auzgdktk
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_brlks_9m'
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_brlks_9m
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0efuy05z
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex__dk9l4m9tmp_ex2.bam'
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_x2ntoo46tmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_2wo6m8qstmp_multi.bam'
PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory
[E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_ji0rguwutmp_largecigar.bam'
PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_69bxv7f0.bcf'
PASSED
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED
tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED
tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED
tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestUnicode::testFromTabix PASSED
tests/tabix_test.py::TestUnicode::testFromVCF PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED
=================================== FAILURES ===================================
________________________ TestIO.testEmptyWithHeaderBAM _________________________
self = <AlignmentFile_test.TestIO testMethod=testEmptyWithHeaderBAM>
def testEmptyWithHeaderBAM(self):
self.assertRaises(
ValueError,
pysam.Samfile,
os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
> "rb")
tests/AlignmentFile_test.py:802:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
________________ TestEmptyHeader.test_bam_without_seq_in_header ________________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_in_header>
def test_bam_without_seq_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
tests/AlignmentFile_test.py:1409:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
________ TestEmptyHeader.test_bam_without_seq_with_null_bytes_in_header ________
self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_with_null_bytes_in_header>
def test_bam_without_seq_with_null_bytes_in_header(self):
> s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header_null_bytes.bam"))
tests/AlignmentFile_test.py:1414:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
___________________ TestHeaderWithProgramOptions.testHeader ____________________
self = <AlignmentFile_test.TestHeaderWithProgramOptions testMethod=testHeader>
def testHeader(self):
s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
> 'rg_with_tab.bam'))
tests/AlignmentFile_test.py:1448:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory
pysam/libcalignmentfile.pyx:940: FileNotFoundError
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/_compile_test.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
/<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py:1472: UserWarning: no BGZF EOF marker; file may be truncated
ignore_truncation=True)
-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 4 failed, 923 passed, 10 skipped, 2 warnings in 470.09 seconds ========
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python2,python3 --buildsystem=pybuild
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py install --root /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython2_2.7_pysam/build/log.txt -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc
running install_egg_info
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/os/*.c'
warning: no files found matching 'htslib/os/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.15.3.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:217: /usr/bin/python3.8 setup.py install --root /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/__init__.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/utils.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/Pileup.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/samtools.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/config.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/version.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/bcftools.cpython-38.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.8_pysam/build/log.txt -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/Pileup.py to Pileup.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__init__.py to __init__.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/bcftools.py to bcftools.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/samtools.py to samtools.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/utils.py to utils.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/version.py to version.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/__init__.py to __init__.cpython-38.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/config.py to config.cpython-38.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/os/*.c'
warning: no files found matching 'htslib/os/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam-0.15.3.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:217: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/__init__.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/utils.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/Pileup.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/samtools.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/config.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/version.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/bcftools.cpython-37.pyc -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.3+ds/.pybuild/cpython3_3.7_pysam/build/log.txt -> /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/Pileup.py to Pileup.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__init__.py to __init__.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/bcftools.py to bcftools.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/samtools.py to samtools.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/utils.py to utils.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/version.py to version.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/__init__.py to __init__.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/config.py to config.cpython-37.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/os/*.c'
warning: no files found matching 'htslib/os/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.15.3+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam-0.15.3.egg-info
Skipping SOURCES.txt
running install_scripts
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
cd tests/pysam_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*.bam" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "pysam_uncompressed.bam" -delete
rm -rf tests/pysam_test_work \
tests/example_htslib.gtf.gz.tbi \
tests/log.txt \
tests/test.bam \
tests/_compile_test.c \
tests/pysam_ex2.sam \
tests/__pycache__ \
pysam/calignmentfile.c \
pysam/cbcf.c \
tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
tests/pysam_data/ex1.fa.gz \
tests/pysam_data/ex1.fa.gz.gzi \
tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh_install -Xtest.gtf.gz
find debian -name log.txt -delete
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.3+ds'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:343: renaming libcalignedsegment.so to libcalignedsegment.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcalignmentfile.so to libcalignmentfile.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcbcf.so to libcbcf.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcbcftools.so to libcbcftools.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcbgzf.so to libcbgzf.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcfaidx.so to libcfaidx.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libchtslib.so to libchtslib.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcsamfile.so to libcsamfile.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcsamtools.so to libcsamtools.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libctabix.so to libctabix.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libctabixproxies.so to libctabixproxies.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcutils.so to libcutils.arm-linux-gnueabihf.so
I: dh_python2 fs:343: renaming libcvcf.so to libcvcf.arm-linux-gnueabihf.so
dh_python3 -a -O--buildsystem=pybuild
dh_installinit -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_lintian -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.15.3+ds-5_armhf.deb'.
dpkg-deb: building package 'python-pysam' in '../python-pysam_0.15.3+ds-5_armhf.deb'.
dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.15.3+ds-5_armhf.deb'.
dpkg-deb: building package 'python-pysam-dbgsym' in '../python-pysam-dbgsym_0.15.3+ds-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pysam_0.15.3+ds-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-01-10T21:16:17Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
python-pysam_0.15.3+ds-5_armhf.changes:
---------------------------------------
Format: 1.8
Date: Mon, 06 Jan 2020 17:44:23 +0100
Source: python-pysam
Binary: python-pysam python-pysam-dbgsym python3-pysam python3-pysam-dbgsym
Architecture: armhf
Version: 0.15.3+ds-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
python-pysam - interface for the SAM/BAM sequence alignment and mapping format (
python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Closes: 948280
Changes:
python-pysam (0.15.3+ds-5) unstable; urgency=medium
.
[ Chris Lamb ]
* make the build reproducible
Closes: #948280
.
[ Andreas Tille ]
* Standards-Version: 4.4.1
* debian/copyright: use spaces rather than tabs to start continuation
lines.
* Set upstream metadata fields: Bug-Database, Repository, Repository-
Browse.
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python-pysam-dbgsym_0.15.3+ds-5_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 5935464 bytes: control archive=1200 bytes.
891 bytes, 12 lines control
1470 bytes, 14 lines md5sums
Package: python-pysam-dbgsym
Source: python-pysam
Version: 0.15.3+ds-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6491
Depends: python-pysam (= 0.15.3+ds-5)
Section: debug
Priority: optional
Description: debug symbols for python-pysam
Build-Ids: 16c77d038f86b6dba827eb42122b169c9c1ff908 22f96e9ec0fd3733c68a7399161b5af220f24de0 29f9bb2f1041a426e8581748cdb2e95e9a89fb3d 413fa67eac62b6ebaa16567ba1333acdeefaa55b 4b79483da7c96e7912d2fb6ad73638cca140f0c6 5fe18242e885dd1354a94148ba10fabe99901524 6ee21eead25ca0c2dfd610eaf201ed9240a45be5 9c5d48da0e7a68b75d270eabb6beb3be6db169a4 ba351194b8e2f5d88760d402f781f0f3dc674630 c7957a5fc34a72dc0302d55ee24c4294e95cf9c3 e11d60637673bc1471cea334fec52fe42f199b1e f81ef821c1e3897c9ec8929c681ab58fe1a15e6f fe6f982e98c44b3fdcb5cdbb608a60f95883a1b5
drwxr-xr-x root/root 0 2020-01-06 16:44 ./
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/16/
-rw-r--r-- root/root 680292 2020-01-06 16:44 ./usr/lib/debug/.build-id/16/c77d038f86b6dba827eb42122b169c9c1ff908.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 1038784 2020-01-06 16:44 ./usr/lib/debug/.build-id/22/f96e9ec0fd3733c68a7399161b5af220f24de0.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/29/
-rw-r--r-- root/root 653960 2020-01-06 16:44 ./usr/lib/debug/.build-id/29/f9bb2f1041a426e8581748cdb2e95e9a89fb3d.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/41/
-rw-r--r-- root/root 701036 2020-01-06 16:44 ./usr/lib/debug/.build-id/41/3fa67eac62b6ebaa16567ba1333acdeefaa55b.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/4b/
-rw-r--r-- root/root 160544 2020-01-06 16:44 ./usr/lib/debug/.build-id/4b/79483da7c96e7912d2fb6ad73638cca140f0c6.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root 88556 2020-01-06 16:44 ./usr/lib/debug/.build-id/5f/e18242e885dd1354a94148ba10fabe99901524.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 350976 2020-01-06 16:44 ./usr/lib/debug/.build-id/6e/e21eead25ca0c2dfd610eaf201ed9240a45be5.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 1189040 2020-01-06 16:44 ./usr/lib/debug/.build-id/9c/5d48da0e7a68b75d270eabb6beb3be6db169a4.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/ba/
-rw-r--r-- root/root 314020 2020-01-06 16:44 ./usr/lib/debug/.build-id/ba/351194b8e2f5d88760d402f781f0f3dc674630.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/c7/
-rw-r--r-- root/root 254056 2020-01-06 16:44 ./usr/lib/debug/.build-id/c7/957a5fc34a72dc0302d55ee24c4294e95cf9c3.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 203848 2020-01-06 16:44 ./usr/lib/debug/.build-id/e1/1d60637673bc1471cea334fec52fe42f199b1e.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/f8/
-rw-r--r-- root/root 35580 2020-01-06 16:44 ./usr/lib/debug/.build-id/f8/1ef821c1e3897c9ec8929c681ab58fe1a15e6f.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.build-id/fe/
-rw-r--r-- root/root 909692 2020-01-06 16:44 ./usr/lib/debug/.build-id/fe/6f982e98c44b3fdcb5cdbb608a60f95883a1b5.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 33852 2020-01-06 16:44 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python-pysam.debug
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/share/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-01-06 16:44 ./usr/share/doc/python-pysam-dbgsym -> python-pysam
python-pysam_0.15.3+ds-5_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 1547704 bytes: control archive=3216 bytes.
726 bytes, 16 lines control
8445 bytes, 88 lines md5sums
162 bytes, 9 lines * postinst #!/bin/sh
263 bytes, 14 lines * prerm #!/bin/sh
Package: python-pysam
Version: 0.15.3+ds-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5836
Depends: libc6 (>= 2.7), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), python2 (<< 2.8), python2 (>= 2.7~), python2:any (<< 2.8), python2:any (>= 2.7~)
Provides: python2.7-pysam
Section: python
Priority: optional
Homepage: https://pysam.readthedocs.org/en/latest
Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
Pysam is a Python module for reading and manipulating Samfiles. It's a
lightweight wrapper of the samtools C-API. Pysam also includes an interface
for tabix.
.
This package installs the module for Python 2.
drwxr-xr-x root/root 0 2020-01-06 16:44 ./
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2020-01-06 16:44 ./usr/lib/python2.7/dist-packages/pysam-0.15.3.egg-info/
-rw-r--r-- root/root 1502 2020-01-06 16:44 ./usr/lib/python2.7/dist-packages/pysam-0.15.3.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2020-01-06 16:44 ./usr/lib/python2.7/dist-packages/pysam-0.15.3.egg-info/dependency_links.txt
-rw-r--r-- root/root 1 2020-01-06 16:44 ./usr/lib/python2.7/dist-packages/pysam-0.15.3.egg-info/not-zip-safe
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python3-pysam-dbgsym_0.15.3+ds-5_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 14361708 bytes: control archive=1800 bytes.
1428 bytes, 12 lines control
2849 bytes, 27 lines md5sums
Package: python3-pysam-dbgsym
Source: python-pysam
Version: 0.15.3+ds-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15528
Depends: python3-pysam (= 0.15.3+ds-5)
Section: debug
Priority: optional
Description: debug symbols for python3-pysam
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python3-pysam_0.15.3+ds-5_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 2358256 bytes: control archive=3592 bytes.
691 bytes, 16 lines control
9944 bytes, 101 lines md5sums
252 bytes, 12 lines * postinst #!/bin/sh
401 bytes, 12 lines * prerm #!/bin/sh
Package: python3-pysam
Source: python-pysam
Version: 0.15.3+ds-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 11184
Depends: libc6 (>= 2.7), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), python3 (<< 3.9), python3 (>= 3.7~), python3:any
Section: python
Priority: optional
Homepage: https://pysam.readthedocs.org/en/latest
Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Pysam is a Python module for reading and manipulating Samfiles. It's a
lightweight wrapper of the samtools C-API. Pysam also includes an interface
for tabix.
.
This package installs the module for Python 3.
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 311524
Build-Time: 7452
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1132
Job: python-pysam_0.15.3+ds-5
Machine Architecture: armhf
Package: python-pysam
Package-Time: 8640
Source-Version: 0.15.3+ds-5
Space: 311524
Status: successful
Version: 0.15.3+ds-5
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Finished at 2020-01-10T21:16:17Z
Build needed 02:24:00, 311524k disc space