python-pysam →
0.17.0+ds-2 →
armhf → 2021-10-17 07:17:12
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| python-pysam 0.17.0+ds-2 (armhf) Sun, 17 Oct 2021 06:21:36 +0000 |
+==============================================================================+
Package: python-pysam
Version: 0.17.0+ds-2
Source Version: 0.17.0+ds-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-3a197beb-74cf-4f84-8748-b156ed063506' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 26s (981 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 1807 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main python-pysam 0.17.0+ds-2 (dsc) [2425 B]
Get:2 http://172.17.0.1/private bookworm-staging/main python-pysam 0.17.0+ds-2 (tar) [1430 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main python-pysam 0.17.0+ds-2 (diff) [374 kB]
Fetched 1807 kB in 0s (7235 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-14xFwZ/python-pysam-0.17.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-14xFwZ' 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-9JFbgR/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-9JFbgR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-9JFbgR/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-9JFbgR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2651 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 35 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-9JFbgR/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 (22.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python3-pytest
Filtered Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-9JFbgR/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-9JFbgR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Sources [586 B]
Get:5 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ Packages [655 B]
Fetched 2574 B in 1s (3099 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3
debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libffi8
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu67
libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev libmagic-mgc
libmagic1 libmpdec3 libncurses6 libnghttp2-14 libpipeline1 libpsl5
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9
libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db media-types po-debconf python3 python3-all python3-all-dev
python3-attr python3-dev python3-distutils python3-importlib-metadata
python3-iniconfig 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-toml
python3-zipp python3.9 python3.9-dev python3.9-minimal samtools
sensible-utils tabix zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib
texlive-latex-recommended cython-doc dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev
libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc
subversion python-pyparsing-doc python-setuptools-doc python3.9-venv
python3.9-doc binfmt-support cwltool
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl python3-pygments
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3
debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libffi8
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu67
libjs-jquery libjs-sphinxdoc libjs-underscore liblzma-dev libmagic-mgc
libmagic1 libmpdec3 libncurses6 libnghttp2-14 libpipeline1 libpsl5
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9
libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db media-types po-debconf python3 python3-all python3-all-dev
python3-attr python3-dev python3-distutils python3-importlib-metadata
python3-iniconfig 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-toml
python3-zipp python3.9 python3.9-dev python3.9-minimal samtools
sbuild-build-depends-python-pysam-dummy sensible-utils tabix zlib1g-dev
0 upgraded, 92 newly installed, 0 to remove and 35 not upgraded.
Need to get 38.5 MB of archives.
After this operation, 133 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-9JFbgR/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
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Get:12 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-3 [21.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
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Get:24 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
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Get:30 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf bcftools armhf 1.13-1 [565 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf cython3 armhf 0.29.21-3+b1 [1234 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
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Get:47 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
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Get:49 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf dh-exec armhf 0.23.4 [25.7 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf dh-python all 4.20201102+nmu1 [99.4 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.8-1 [40.4 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.1-2 [135 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libjs-underscore all 1.9.1~dfsg-4 [100 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.2.0-4 [137 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.7-4+rpi1 [1416 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.7-4+rpi1 [3060 kB]
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Get:72 http://172.17.0.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.9.2-3 [1068 B]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf python3-all armhf 3.9.2-3 [1056 B]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.7-4+rpi1 [501 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf python3-dev armhf 3.9.2-3 [24.8 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf python3-all-dev armhf 3.9.2-3 [1064 B]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf python3-attr all 20.3.0-1 [52.9 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf python3-six all 1.16.0-2 [17.5 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf python3-more-itertools all 4.2.0-3 [42.7 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf python3-zipp all 1.0.0-3 [6060 B]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf python3-importlib-metadata all 4.6.4-1 [22.5 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-1 [6308 B]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf python3-pyparsing all 2.4.7-1 [109 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf python3-packaging all 21.0-1 [33.5 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf python3-pkg-resources all 58.2.0-1 [192 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf python3-pluggy all 0.13.0-6 [22.3 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf python3-py all 1.10.0-1 [94.2 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf python3-toml all 0.10.2-1 [16.2 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf python3-pytest all 6.2.5-1 [218 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf python3-setuptools all 58.2.0-1 [396 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-2 [525 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf tabix armhf 1.13+ds-2 [292 kB]
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Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 bcftools_1.13-1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 cython3_0.29.21-3+b1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-exec_0.23.4 dh-python_4.20201102+nmu1 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libexpat1-dev_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-sphinxdoc_4.2.0-4 libjs-underscore_1.9.1~dfsg-4 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libpython3-all-dev_3.9.2-3 libpython3-dev_3.9.2-3 libpython3-stdlib_3.9.2-3 libpython3.9_3.9.7-4+rpi1 libpython3.9-dev_3.9.7-4+rpi1 libpython3.9-minimal_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-all_3.9.2-3 python3-all-dev_3.9.2-3 python3-attr_20.3.0-1 python3-dev_3.9.2-3 python3-distutils_3.9.7-1 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3-more-itertools_4.2.0-3 python3-packaging_21.0-1 python3-pkg-resources_58.2.0-1 python3-pluggy_0.13.0-6 python3-py_1.10.0-1 python3-pyparsing_2.4.7-1 python3-pytest_6.2.5-1 python3-setuptools_58.2.0-1 python3-six_1.16.0-2 python3-toml_0.10.2-1 python3-zipp_1.0.0-3 python3.9_3.9.7-4+rpi1 python3.9-dev_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 samtools_1.13-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tabix_1.13+ds-2 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig._xxPvrzz/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 15 07:58:45 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.17.0+ds-2.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.17.0+ds
dpkg-source: info: unpacking python-pysam_0.17.0+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.17.0+ds-2.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 clean_less
dpkg-source: info: applying skip-test-on-32-bit.patch
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-3a197beb-74cf-4f84-8748-b156ed063506
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 0.17.0+ds-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
all.stamp *~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/cbcf_data'
rm -f all.stamp *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+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 python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds'
dh_auto_clean
I: pybuild base:232: python3.9 setup.py clean
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.9' 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-0.17.0+ds'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with 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:232: python3.9 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
# 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:232: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
# 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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/version.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/abuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/dist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/extsort.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/str_finder.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/utlist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/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-0.17.0+ds/pysam/libchtslib.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/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-0.17.0+ds/pysam/libcsamtools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/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-0.17.0+ds/pysam/libcbcftools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/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-0.17.0+ds/pysam/libcutils.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/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-0.17.0+ds/pysam/libcalignmentfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/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-0.17.0+ds/pysam/libcsamfile.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/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-0.17.0+ds/pysam/libcalignedsegment.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/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-0.17.0+ds/pysam/libctabix.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/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-0.17.0+ds/pysam/libcfaidx.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/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-0.17.0+ds/pysam/libcbcf.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/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-0.17.0+ds/pysam/libcbgzf.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/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-0.17.0+ds/pysam/libctabixproxies.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/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-0.17.0+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-3.9
creating build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-armhf-3.9/pysam/htslib_util.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-armhf-3.9/pysam/libchtslib.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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/htslib_util.o build/temp.linux-armhf-3.9/pysam/libchtslib.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.9/samtools
creating build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-armhf-3.9/samtools/amplicon_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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-armhf-3.9/samtools/bam_ampliconclip.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.9/samtools/bam_import.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.9/samtools/lz4/lz4.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.9/samtools/tmp_file.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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcsamtools.o build/temp.linux-armhf-3.9/samtools/amplicon_stats.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_fastq.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.9/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.9/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.9/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.9/samtools/coverage.c.pysam.o build/temp.linux-armhf-3.9/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.9/samtools/dict.c.pysam.o build/temp.linux-armhf-3.9/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.9/samtools/lz4/lz4.o build/temp.linux-armhf-3.9/samtools/padding.c.pysam.o build/temp.linux-armhf-3.9/samtools/phase.c.pysam.o build/temp.linux-armhf-3.9/samtools/sam.c.pysam.o build/temp.linux-armhf-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.9/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.9/samtools/sample.c.pysam.o build/temp.linux-armhf-3.9/samtools/samtools.pysam.o build/temp.linux-armhf-3.9/samtools/stats.c.pysam.o build/temp.linux-armhf-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.9/samtools/tmp_file.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.linux-armhf-3.9/bcftools/abuf.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.linux-armhf-3.9/bcftools/dist.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.linux-armhf-3.9/bcftools/extsort.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-armhf-3.9/bcftools/str_finder.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.9/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:733:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
733 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
from /usr/include/htslib/hts.h:37,
from /usr/include/htslib/vcf.h:39,
from bcftools/vcfmerge.c.pysam.c:35:
/usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
542 | 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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.9/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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.9/bcftools/version.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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.9/pysam/libcbcftools.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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.9/bcftools/abuf.c.pysam.o build/temp.linux-armhf-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.9/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.9/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.9/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.9/bcftools/cols.c.pysam.o build/temp.linux-armhf-3.9/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.9/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.9/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.9/bcftools/dist.c.pysam.o build/temp.linux-armhf-3.9/bcftools/em.c.pysam.o build/temp.linux-armhf-3.9/bcftools/extsort.c.pysam.o build/temp.linux-armhf-3.9/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.9/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.9/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.9/bcftools/main.c.pysam.o build/temp.linux-armhf-3.9/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.9/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.9/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.9/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.9/bcftools/str_finder.c.pysam.o build/temp.linux-armhf-3.9/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.9/bcftools/version.c.pysam.o build/temp.linux-armhf-3.9/pysam/libcbcftools.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-armhf-3.9/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_15_pysam_dispatch’:
pysam/libcutils.c:524:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
524 | #define PyInt_FromLong PyLong_FromLong
| ^~~~~~~~~~~~~~~
pysam/libcutils.c:6763:7: note: ‘__pyx_v_retval’ was declared here
6763 | 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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcutils.o build/temp.linux-armhf-3.9/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcsamtools.cpython-39-arm-linux-gnueabihf -lcbcftools.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.9/pysam/libcalignmentfile.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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-armhf-3.9/pysam/libctabix.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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.9/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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-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 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-armhf-3.9/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.constprop’:
pysam/libcvcf.c:25060:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
25060 | __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 -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools view --no-PG -bo ex1.bam -t ex1.fa.fai 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 --no-PG -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view --no-PG -bo ex2.bam ex2.sam
samtools index ex2.bam
samtools calmd --no-PG --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 --no-PG -bo with_md.bam with_md.sam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view --no-PG -bu -o uncompressed.bam ex2.sam
samtools view --no-PG -bo ex10.bam ex10.sam
samtools view --no-PG -bo ex3.bam ex3.sam
samtools view --no-PG -bo ex4.bam ex4.sam
samtools view --no-PG -bo ex5.bam ex5.sam
samtools view --no-PG -bo ex6.bam ex6.sam
samtools view --no-PG -bo ex8.bam ex8.sam
samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam
samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam
samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam
samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam
samtools view --no-PG -bo example_btag.bam example_btag.sam
samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam
samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam
samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam
samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam
touch tmp.list
samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view --no-PG -bo issue100.bam issue100.sam
samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam
samtools view --no-PG -bo softclip.bam softclip.sam
samtools view --no-PG -bo tag_bug.bam tag_bug.sam
samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam
samtools view --no-PG -bo test_query_position.bam test_query_position.sam
samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam
samtools index ex10.bam
samtools index ex3.bam
samtools index ex4.bam
samtools index ex5.bam
samtools index ex6.bam
samtools index ex8.bam
samtools index ex9_fail.bam
samtools index ex9_nofail.bam
samtools index ex_spliced.bam
samtools index example_aligned_pairs.bam
samtools index example_btag.bam
samtools index example_dash_in_chr.bam
samtools index example_empty_header.bam
samtools index example_empty_with_header.bam
samtools index example_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.bam
samtools index rg_with_tab.bam
samtools index softclip.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index test_query_position.bam
samtools index test_unaligned.bam
samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam
samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam
samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam
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
(bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam
grep "^@" ex2.sam | samtools view --no-PG -bo 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
touch all.stamp
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/cbcf_data'
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_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
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_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 < 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 < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz # create tbi index
bcftools index gnomad.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 < 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
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.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
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_vcf43.vcf.gz -o example_vcf43.bcf
bcftools index example_vcf43.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 gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.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 missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
touch all.stamp
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:232: cd /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build; python3.9 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.9.7, pytest-6.2.5, py-1.10.0, pluggy-0.13.0 -- /usr/bin/python3.9
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.17.0+ds, configfile: 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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___4ulw4yg9negative_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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_edren3fg'
/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_edren3fg
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vop00e69'
/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_vop00e69
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_p3zg5ts0
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_fe_xdrgg'
/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_fe_xdrgg
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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_iqe69a6p'
/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_iqe69a6p
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_xejs7wcf
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": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
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": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
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": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
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::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": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_6kg_ov0gtmp_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": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
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": Protocol not supported
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": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_o9melqy0tmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_ofvqi871tmp_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::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam'
PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam'
PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex2_truncated.bam'
[E::bgzf_read_block] Failed to read BGZF block data at offset 106529 expected 17790 bytes; hread returned 17453
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex2_corrupt.bam'
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": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Protocol not supported
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-0.17.0+ds/.pybuild/cpython3_3.9_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::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_xiocdtiutmp_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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_0x2331t_.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/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error 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 (skipping us...)
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 (skipping usage...)
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' at 20:676148 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' at 20:669442 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] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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] 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' at 20:439104 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] 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] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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] 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] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse_info] 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] 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' at 20:249843 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] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' at 20:669442 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' at 20:249843 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' at 20:676148 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] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 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
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1233
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:1233: PytestConfigWarning: Unknown config option: pep8ignore
self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1233
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:1233: PytestConfigWarning: Unknown config option: pep8maxlinelength
self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
../../../../../../usr/lib/python3/dist-packages/pyximport/pyximport.py:51
/usr/lib/python3/dist-packages/pyximport/pyximport.py:51: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
../../../../../../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-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/_compile_test.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
.pybuild/cpython3_3.9_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
/<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/tests/AlignmentFile_test.py:1449: 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/stable/warnings.html
=========== 927 passed, 10 skipped, 5 warnings in 522.33s (0:08:42) ============
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead
warnings.warn(
/usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead
warnings.warn(
# 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-0.17.0+ds/.pybuild/cpython3_3.9_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)
copying samtools/samtools_config_vars.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
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)
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/abuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/dist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/extsort.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/str_finder.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/utlist.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.h -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/__init__.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/utils.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/Pileup.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/samtools.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/config.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/version.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/bcftools.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/Pileup.py to Pileup.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/bcftools.py to bcftools.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/samtools.py to samtools.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/utils.py to utils.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/version.py to version.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/config.py to config.cpython-39.pyc
running install_egg_info
running egg_info
creating pysam.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
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 'htslib/LICENSE'
warning: no files found matching 'htslib/README'
warning: no files found matching '*.[ch]' under directory 'htslib'
warning: no previously-included files found matching 'htslib/*config*.h'
warning: no files found matching 'htslib/configure.ac'
warning: no files found matching 'htslib/m4/*.m4'
warning: no files found matching 'htslib/*.in'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/version.sh'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/*.mk'
warning: no previously-included files found matching 'htslib/config.mk'
warning: no previously-included files found matching 'htslib/htscodecs.mk'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam-0.17.0.egg-info
Skipping SOURCES.txt
running install_scripts
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds'
cd tests/pysam_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
all.stamp *~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
with_md.sam.gz \
*.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.17.0+ds/tests/cbcf_data'
rm -f all.stamp *.gz *.tbi *.csi *.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.17.0+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-0.17.0+ds'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_python3 -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
dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so: DWARF compression not beneficial - old size 1068854 new size 1075716
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 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 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' in '../python3-pysam_0.17.0+ds-2_armhf.deb'.
dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.17.0+ds-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pysam_0.17.0+ds-2_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 2021-10-17T07:17:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
python-pysam_0.17.0+ds-2_armhf.changes:
---------------------------------------
Format: 1.8
Date: Fri, 15 Oct 2021 13:17:18 +0530
Source: python-pysam
Binary: python3-pysam python3-pysam-dbgsym
Architecture: armhf
Version: 0.17.0+ds-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Changes:
python-pysam (0.17.0+ds-2) unstable; urgency=medium
.
* Team Upload.
* Move from experimental to unstable
* Skip failing test on 32-bit
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aab75f4c32ebd02124796ef13317c1bb8ab0de69 1410596 python3-pysam_0.17.0+ds-2_armhf.deb
Checksums-Sha256:
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3376d4f78579a6353db1751193ccab119809e42530ebb60001f8f0acb03b151e 6883988 python3-pysam-dbgsym_0.17.0+ds-2_armhf.deb
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Files:
a07dad894538ec6abcc14f67f45c56cc 7163 python optional python-pysam_0.17.0+ds-2_armhf.buildinfo
4ed0b6376477c0b5620ec7d7709ac1b4 6883988 debug optional python3-pysam-dbgsym_0.17.0+ds-2_armhf.deb
f9610053d82125a455c7a1b80dfe30c5 1410596 python optional python3-pysam_0.17.0+ds-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python3-pysam-dbgsym_0.17.0+ds-2_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 6883988 bytes: control archive=1208 bytes.
894 bytes, 12 lines control
1471 bytes, 14 lines md5sums
Package: python3-pysam-dbgsym
Source: python-pysam
Version: 0.17.0+ds-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7436
Depends: python3-pysam (= 0.17.0+ds-2)
Section: debug
Priority: optional
Description: debug symbols for python3-pysam
Build-Ids: 0eed8c349f57e2e6b3921a2b4ccda2912415165d 1d9f52d81ee36b8114d9363c5e7c025c3d8bcf3f 2b35e9a4e052dcddc34b67f85a5cd12906cbdcc8 3135793adaaaa3792390cab9c44823cb914965b2 4af904db41819c513af3b866a019b9aa0271e1a6 5df5ee25297b6224c98bd490a72efff4af210e92 6ee4d34245005638859d39be67f44088881cd713 859bd78544fe86d452f8a7b915226b266eb0ffc4 cfae721062681b8b36e0012c12e12aad837941a1 d6ef20c501bc2b883fc7a6819b39cebc3e74808c e451316ec7ac2afcf18aad744f2f70de642b7397 f7fab7908fdebbaa3362bb164ee7b4fc6575e439 fd9fbbec983c2e167d081a54c74a36b603072373
drwxr-xr-x root/root 0 2021-10-15 07:47 ./
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 1010348 2021-10-15 07:47 ./usr/lib/debug/.build-id/0e/ed8c349f57e2e6b3921a2b4ccda2912415165d.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 362840 2021-10-15 07:47 ./usr/lib/debug/.build-id/1d/9f52d81ee36b8114d9363c5e7c025c3d8bcf3f.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 247364 2021-10-15 07:47 ./usr/lib/debug/.build-id/2b/35e9a4e052dcddc34b67f85a5cd12906cbdcc8.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/31/
-rw-r--r-- root/root 761400 2021-10-15 07:47 ./usr/lib/debug/.build-id/31/35793adaaaa3792390cab9c44823cb914965b2.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/4a/
-rw-r--r-- root/root 282340 2021-10-15 07:47 ./usr/lib/debug/.build-id/4a/f904db41819c513af3b866a019b9aa0271e1a6.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root 851128 2021-10-15 07:47 ./usr/lib/debug/.build-id/5d/f5ee25297b6224c98bd490a72efff4af210e92.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root 208856 2021-10-15 07:47 ./usr/lib/debug/.build-id/6e/e4d34245005638859d39be67f44088881cd713.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/85/
-rw-r--r-- root/root 1424092 2021-10-15 07:47 ./usr/lib/debug/.build-id/85/9bd78544fe86d452f8a7b915226b266eb0ffc4.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/cf/
-rw-r--r-- root/root 106780 2021-10-15 07:47 ./usr/lib/debug/.build-id/cf/ae721062681b8b36e0012c12e12aad837941a1.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/d6/
-rw-r--r-- root/root 42548 2021-10-15 07:47 ./usr/lib/debug/.build-id/d6/ef20c501bc2b883fc7a6819b39cebc3e74808c.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 1106032 2021-10-15 07:47 ./usr/lib/debug/.build-id/e4/51316ec7ac2afcf18aad744f2f70de642b7397.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root 389208 2021-10-15 07:47 ./usr/lib/debug/.build-id/f7/fab7908fdebbaa3362bb164ee7b4fc6575e439.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root 756612 2021-10-15 07:47 ./usr/lib/debug/.build-id/fd/9fbbec983c2e167d081a54c74a36b603072373.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 33340 2021-10-15 07:47 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-pysam.debug
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/share/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-15 07:47 ./usr/share/doc/python3-pysam-dbgsym -> python3-pysam
python3-pysam_0.17.0+ds-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1410596 bytes: control archive=3472 bytes.
692 bytes, 16 lines control
9004 bytes, 94 lines md5sums
251 bytes, 12 lines * postinst #!/bin/sh
400 bytes, 12 lines * prerm #!/bin/sh
Package: python3-pysam
Source: python-pysam
Version: 0.17.0+ds-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5057
Depends: libc6 (>= 2.11), libhts3 (>= 1.13), zlib1g (>= 1:1.1.4), python3 (<< 3.10), python3 (>= 3.9~), 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.
drwxr-xr-x root/root 0 2021-10-15 07:47 ./
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/python3/
drwxr-xr-x root/root 0 2021-10-15 07:47 ./usr/lib/python3/dist-packages/
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-rw-r--r-- root/root 1394 2021-10-15 07:47 ./usr/lib/python3/dist-packages/pysam-0.17.0.egg-info/PKG-INFO
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+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 122188
Build-Time: 2607
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 668
Job: python-pysam_0.17.0+ds-2
Machine Architecture: armhf
Package: python-pysam
Package-Time: 3327
Source-Version: 0.17.0+ds-2
Space: 122188
Status: successful
Version: 0.17.0+ds-2
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Finished at 2021-10-17T07:17:03Z
Build needed 00:55:27, 122188k disc space