Raspbian Package Auto-Building

python-pysam → 0.15.4+ds-3+b1 → armhf → 2020-12-09 09:04:09

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| python-pysam 0.15.4+ds-3+b1 (armhf)          Wed, 09 Dec 2020 08:39:13 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.15.4+ds-3+b1
Source Version: 0.15.4+ds-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-6824dc37-9f9d-4fa5-867e-23f878a62ec8' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.9 MB in 10s (2564 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 1738 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.4+ds-3 (dsc) [2425 B]
Get:2 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.4+ds-3 (tar) [1362 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main python-pysam 0.15.4+ds-3 (diff) [374 kB]
Fetched 1738 kB in 1s (3001 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-y8Qw6W/python-pysam-0.15.4+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-y8Qw6W' 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-U8pFwt/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-U8pFwt/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-U8pFwt/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-U8pFwt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9408 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 packages were automatically installed and are no longer required:
  bsdextrautils krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 59 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (64.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12762 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 (= 12), 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 (= 12), 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-U8pFwt/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-U8pFwt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Sources [587 B]
Get:5 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ Packages [655 B]
Fetched 2575 B in 0s (11.3 kB/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 packages were automatically installed and are no longer required:
  krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools cython3 debhelper
  dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1
  libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
  liblzma-dev libmagic-mgc libmagic1 libncurses6 libncursesw6 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 libtinfo6 libtool
  libuchardet0 libxml2 m4 mailcap man-db media-types mime-support po-debconf
  python3 python3-all python3-all-dev python3-atomicwrites python3-attr
  python3-dev python3-distutils python3-importlib-metadata python3-lib2to3
  python3-minimal python3-more-itertools python3-packaging
  python3-pkg-resources python3-pluggy python3-py python3-pyparsing
  python3-pytest python3-setuptools python3-six python3-wcwidth python3-zipp
  python3.9 python3.9-dev python3.9-minimal samtools 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 libglib2.0-data
  shared-mime-info xdg-user-dirs libgpm2 publicsuffix libltdl-dev
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools cython3 debhelper
  dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1
  libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
  libdeflate-dev libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
  liblzma-dev libmagic-mgc libmagic1 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
  mailcap man-db media-types mime-support po-debconf python3 python3-all
  python3-all-dev python3-atomicwrites python3-attr python3-dev
  python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal
  python3-more-itertools python3-packaging python3-pkg-resources
  python3-pluggy python3-py python3-pyparsing python3-pytest
  python3-setuptools python3-six python3-wcwidth python3-zipp python3.9
  python3.9-dev python3.9-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
The following packages will be upgraded:
  libncursesw6 libtinfo6
2 upgraded, 88 newly installed, 0 to remove and 57 not upgraded.
Need to get 39.6 MB of archives.
After this operation, 136 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-U8pFwt/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1~rc1-2+rpi1 [789 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1~rc1-2+rpi1 [1624 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.0-4 [37.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 1.0.1 [18.2 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.67 [31.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-1 [328 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-1 [105 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1~rc1-2+rpi1 [1653 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.1~rc1-2+rpi1 [460 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.0-4 [21.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.0-4 [64.1 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf bcftools armhf 1.11-1 [531 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf cython3 armhf 0.29.21-3+b1 [1234 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2+b3 [25.7 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.6-1 [78.4 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.6-1 [145 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102 [99.3 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.10-1 [121 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-1 [79.5 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9 armhf 3.9.1~rc1-2+rpi1 [1412 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-dev armhf 3.9.1~rc1-2+rpi1 [3057 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.9.0-4 [21.2 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libpython3-all-dev armhf 3.9.0-4 [1068 B]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf python3-all armhf 3.9.0-4 [1056 B]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf python3.9-dev armhf 3.9.1~rc1-2+rpi1 [501 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.9.0-4 [1164 B]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.9.0-4 [1060 B]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf python3-atomicwrites all 1.4.0-1 [10.2 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf python3-attr all 20.3.0-1 [52.9 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf python3-six all 1.15.0-2 [16.9 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf python3-more-itertools all 4.2.0-3 [42.7 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf python3-zipp all 1.0.0-3 [6060 B]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf python3-importlib-metadata all 1.6.0-2 [10.3 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf python3-pyparsing all 2.4.7-1 [109 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf python3-packaging all 20.4-1 [30.4 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 50.3.0-1 [187 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf python3-pluggy all 0.13.0-5 [22.1 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf python3-py all 1.9.0-2 [94.1 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf python3-wcwidth all 0.1.9+dfsg1-2 [18.2 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf python3-pytest all 4.6.11-1 [268 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf python3-setuptools all 50.3.0-1 [511 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf tabix armhf 1.11-2 [283 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 39.6 MB in 6s (6947 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12762 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 bcftools_1.11-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 cython3_0.29.21-3+b1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-exec_0.23.2+b3 dh-python_4.20201102 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libasan6_10.2.0-16+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-16+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libexpat1_2.2.10-1 libexpat1-dev_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-1 libncursesw6_6.2+20201114-1 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.1 libpython3-all-dev_3.9.0-4 libpython3-dev_3.9.0-4 libpython3-stdlib_3.9.0-4 libpython3.9_3.9.1~rc1-2+rpi1 libpython3.9-dev_3.9.1~rc1-2+rpi1 libpython3.9-minimal_3.9.1~rc1-2+rpi1 libpython3.9-stdlib_3.9.1~rc1-2+rpi1 libreadline8_8.1~rc2-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.3 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 mailcap_3.67 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_1.0.1 mime-support_3.66 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 python3_3.9.0-4 python3-all_3.9.0-4 python3-all-dev_3.9.0-4 python3-atomicwrites_1.4.0-1 python3-attr_20.3.0-1 python3-dev_3.9.0-4 python3-distutils_3.8.6-1 python3-importlib-metadata_1.6.0-2 python3-lib2to3_3.8.6-1 python3-minimal_3.9.0-4 python3-more-itertools_4.2.0-3 python3-packaging_20.4-1 python3-pkg-resources_50.3.0-1 python3-pluggy_0.13.0-5 python3-py_1.9.0-2 python3-pyparsing_2.4.7-1 python3-pytest_4.6.11-1 python3-setuptools_50.3.0-1 python3-six_1.15.0-2 python3-wcwidth_0.1.9+dfsg1-2 python3-zipp_1.0.0-3 python3.9_3.9.1~rc1-2+rpi1 python3.9-dev_3.9.1~rc1-2+rpi1 python3.9-minimal_3.9.1~rc1-2+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tabix_1.11-2 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 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.BcK3onhi/trustedkeys.kbx': General error
gpgv: Signature made Fri May  8 18:41:05 2020 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.4+ds-3.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.15.4+ds
dpkg-source: info: unpacking python-pysam_0.15.4+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.15.4+ds-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying hts1.10
dpkg-source: info: applying samtools_v1.10_full
dpkg-source: info: applying bcftools_v1.10_full
dpkg-source: info: applying clean_less

Check disk space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 0.15.4+ds-3+b1

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-6824dc37-9f9d-4fa5-867e-23f878a62ec8
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.15.4+ds-3+b1
dpkg-buildpackage: info: source distribution bullseye-staging
 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-0.15.4+ds/tests/pysam_data'
rm -fr *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds'
dh_auto_clean
I: pybuild base:232: python3.9 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 
# 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 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools
/usr/lib/python3/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process.
  warnings.warn(
Fixing /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+ds/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2528:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2533:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2538:49: 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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libchtslib.c: In function ‘__Pyx_PyUnicode_Equals.constprop’:
pysam/libchtslib.c:17155:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
17155 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libchtslib.c:17155:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libchtslib.c:17155:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libchtslib.c:17155:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
samtools/bam_addrprg.c.pysam.c: In function ‘main_addreplacerg’:
samtools/bam_addrprg.c.pysam.c:452:5: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
  452 | int main_addreplacerg(int argc, char** argv)
      |     ^~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
samtools/padding.c.pysam.c: In function ‘load_unpadded_ref’:
samtools/padding.c.pysam.c:116:5: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
  116 | int load_unpadded_ref(faidx_t *fai, const char *ref_name, hts_pos_t ref_len, kstring_t *seq)
      |     ^~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
samtools/phase.c.pysam.c: In function ‘main_phase’:
samtools/phase.c.pysam.c:585:5: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
  585 | int main_phase(int argc, char *argv[])
      |     ^~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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/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_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_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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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:694:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
  694 |         ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
                 from /usr/include/htslib/hts.h:37,
                 from /usr/include/htslib/vcf.h:39,
                 from bcftools/vcfmerge.c.pysam.c:34:
/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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/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/em.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/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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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_PyUnicode_Equals’:
pysam/libcutils.c:10700:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
10700 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:10700:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcutils.c:10700:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcutils.c:10700:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcutils.c: In function ‘__pyx_f_5pysam_9libcutils_parse_region’:
pysam/libcutils.c:4023:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
 4023 | static PyObject *__pyx_f_5pysam_9libcutils_parse_region(CYTHON_UNUSED int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_9libcutils_parse_region *__pyx_optional_args) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_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:5971:7: note: ‘__pyx_v_retval’ was declared here
 5971 |   int __pyx_v_retval;
      |       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29761:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
29761 |   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
      |                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
      |                                                                                                                               |
      |                                                                                                                               bam_pileup1_t **
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:616:
/usr/include/htslib/sam.h:1939:96: note: expected ‘const bam_pileup1_t **’ but argument is of type ‘bam_pileup1_t **’
 1939 |     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
      |                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__Pyx_PyUnicode_Equals.constprop’:
pysam/libcalignmentfile.c:40602:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
40602 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c:40602:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c:40602:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c:40602:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_reset’:
pysam/libcalignmentfile.c:30674:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
30674 | static PyObject *__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_reset(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_stop) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_2__next__’:
pysam/libcalignmentfile.c:32310:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
32310 | static PyObject *__pyx_pf_5pysam_17libcalignmentfile_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorColumnAllRefs *__pyx_v_self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_6__next__’:
pysam/libcalignmentfile.c:27235:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
27235 | static PyObject *__pyx_pf_5pysam_17libcalignmentfile_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_17libcalignmentfile_IteratorRowAllRefs *__pyx_v_self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c:27235:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c: In function ‘__pyx_pw_5pysam_17libcalignmentfile_7SNPCall_3__reduce_cython__’:
pysam/libcalignmentfile.c:33288:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
33288 | static PyObject *__pyx_pw_5pysam_17libcalignmentfile_7SNPCall_3__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c:33288:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c:33288:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c:33288:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignmentfile.c: In function ‘__pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_1__init__’:
pysam/libcalignmentfile.c:33638:12: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
33638 | static int __pyx_pw_5pysam_17libcalignmentfile_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnRegion’:
pysam/libcalignmentfile.c:37331:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
37331 | static PyObject *__pyx_tp_new_5pysam_17libcalignmentfile_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_21find_introns_slow’:
pysam/libcalignmentfile.c:19067:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
19067 | static PyObject *__pyx_pw_5pysam_17libcalignmentfile_13AlignmentFile_21find_introns_slow(PyObject *__pyx_v_self, PyObject *__pyx_v_read_iterator) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+ds -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-arm-linux-gnueabihf -lcutils.cpython-39-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -Wl,-rpath,$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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libcalignedsegment.c: In function ‘__Pyx_PyUnicode_Equals.constprop’:
pysam/libcalignedsegment.c:62591:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
62591 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:62591:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c:62591:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c:62591:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c: In function ‘__pyx_getprop_5pysam_18libcalignedsegment_14AlignedSegment_reference_length’:
pysam/libcalignedsegment.c:54447:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
54447 | static PyObject *__pyx_getprop_5pysam_18libcalignedsegment_14AlignedSegment_reference_length(PyObject *o, CYTHON_UNUSED void *x) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_pw_5pysam_18libcalignedsegment_14AlignedSegment_35get_forward_sequence’:
pysam/libcalignedsegment.c:22732:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
22732 | static PyObject *__pyx_pw_5pysam_18libcalignedsegment_14AlignedSegment_35get_forward_sequence(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_pw___pyx_MemviewEnum_1__reduce_cython__’:
pysam/libcalignedsegment.c:42658:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
42658 | static PyObject *__pyx_pw___pyx_MemviewEnum_1__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:42658:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c:42658:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c:42658:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c: In function ‘__Pyx_Coroutine_Close’:
pysam/libcalignedsegment.c:67425:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
67425 | static PyObject *__Pyx_Coroutine_Close(PyObject *self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:67425:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcalignedsegment.c: In function ‘__pyx_f_5pysam_18libcalignedsegment_14AlignedSegment_get_tag’:
pysam/libcalignedsegment.c:27330:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
27330 | static PyObject *__pyx_f_5pysam_18libcalignedsegment_14AlignedSegment_get_tag(struct __pyx_obj_5pysam_18libcalignedsegment_AlignedSegment *__pyx_v_self, PyObject *__pyx_v_tag, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_18libcalignedsegment_14AlignedSegment_get_tag *__pyx_optional_args) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8763:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
 8763 |         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
      |                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13958:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13958 |   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
      |                                       ^~~~~~~~
pysam/libctabix.c:13990:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13990 |   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
      |                                       ^~~~~~~~
pysam/libctabix.c:14360:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14360 |       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
      |                                           ^~~~~~~~
pysam/libctabix.c: In function ‘__Pyx_PyUnicode_Equals’:
pysam/libctabix.c:24295:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
24295 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libctabix.c:24295:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libctabix.c:24295:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libctabix.c:24295:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libctabix.c: In function ‘__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator’:
pysam/libctabix.c:20151:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
20151 | static PyObject *__pyx_tp_new_5pysam_9libctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libctabix.c: In function ‘__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__’:
pysam/libctabix.c:15882:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
15882 | static PyObject *__pyx_pw_5pysam_9libctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libcbcf.c: In function ‘__Pyx_PyUnicode_Equals’:
pysam/libcbcf.c:90619:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
90619 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:90619:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcbcf.c:90619:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcbcf.c:90619:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcbcf.c: In function ‘__pyx_getprop_5pysam_7libcbcf_19VariantHeaderRecord_type’:
pysam/libcbcf.c:78175:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
78175 | static PyObject *__pyx_getprop_5pysam_7libcbcf_19VariantHeaderRecord_type(PyObject *o, CYTHON_UNUSED void *x) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_makeVariantRecordSample’:
pysam/libcbcf.c:58727:62: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
58727 | static struct __pyx_obj_5pysam_7libcbcf_VariantRecordSample *__pyx_f_5pysam_7libcbcf_makeVariantRecordSample(struct __pyx_obj_5pysam_7libcbcf_VariantRecord *__pyx_v_record, int32_t __pyx_v_sample_index) {
      |                                                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_getprop_5pysam_7libcbcf_15VariantMetadata_description’:
pysam/libcbcf.c:79238:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
79238 | static PyObject *__pyx_getprop_5pysam_7libcbcf_15VariantMetadata_description(PyObject *o, CYTHON_UNUSED void *x) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__Pyx_Coroutine_Close’:
pysam/libcbcf.c:94319:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
94319 | static PyObject *__Pyx_Coroutine_Close(PyObject *self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:94319:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_makeVariantMetadata’:
pysam/libcbcf.c:23548:58: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
23548 | static struct __pyx_obj_5pysam_7libcbcf_VariantMetadata *__pyx_f_5pysam_7libcbcf_makeVariantMetadata(struct __pyx_obj_5pysam_7libcbcf_VariantHeader *__pyx_v_header, int __pyx_v_type, int __pyx_v_id) {
      |                                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_bcf_array_to_object’:
pysam/libcbcf.c:6114:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
 6114 | static PyObject *__pyx_f_5pysam_7libcbcf_bcf_array_to_object(void *__pyx_v_data, int __pyx_v_type, Py_ssize_t __pyx_v_n, Py_ssize_t __pyx_v_count, int __pyx_v_scalar) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_bcf_check_values’:
pysam/libcbcf.c:9875:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
 9875 | static PyObject *__pyx_f_5pysam_7libcbcf_bcf_check_values(struct __pyx_obj_5pysam_7libcbcf_VariantRecord *__pyx_v_record, PyObject *__pyx_v_value, int __pyx_v_sample, int __pyx_v_hl_type, int __pyx_v_ht_type, int __pyx_v_id, int __pyx_v_bt_type, Py_ssize_t __pyx_v_bt_len, Py_ssize_t *__pyx_v_value_count, int *__pyx_v_scalar, int *__pyx_v_realloc) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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
pysam/libctabixproxies.c: In function ‘__Pyx_PyUnicode_Equals.constprop’:
pysam/libctabixproxies.c:20815:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
20815 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:20815:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libctabixproxies.c:20815:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libctabixproxies.c:20815:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.4+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.4+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_PyUnicode_Equals’:
pysam/libcvcf.c:35921:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
35921 | static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
      |                          ^~~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c:35921:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcvcf.c:35921:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcvcf.c:35921:26: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcvcf.c: In function ‘__Pyx_Coroutine_Close’:
pysam/libcvcf.c:39642:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
39642 | static PyObject *__Pyx_Coroutine_Close(PyObject *self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c:39642:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
pysam/libcvcf.c: In function ‘__pyx_pw_5pysam_7libcvcf_3VCF_84close’:
pysam/libcvcf.c:29972:18: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
29972 | static PyObject *__pyx_pw_5pysam_7libcvcf_3VCF_84close(PyObject *__pyx_self, PyObject *__pyx_v_self) {
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’:
pysam/libcvcf.c:25041:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
25041 |   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+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-0.15.4+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view -bS with_md.sam > with_md.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS ex3.sam > ex3.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS ex6.sam > ex6.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS ex_spliced.sam > ex_spliced.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam
touch tmp.list
samtools view -bt tmp.list -o example_unmapped_reads_no_sq.bam example_unmapped_reads_no_sq.sam
rm -f tmp.list
samtools view -bS issue100.sam > issue100.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS test_query_position.sam > test_query_position.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
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_reverse_complement.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index issue100.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 -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+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
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/cbcf_data'
export PYBUILD_TEST_ARGS='|| true' ; dh_auto_test
I: pybuild base:232: cd /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build; python3.9 -m pytest || true
============================= test session starts ==============================
platform linux -- Python 3.9.1rc1, pytest-4.6.11, py-1.9.0, pluggy-0.13.0 -- /usr/bin/python3.9
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.15.4+ds, inifile: setup.cfg
collecting ... collected 937 items

tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp___enter___ztawc9c7negative_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 FAILED
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 FAILED
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 FAILED
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 FAILED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_uwbunhxi'
/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_uwbunhxi
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_amdl3_rx'
/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_amdl3_rx
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ic__a11_
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_inlts30b'
/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_inlts30b
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
[E::cram_index_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_kz5owivm'
/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_kz5owivm
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_wn_s4l0t
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
FAILED
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
FAILED
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
FAILED
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
FAILED
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
FAILED
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
FAILED
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
FAILED
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
FAILED
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 FAILED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [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
FAILED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM FAILED
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 [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject FAILED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename FAILED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_4cqhllw1tmp_ex2.bam'
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED
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 FAILED
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 FAILED
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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_zo91gjn2tmp_single.bam'
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_2yg57huotmp_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 FAILED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED
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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/example_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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam'
PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory
FAILED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+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 106622 expected 17790 bytes; hread returned 17360
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
FileNotFoundError: [Errno 2] No such file or directory
Exception ignored in: 'pysam.libcalignmentfile.AlignmentFile.__dealloc__'
Traceback (most recent call last):
  File "/usr/lib/python3.9/unittest/case.py", line 550, in _callTestMethod
    method()
FileNotFoundError: [Errno 2] No such file or directory
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-0.15.4+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::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_check_read_ocakxxcdtmp_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 FAILED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_j466c5hp.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 FAILED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements FAILED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements FAILED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' 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

=================================== FAILURES ===================================
__________________ TestHeaderBAM.test_dictionary_access_works __________________

self = <AlignmentFileHeader_test.TestHeaderBAM testMethod=test_dictionary_access_works>

    def test_dictionary_access_works(self):
        for key in self.header.keys():
>           self.compare_headers({key: self.header[key]},
                                 {key: self.samfile.header[key]})

tests/AlignmentFileHeader_test.py:169: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFileHeader_test.py:143: in compare_headers
    self.assertEqual(av, b[ak])
E   AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[54 chars]am'}]
E   
E   Second list contains 1 additional elements.
E   First extra element 2:
E   {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P2', 'VN': '1.11', 'CL': 'samtools view -bS ex3.sam'}
E   
E   - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}]
E   + [{'ID': 'P1', 'VN': '1.0'},
E   +  {'ID': 'P2', 'VN': '1.1'},
E   +  {'CL': 'samtools view -bS ex3.sam',
E   +   'ID': 'samtools',
E   +   'PN': 'samtools',
E   +   'PP': 'P2',
E   +   'VN': '1.11'}]
_______________ TestHeaderBAM.test_header_content_is_as_expected _______________

self = <AlignmentFileHeader_test.TestHeaderBAM testMethod=test_header_content_is_as_expected>

    def test_header_content_is_as_expected(self):
>       self.compare_headers(self.header, self.samfile.header.to_dict())

tests/AlignmentFileHeader_test.py:151: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFileHeader_test.py:143: in compare_headers
    self.assertEqual(av, b[ak])
E   AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[54 chars]am'}]
E   
E   Second list contains 1 additional elements.
E   First extra element 2:
E   {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P2', 'VN': '1.11', 'CL': 'samtools view -bS ex3.sam'}
E   
E   - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}]
E   + [{'ID': 'P1', 'VN': '1.0'},
E   +  {'ID': 'P2', 'VN': '1.1'},
E   +  {'CL': 'samtools view -bS ex3.sam',
E   +   'ID': 'samtools',
E   +   'PN': 'samtools',
E   +   'PP': 'P2',
E   +   'VN': '1.11'}]
_________________ TestHeaderCRAM.test_dictionary_access_works __________________

self = <AlignmentFileHeader_test.TestHeaderCRAM testMethod=test_dictionary_access_works>

    def test_dictionary_access_works(self):
        for key in self.header.keys():
>           self.compare_headers({key: self.header[key]},
                                 {key: self.samfile.header[key]})

tests/AlignmentFileHeader_test.py:169: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFileHeader_test.py:229: in compare_headers
    self.assertEqual(av, b[ak])
E   AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[64 chars]am'}]
E   
E   Second list contains 1 additional elements.
E   First extra element 2:
E   {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P2', 'VN': '1.11', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'}
E   
E   - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}]
E   + [{'ID': 'P1', 'VN': '1.0'},
E   +  {'ID': 'P2', 'VN': '1.1'},
E   +  {'CL': 'samtools view -bC -T ex1.fa ex3.sam',
E   +   'ID': 'samtools',
E   +   'PN': 'samtools',
E   +   'PP': 'P2',
E   +   'VN': '1.11'}]
______________ TestHeaderCRAM.test_header_content_is_as_expected _______________

self = <AlignmentFileHeader_test.TestHeaderCRAM testMethod=test_header_content_is_as_expected>

    def test_header_content_is_as_expected(self):
>       self.compare_headers(self.header, self.samfile.header.to_dict())

tests/AlignmentFileHeader_test.py:151: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFileHeader_test.py:229: in compare_headers
    self.assertEqual(av, b[ak])
E   AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[64 chars]am'}]
E   
E   Second list contains 1 additional elements.
E   First extra element 2:
E   {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P2', 'VN': '1.11', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'}
E   
E   - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}]
E   + [{'ID': 'P1', 'VN': '1.0'},
E   +  {'ID': 'P2', 'VN': '1.1'},
E   +  {'CL': 'samtools view -bC -T ex1.fa ex3.sam',
E   +   'ID': 'samtools',
E   +   'PN': 'samtools',
E   +   'PP': 'P2',
E   +   'VN': '1.11'}]
_______________ BasicTestCRAMFromFetch.testPresentOptionalFields _______________

self = <AlignmentFile_test.BasicTestCRAMFromFetch testMethod=testPresentOptionalFields>

    def testPresentOptionalFields(self):
>       self.assertEqual(
            self.reads[0].opt('NM'), 22,
            "optional field mismatch in read 1, NM: %s != %s" %
            (self.reads[0].opt('NM'), 22))
E       AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22

tests/AlignmentFile_test.py:256: AssertionError
_______________________ BasicTestCRAMFromFetch.testTags ________________________

self = <AlignmentFile_test.BasicTestCRAMFromFetch testMethod=testTags>

    def testTags(self):
>       self.assertEqual(
            sorted(self.reads[0].tags),
            sorted([('RG', 'L1'),
                    ('NM', 22),
                    ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
                    ('PG', 'P1'),
                    ('XT', 'U'),
                    ]))
E       AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')]
E       
E       First differing element 1:
E       ('NM', 1)
E       ('NM', 22)
E       
E         [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
E       -  ('NM', 1),
E       ?         ^
E       
E       +  ('NM', 22),
E       ?         ^^
E       
E          ('PG', 'P1'),
E          ('RG', 'L1'),
E          ('XT', 'U')]

tests/AlignmentFile_test.py:237: AssertionError
_____________ BasicTestCRAMFromFilename.testPresentOptionalFields ______________

self = <AlignmentFile_test.BasicTestCRAMFromFilename testMethod=testPresentOptionalFields>

    def testPresentOptionalFields(self):
>       self.assertEqual(
            self.reads[0].opt('NM'), 22,
            "optional field mismatch in read 1, NM: %s != %s" %
            (self.reads[0].opt('NM'), 22))
E       AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22

tests/AlignmentFile_test.py:256: AssertionError
______________________ BasicTestCRAMFromFilename.testTags ______________________

self = <AlignmentFile_test.BasicTestCRAMFromFilename testMethod=testTags>

    def testTags(self):
>       self.assertEqual(
            sorted(self.reads[0].tags),
            sorted([('RG', 'L1'),
                    ('NM', 22),
                    ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
                    ('PG', 'P1'),
                    ('XT', 'U'),
                    ]))
E       AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')]
E       
E       First differing element 1:
E       ('NM', 1)
E       ('NM', 22)
E       
E         [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
E       -  ('NM', 1),
E       ?         ^
E       
E       +  ('NM', 22),
E       ?         ^^
E       
E          ('PG', 'P1'),
E          ('RG', 'L1'),
E          ('XT', 'U')]

tests/AlignmentFile_test.py:237: AssertionError
_______________ BasicTestCRAMFromFile.testPresentOptionalFields ________________

self = <AlignmentFile_test.BasicTestCRAMFromFile testMethod=testPresentOptionalFields>

    def testPresentOptionalFields(self):
>       self.assertEqual(
            self.reads[0].opt('NM'), 22,
            "optional field mismatch in read 1, NM: %s != %s" %
            (self.reads[0].opt('NM'), 22))
E       AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22

tests/AlignmentFile_test.py:256: AssertionError
________________________ BasicTestCRAMFromFile.testTags ________________________

self = <AlignmentFile_test.BasicTestCRAMFromFile testMethod=testTags>

    def testTags(self):
>       self.assertEqual(
            sorted(self.reads[0].tags),
            sorted([('RG', 'L1'),
                    ('NM', 22),
                    ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
                    ('PG', 'P1'),
                    ('XT', 'U'),
                    ]))
E       AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')]
E       
E       First differing element 1:
E       ('NM', 1)
E       ('NM', 22)
E       
E         [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
E       -  ('NM', 1),
E       ?         ^
E       
E       +  ('NM', 22),
E       ?         ^^
E       
E          ('PG', 'P1'),
E          ('RG', 'L1'),
E          ('XT', 'U')]

tests/AlignmentFile_test.py:237: AssertionError
______________ BasicTestCRAMFromFileNo.testPresentOptionalFields _______________

self = <AlignmentFile_test.BasicTestCRAMFromFileNo testMethod=testPresentOptionalFields>

    def testPresentOptionalFields(self):
>       self.assertEqual(
            self.reads[0].opt('NM'), 22,
            "optional field mismatch in read 1, NM: %s != %s" %
            (self.reads[0].opt('NM'), 22))
E       AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22

tests/AlignmentFile_test.py:256: AssertionError
_______________________ BasicTestCRAMFromFileNo.testTags _______________________

self = <AlignmentFile_test.BasicTestCRAMFromFileNo testMethod=testTags>

    def testTags(self):
>       self.assertEqual(
            sorted(self.reads[0].tags),
            sorted([('RG', 'L1'),
                    ('NM', 22),
                    ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
                    ('PG', 'P1'),
                    ('XT', 'U'),
                    ]))
E       AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')]
E       
E       First differing element 1:
E       ('NM', 1)
E       ('NM', 22)
E       
E         [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'),
E       -  ('NM', 1),
E       ?         ^
E       
E       +  ('NM', 22),
E       ?         ^^
E       
E          ('PG', 'P1'),
E          ('RG', 'L1'),
E          ('XT', 'U')]

tests/AlignmentFile_test.py:237: AssertionError
______________________________ TestIO.testBAM2BAM ______________________________

self = <AlignmentFile_test.TestIO testMethod=testBAM2BAM>

    def testBAM2BAM(self):
>       self.checkEcho("ex2.bam",
                       "ex2.bam",
                       "tmp_ex2.bam",
                       "rb", "wb",
                       checkf=checkGZBinaryEqual)

tests/AlignmentFile_test.py:470: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files ex2.bam and tmp_ex2.bam are not the same
_____________________________ TestIO.testBAM2CRAM ______________________________

self = <AlignmentFile_test.TestIO testMethod=testBAM2CRAM>

    def testBAM2CRAM(self):
        # ignore header (md5 sum)
>       self.checkEcho("ex2.bam",
                       "ex2.cram",
                       "tmp_ex2.cram",
                       "rb", "wc",
                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
                       checkf=partial(
                           check_samtools_view_equal,
                           without_header=True))

tests/AlignmentFile_test.py:504: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files ex2.cram and tmp_ex2.cram are not the same
______________________________ TestIO.testBAM2SAM ______________________________

self = <AlignmentFile_test.TestIO testMethod=testBAM2SAM>

    def testBAM2SAM(self):
>       self.checkEcho("ex2.bam",
                       "ex2.sam",
                       "tmp_ex2.sam",
                       "rb", "wh")

tests/AlignmentFile_test.py:497: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files ex2.sam and tmp_ex2.sam are not the same
________________________ TestIO.testEmptyWithHeaderBAM _________________________

self = <AlignmentFile_test.TestIO testMethod=testEmptyWithHeaderBAM>

    def testEmptyWithHeaderBAM(self):
>       self.assertRaises(
            ValueError,
            pysam.Samfile,
            os.path.join(BAM_DATADIR, "example_empty_with_header.bam"),
            "rb")

tests/AlignmentFile_test.py:798: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory

pysam/libcalignmentfile.pyx:940: FileNotFoundError
_____________________ TestIO.testFetchFromClosedFileObject _____________________

self = <AlignmentFile_test.TestIO testMethod=testFetchFromClosedFileObject>

    def testFetchFromClosedFileObject(self):
    
        f = open(os.path.join(BAM_DATADIR, "ex1.bam"))
        samfile = pysam.AlignmentFile(f, "rb")
        f.close()
        self.assertTrue(f.closed)
        # access to Samfile still works
>       self.checkEcho("ex1.bam",
                       "ex1.bam",
                       "tmp_ex1.bam",
                       "rb", "wb",
                       checkf=checkGZBinaryEqual)

tests/AlignmentFile_test.py:667: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files ex1.bam and tmp_ex1.bam are not the same
_________________________ TestIO.testOpenFromFilename __________________________

self = <AlignmentFile_test.TestIO testMethod=testOpenFromFilename>

    def testOpenFromFilename(self):
    
        samfile = pysam.AlignmentFile(
            filename=os.path.join(BAM_DATADIR, "ex1.bam"),
            mode="rb")
>       self.assertEqual(len(list(samfile.fetch())), 3270)
E       AssertionError: 3269 != 3270

tests/AlignmentFile_test.py:818: AssertionError
______________________________ TestIO.testSAM2BAM ______________________________

self = <AlignmentFile_test.TestIO testMethod=testSAM2BAM>

    def testSAM2BAM(self):
>       self.checkEcho("ex2.sam",
                       "ex2.bam",
                       "tmp_ex2.bam",
                       "r", "wb",
                       checkf=checkGZBinaryEqual)

tests/AlignmentFile_test.py:490: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files ex2.bam and tmp_ex2.bam are not the same
_____________________ TestIO.testWriteUncompressedBAMFile ______________________

self = <AlignmentFile_test.TestIO testMethod=testWriteUncompressedBAMFile>

    def testWriteUncompressedBAMFile(self):
        '''read from uncompressed BAM file, see issue #43'''
    
        input_filename = "ex2.sam"
        output_filename = "pysam_uncompressed.bam"
        reference_filename = "uncompressed.bam"
    
>       self.checkEcho(input_filename,
                       reference_filename,
                       output_filename,
                       "r", "wb0")

tests/AlignmentFile_test.py:780: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignmentFile_test.py:447: in checkEcho
    self.assertTrue(checkf(
E   AssertionError: False is not true : files uncompressed.bam and pysam_uncompressed.bam are not the same
______________________ TestIteratorRowAllBAM.testIterate _______________________

self = <AlignmentFile_test.TestIteratorRowAllBAM testMethod=testIterate>

    def testIterate(self):
        '''compare results from iterator with those from samtools.'''
        ps = list(self.samfile.fetch())
        sa = pysam.samtools.view(self.filename,
                                 raw=True).splitlines()
>       self.assertEqual(
            len(ps), len(sa),
            "unequal number of results: %i != %i" %
            (len(ps), len(sa)))
E       AssertionError: 3269 != 3270 : unequal number of results: 3269 != 3270

tests/AlignmentFile_test.py:973: AssertionError
___________________ TestDeNovoConstruction.testBAMWholeFile ____________________

self = <AlignmentFile_test.TestDeNovoConstruction testMethod=testBAMWholeFile>

    def testBAMWholeFile(self):
    
        tmpfilename = "tmp_%i.bam" % id(self)
    
        outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header)
    
        for x in self.reads:
            outfile.write(x)
        outfile.close()
    
>       self.assertTrue(
            checkGZBinaryEqual(tmpfilename, self.bamfile),
            "mismatch when construction BAM file, see %s %s" %
            (tmpfilename, self.bamfile))
E       AssertionError: False is not true : mismatch when construction BAM file, see tmp_4124248048.bam /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/ex6.bam

tests/AlignmentFile_test.py:1377: AssertionError
_______________________ TestEmptyHeader.testEmptyHeader ________________________

self = <AlignmentFile_test.TestEmptyHeader testMethod=testEmptyHeader>

    def testEmptyHeader(self):
        s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
                                             'example_empty_header.bam'))
>       self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})
E       AssertionError: OrderedDict([('SQ', [{'SN': 'chr1', 'LN':[119 chars]}])]) != {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}

tests/AlignmentFile_test.py:1406: AssertionError
___________________ TestHeaderWithProgramOptions.testHeader ____________________

self = <AlignmentFile_test.TestHeaderWithProgramOptions testMethod=testHeader>

    def testHeader(self):
>       s = pysam.AlignmentFile(os.path.join(BAM_DATADIR,
                                             'rg_with_tab.bam'))

tests/AlignmentFile_test.py:1447: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   FileNotFoundError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory

pysam/libcalignmentfile.pyx:940: FileNotFoundError
_______________________ StreamTest.test_text_processing ________________________

self = <StreamFiledescriptors_test.StreamTest testMethod=test_text_processing>

    @unittest.skipIf(IS_PYTHON2, "no context manager in py2")
    def test_text_processing(self):
    
        with subprocess.Popen('head -n200',
                              stdin=subprocess.PIPE,
                              stdout=subprocess.PIPE,
                              shell=True) as proc:
    
            in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam'))
            out_stream = AlignmentFile(
                proc.stdin, 'wh', header=in_stream.header)
            writer = alignmentfile_writer_thread(in_stream,
                                                 out_stream)
    
            written, read = self.stream_process(proc,
                                                in_stream,
                                                out_stream,
                                                writer)
>           self.assertEqual(read, 198)
E           AssertionError: 197 != 198

tests/StreamFiledescriptors_test.py:61: AssertionError
______________________________ BAMTest.testCount _______________________________

self = <compile_test.BAMTest testMethod=testCount>

    def testCount(self):
    
        nread = _compile_test.testCountBAM(
            pysam.Samfile(self.input_filename))
>       self.assertEqual(nread, 3270)
E       AssertionError: 3269 != 3270

tests/compile_test.py:34: AssertionError
_________________________ SamtoolsTest.testStatements __________________________

self = <samtools_test.SamtoolsTest testMethod=testStatements>

    def testStatements(self):
        for statement in self.statements:
            command = self.get_command(statement, map_to_internal=False)
            # bam2fq differs between version 1.5 and 1.6 - reenable if
            # bioconda samtools will be available.
            if command in ("bedcov", "stats", "dict", "bam2fq"):
                continue
    
            if (command == "calmd" and
                    list(sys.version_info[:2]) == [3, 3]):
                # skip calmd test, fails only on python 3.3.5
                # in linux (empty output). Works in OsX and passes
                # for 3.4 and 3.5, see issue #293
                continue
>           self.check_statement(statement)

tests/samtools_test.py:256: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/samtools_test.py:233: in check_statement
    check_samtools_view_equal(
tests/TestUtils.py:124: in check_samtools_view_equal
    lines2 = pysam.samtools.view(*(args + [filename2]))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pysam.utils.PysamDispatcher object at 0xf72b37c0>
args = ('-x', 'MD', '-x', 'NM', 'pysam_ex1.calmd.bam'), kwargs = {}, retval = 1
stderr = '[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n'
stdout = ''

    def __call__(self, *args, **kwargs):
        '''execute a samtools command.
    
        Keyword arguments:
        catch_stdout -- redirect stdout from the samtools command and
            return as variable (default True)
        save_stdout -- redirect stdout to a filename.
        raw -- ignore any parsers associated with this samtools command.
        split_lines -- return stdout (if catch_stdout is True and stderr
                       as a list of strings.
        '''
        retval, stderr, stdout = _pysam_dispatch(
            self.collection,
            self.dispatch,
            args,
            catch_stdout=kwargs.get("catch_stdout", True),
            save_stdout=kwargs.get("save_stdout", None))
    
        if kwargs.get("split_lines", False):
            stdout = stdout.splitlines()
            if stderr:
                stderr = stderr.splitlines()
    
        if retval:
>           raise SamtoolsError(
                "%s returned with error %i: "
                "stdout=%s, stderr=%s" %
                (self.collection,
                 retval,
                 stdout,
                 stderr))
E           pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n'

pysam/utils.py:69: SamtoolsError
___________________________ PysamTest.testStatements ___________________________

self = <samtools_test.PysamTest testMethod=testStatements>

    def testStatements(self):
        for statement in self.statements:
            command = self.get_command(statement, map_to_internal=False)
            # bam2fq differs between version 1.5 and 1.6 - reenable if
            # bioconda samtools will be available.
            if command in ("bedcov", "stats", "dict", "bam2fq"):
                continue
    
            if (command == "calmd" and
                    list(sys.version_info[:2]) == [3, 3]):
                # skip calmd test, fails only on python 3.3.5
                # in linux (empty output). Works in OsX and passes
                # for 3.4 and 3.5, see issue #293
                continue
>           self.check_statement(statement)

tests/samtools_test.py:256: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/samtools_test.py:233: in check_statement
    check_samtools_view_equal(
tests/TestUtils.py:124: in check_samtools_view_equal
    lines2 = pysam.samtools.view(*(args + [filename2]))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pysam.utils.PysamDispatcher object at 0xf72b37c0>
args = ('-x', 'MD', '-x', 'NM', 'pysam_ex1.calmd.bam'), kwargs = {}, retval = 1
stderr = '[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n'
stdout = ''

    def __call__(self, *args, **kwargs):
        '''execute a samtools command.
    
        Keyword arguments:
        catch_stdout -- redirect stdout from the samtools command and
            return as variable (default True)
        save_stdout -- redirect stdout to a filename.
        raw -- ignore any parsers associated with this samtools command.
        split_lines -- return stdout (if catch_stdout is True and stderr
                       as a list of strings.
        '''
        retval, stderr, stdout = _pysam_dispatch(
            self.collection,
            self.dispatch,
            args,
            catch_stdout=kwargs.get("catch_stdout", True),
            save_stdout=kwargs.get("save_stdout", None))
    
        if kwargs.get("split_lines", False):
            stdout = stdout.splitlines()
            if stderr:
                stderr = stderr.splitlines()
    
        if retval:
>           raise SamtoolsError(
                "%s returned with error %i: "
                "stdout=%s, stderr=%s" %
                (self.collection,
                 retval,
                 stdout,
                 stderr))
E           pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[main_samview] fail to read the header from "pysam_ex1.calmd.bam".\n'

pysam/utils.py:69: SamtoolsError
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/AlignmentFile_test.py:1471: UserWarning: no BGZF EOF marker; file may be truncated
    s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'),

.pybuild/cpython3_3.9_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements
.pybuild/cpython3_3.9_pysam/build/tests/samtools_test.py::PysamTest::testStatements
  /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tests/samtools_test.py:136: UserWarning: versions of pysam.samtools and samtools differ: 1.9 != 1.11
    warnings.warn(

-- Docs: https://docs.pytest.org/en/latest/warnings.html
======= 28 failed, 899 passed, 10 skipped, 4 warnings in 202.85 seconds ========
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+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-0.15.4+ds/debian/python3-pysam 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.4+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)
/usr/lib/python3/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process.
  warnings.warn(
Fixing /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/cols.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hex.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/variantkey.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/__init__.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/utils.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/Pileup.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/samtools.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/config.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/version.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__pycache__/bcftools.cpython-39.pyc -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__pycache__
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex1.bam -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_ex2.bam -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/pysam_uncompressed.bam -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/tmp_4124248048.bam -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
copying /<<BUILDDIR>>/python-pysam-0.15.4+ds/.pybuild/cpython3_3.9_pysam/build/log.txt -> /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/Pileup.py to Pileup.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/bcftools.py to bcftools.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/samtools.py to samtools.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/utils.py to utils.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/version.py to version.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/__init__.py to __init__.cpython-39.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.15.4+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 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/os/*.c'
warning: no files found matching 'htslib/os/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.15.4+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam-0.15.4.egg-info
Skipping SOURCES.txt
running install_scripts
   debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds'
cd tests/pysam_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/pysam_data'
rm -fr *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*.bam" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "pysam_uncompressed.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c \
	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
	tests/pysam_data/ex1.fa.gz \
	tests/pysam_data/ex1.fa.gz.gzi \
	tests/pysam_data/ex1_csi.bam.csi
rm -rf .pytest_cache/
dh_install -Xtest.gtf.gz
find debian -name log.txt -delete
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.4+ds'
   dh_installdocs -a -O--buildsystem=pybuild
   dh_installchangelogs -a -O--buildsystem=pybuild
   dh_python3 -a -O--buildsystem=pybuild
   dh_installinit -a -O--buildsystem=pybuild
   dh_installsystemduser -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
   dh_fixperms -a -O--buildsystem=pybuild
   dh_missing -a -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-39-arm-linux-gnueabihf.so: DWARF compression not beneficial - old size 1064768 new size 1071383
   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_0.15.4+ds-3+b1_armhf.deb'.
dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.15.4+ds-3+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../python-pysam_0.15.4+ds-3+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-12-09T09:04:03Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


python-pysam_0.15.4+ds-3+b1_armhf.changes:
------------------------------------------

Format: 1.8
Date: Fri, 08 May 2020 20:27:35 +0200
Source: python-pysam (0.15.4+ds-3)
Binary: python3-pysam python3-pysam-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 0.15.4+ds-3+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Changes:
 python-pysam (0.15.4+ds-3+b1) bullseye-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
 ebdf7ea9ce9c7b5e959f36c80733fdfe6d46dcab 7490 python-pysam_0.15.4+ds-3+b1_armhf.buildinfo
 d5157f5a12675e22b8225501b65767c1e3b5f9eb 6675636 python3-pysam-dbgsym_0.15.4+ds-3+b1_armhf.deb
 7e2aca3ee6356ab3cdff7a120ab1cb123f446423 1343752 python3-pysam_0.15.4+ds-3+b1_armhf.deb
Checksums-Sha256:
 2c8890c932fd12c56fa4e08be61eba0a7253f3f20ecd471f74374646446467d9 7490 python-pysam_0.15.4+ds-3+b1_armhf.buildinfo
 d2efba7f82a0934c82233e9b27fcc69673cc19be0f0e1ed9a1e3ca8bfd861ce3 6675636 python3-pysam-dbgsym_0.15.4+ds-3+b1_armhf.deb
 12b2f5cc9192f0ebfcc64bfb2b4a79d054592b204446cc2d4479274c6949575e 1343752 python3-pysam_0.15.4+ds-3+b1_armhf.deb
Files:
 bb3fd37132074899d8c67822a81b8bb8 7490 python optional python-pysam_0.15.4+ds-3+b1_armhf.buildinfo
 32ff42a1fc08441a25f8e1b8ccddb6f8 6675636 debug optional python3-pysam-dbgsym_0.15.4+ds-3+b1_armhf.deb
 77fe532ee900e921bf24f806183c0773 1343752 python optional python3-pysam_0.15.4+ds-3+b1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


python3-pysam-dbgsym_0.15.4+ds-3+b1_armhf.deb
---------------------------------------------

 new Debian package, version 2.0.
 size 6675636 bytes: control archive=1216 bytes.
     914 bytes,    12 lines      control              
    1471 bytes,    14 lines      md5sums              
 Package: python3-pysam-dbgsym
 Source: python-pysam (0.15.4+ds-3)
 Version: 0.15.4+ds-3+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 7227
 Depends: python3-pysam (= 0.15.4+ds-3+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for python3-pysam
 Build-Ids: 22a74987b9b6bf67146840d330fc330dfe8a4ae7 26e0d83399e8fcfde7daaed0882a2c2022efcf4d 734daf0006e6c03023d607a6e721965f7415286b 7e6487ae8246378fcaa8fbaac93c4fb3ad15ff2f 8f7ee60106fd1e5a41f116f4ea442b07047c5e7d 93840275eb06d97926069fbacd68f7defddf3401 9dc3794050c9fb12381154b86673bf2a27bb74f6 c5c2e573d3022b8670c42204a8af6e6fe367a0d4 d8c83d6e47c91242c76967cdf1807ef1ed5595a6 df46b3fe4057c47e0fed1d919e136f0b7537b39b e2b023b2d02377e3ac6f516fef788aed54dcdbe8 e357cb336ba564936e25da59f49d23da4102577c f71a932e107c722b97ba113bb72a09c6b8629b96

drwxr-xr-x root/root         0 2020-05-08 18:27 ./
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root   1009920 2020-05-08 18:27 ./usr/lib/debug/.build-id/22/a74987b9b6bf67146840d330fc330dfe8a4ae7.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/26/
-rw-r--r-- root/root    670312 2020-05-08 18:27 ./usr/lib/debug/.build-id/26/e0d83399e8fcfde7daaed0882a2c2022efcf4d.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/73/
-rw-r--r-- root/root    855412 2020-05-08 18:27 ./usr/lib/debug/.build-id/73/4daf0006e6c03023d607a6e721965f7415286b.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/7e/
-rw-r--r-- root/root    193188 2020-05-08 18:27 ./usr/lib/debug/.build-id/7e/6487ae8246378fcaa8fbaac93c4fb3ad15ff2f.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/8f/
-rw-r--r-- root/root    405060 2020-05-08 18:27 ./usr/lib/debug/.build-id/8f/7ee60106fd1e5a41f116f4ea442b07047c5e7d.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/93/
-rw-r--r-- root/root    995428 2020-05-08 18:27 ./usr/lib/debug/.build-id/93/840275eb06d97926069fbacd68f7defddf3401.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root    247624 2020-05-08 18:27 ./usr/lib/debug/.build-id/9d/c3794050c9fb12381154b86673bf2a27bb74f6.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root     42636 2020-05-08 18:27 ./usr/lib/debug/.build-id/c5/c2e573d3022b8670c42204a8af6e6fe367a0d4.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/d8/
-rw-r--r-- root/root    741772 2020-05-08 18:27 ./usr/lib/debug/.build-id/d8/c83d6e47c91242c76967cdf1807ef1ed5595a6.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/df/
-rw-r--r-- root/root    364488 2020-05-08 18:27 ./usr/lib/debug/.build-id/df/46b3fe4057c47e0fed1d919e136f0b7537b39b.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root    106868 2020-05-08 18:27 ./usr/lib/debug/.build-id/e2/b023b2d02377e3ac6f516fef788aed54dcdbe8.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/e3/
-rw-r--r-- root/root   1420072 2020-05-08 18:27 ./usr/lib/debug/.build-id/e3/57cb336ba564936e25da59f49d23da4102577c.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.build-id/f7/
-rw-r--r-- root/root    282748 2020-05-08 18:27 ./usr/lib/debug/.build-id/f7/1a932e107c722b97ba113bb72a09c6b8629b96.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root     32932 2020-05-08 18:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-pysam.debug
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/share/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-05-08 18:27 ./usr/share/doc/python3-pysam-dbgsym -> python3-pysam


python3-pysam_0.15.4+ds-3+b1_armhf.deb
--------------------------------------

 new Debian package, version 2.0.
 size 1343752 bytes: control archive=3352 bytes.
     708 bytes,    16 lines      control              
    8509 bytes,    89 lines      md5sums              
     251 bytes,    12 lines   *  postinst             #!/bin/sh
     400 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-pysam
 Source: python-pysam (0.15.4+ds-3)
 Version: 0.15.4+ds-3+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4809
 Depends: libc6 (>= 2.7), libhts3 (>= 1.10), 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 2020-05-08 18:27 ./
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/python3/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2020-05-08 18:27 ./usr/lib/python3/dist-packages/pysam-0.15.4.egg-info/
-rw-r--r-- root/root      1505 2020-05-08 18:27 ./usr/lib/python3/dist-packages/pysam-0.15.4.egg-info/PKG-INFO
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| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 126296
Build-Time: 1252
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 218
Job: python-pysam_0.15.4+ds-3
Machine Architecture: armhf
Package: python-pysam
Package-Time: 1490
Source-Version: 0.15.4+ds-3
Space: 126296
Status: successful
Version: 0.15.4+ds-3+b1
--------------------------------------------------------------------------------
Finished at 2020-12-09T09:04:03Z
Build needed 00:24:50, 126296k disk space

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