Truncate ex2.bam irrespective of its size

Bug: https://github.com/pysam-developers/pysam/issues/1128
Applied-Upstream: 56b1624c21b02762fdcea3aa5f657a4152ca178e
Reviewed-by: Étienne Mollier <emollier@debian.org>
Last-Update: 2022-10-02

The Makefile also builds ex2.bam from ex2.sam via `samtools view`.
Samtools as traditionally built using zlib typically generates a
124703-byte file, whereas when built using libdeflate it typically
generates a 122804-byte file -- but `head -c 124000` leaves that unchanged
and the test cases fail because ex2_truncated.bam is unexpectedly valid.

Rewrite the truncation rule to remove the final 512 bytes, irrespective
of ex2.bam's length. (No practical compression will reduce it to less
than 512 bytes in total, so this is safe.) Fixes #1128.
Last-Update: 2022-10-02
Gbp-Pq: Name test-truncated-bam.patch

skip-test-on-32-bit

Gbp-Pq: Name skip-test-on-32-bit.patch

Do not clean *.bam files

Last-Update: 2020-01-23 14:31:06 +0100

Gbp-Pq: Name clean_less

Skip tests trying to access remote site

Last-Update: Tue, 11 Sep 2018 14:12:55 +0200

Gbp-Pq: Name skip_test_remote.patch

ready to upload to unstable.

d/*.lintian-overrides: remove unused overrides.

d/control: add myself to uploaders.

d/*.lintian-overrides: refresh mismatches.

test-truncated-bam.patch: added; fix test truncated BAM failure.

Thanks: John Marshall

Remove unused license definitions for LGPL-2.1+, BSD-3-clause.

Changes-By: lintian-brush
Fixes: lintian: unused-license-paragraph-in-dep5-copyright
See-also: https://lintian.debian.org/tags/unused-license-paragraph-in-dep5-copyright.html

routine-update: Standards-Version: 4.6.1

Update upstream source from tag 'upstream/0.19.1+ds'

Update to upstream version '0.19.1+ds'
with Debian dir 8d6067cf8e6433e7474d1bfcaaa7dc7205ee6434

routine-update: New upstream version

New upstream version 0.19.1+ds

Upload to experimental

Bump Build-Depends: libhts-dev (>= 1.14~)

Remove superflous file patterns from debian/copyright

Upload to experimental

Update upstream source from tag 'upstream/0.18.0+ds'

Update to upstream version '0.18.0+ds'
with Debian dir fbe513c606d10f93e294607f45f5cce098219fe3

New upstream version 0.18.0+ds

Remove also win32 dir from upstream code (and when beeing at it also .github and .gitignore)

Drop outdated and unused tests

Remove constraints unnecessary since buster

* Build-Depends: Drop versioned constraint on bcftools, libhts-dev and samtools.

Changes-By: deb-scrub-obsolete

Avoid explicitly specifying -Wl,--as-needed linker flag.

Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html

Update renamed lintian tag names in lintian overrides.

Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html

routine-update: No tab in license text

Update upstream source from tag 'upstream/0.18.0+ds'

Update to upstream version '0.18.0+ds'
with Debian dir 56361846805f33ba070134821867efdb2fd1768a

New upstream version 0.18.0+ds

routine-update: New upstream version

Upload to unstable

Attempt skipping failing test on 32-bit

Upload to experimental

Interim changelog entry

Rediff patches

Bump watch file version to 4

Standards version: 4.6.0

Update upstream source from tag 'upstream/0.17.0+ds'

Update to upstream version '0.17.0+ds'
with Debian dir e8cdf682c37aedf7f1618ff50f6680765468f2f5

New upstream version 0.17.0+ds

Exclude another test that is failing

Do not ignore test results via '|| true'

Update copyright

Adapt patches to new upstream version.  Patches targeting at version 1.10 were deactivated

routine-update: debhelper-compat 13

Update upstream source from tag 'upstream/0.16.0.1+ds'

Update to upstream version '0.16.0.1+ds'
with Debian dir fd4ab3584641ae7025d3b069d5d1b44aa885e82b

New upstream version 0.16.0.1+ds

routine-update: New upstream version

DEP3

Upload to unstable

Remove Python2 also from d/rules

Set upstream metadata fields: Bug-Submit.

Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

routine-update: Rules-Requires-Root: no

routine-update: Add salsa-ci file

routine-update: Standards-Version: 4.5.0

Remove unneeded debian/gbp.conf

Remove Python2 package

releasing package python-pysam version 0.15.4+ds-2

Dont run unittests for python2 binary, to reduce pytest rdeps

0.15.4+ds-1

Try to keep example_no_seq_in_header_null_bytes.bam from being deleted

python-pysam-tests: Multi-Arch: foreign

Update upstream source from tag 'upstream/0.15.4+ds'

Update to upstream version '0.15.4+ds'
with Debian dir 8d163184d585b58f150119376d9fd11764076f8c

New upstream version 0.15.4+ds

routine-update: New upstream version

routine-update: Ready to upload to unstable

Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.

debian/copyright: use spaces rather than tabs to start continuation lines.

Fixes lintian: tab-in-licence-text
See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.

routine-update: Standards-Version: 4.4.1

make the build reproducible

try to fix seeking in uncompressed files

don't try to ship nonexistent debian/tests/run-nose{3,}-tests

update samtools & bcftools to v1.10

samtools import →  samtools view

Remove hts_utell, no longer in libhts3

sga already removed python2

Update metadata - added ref to bioconda, yamllinting

set HOME for autopkgtests

remove unused autopkgtests

Set upstream metadata fields: Repository.

Use secure URI in Homepage field.

Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.

Trim trailing whitespace.

Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.

Standards-Version: 4.4.0

debhelper-compat 12

document why we aren't dropping py2 yet

Revert "drop python2"

This reverts commit feea4660e2dfdd2702594e1eee0bae3c53c6d3cb.

drop python2

0.15.3+ds-1

Update upstream source from tag 'upstream/0.15.3+ds'

Update to upstream version '0.15.3+ds'
with Debian dir 307bac42b790b1d11795bf9ce3e9403377717f16

New upstream version 0.15.3+ds

release to unstable

cope with change to Tabix index format

Remove myself from Uploaders

python3:Provides is deprecated

upload to unstable.

remove errant log.txt from the packages.

debian/tests/control.autodep8 → debian/tests/control.

Fix lintian found spelling typos.

Provides: ${python:Provides}

New upstream version

Update upstream source from tag 'upstream/0.15.2+ds'

Update to upstream version '0.15.2+ds'
with Debian dir 528859a225bdaf3bf87eae5371d0cf5153a05354

New upstream version 0.15.2+ds