[med-svn] samtools annotated tag upstream/1.6 created (now 51d1784)
Andreas Tille
tille at debian.org
Mon Dec 11 14:22:09 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag upstream/1.6
in repository samtools.
at 51d1784 (tag)
tagging 8abd692651ac07ea7138fe705c83b3253081f3be (commit)
replaces 1.4.1
tagged by Andreas Tille
on Mon Dec 11 15:19:04 2017 +0100
- Log -----------------------------------------------------------------
Upstream version 1.6
Afif Elghraoui (9):
Set up a new changelog entry
Add patch to fix building on i386
Remove source files not present in upstream tarball
Allow all scripts to be called without language extensions
Update changelog for 1.2-2 release
Mark release and remove redundant changelog entry
Revert "Allow all scripts to be called without language extensions"
Revert "Remove source files not present in upstream tarball"
Prepare for upload
Andreas Tille (28):
debian/upstream: replace a perfectly valid BibTeX entry which happens to cause problems in the replacement algorith for the tasks pages written by Michael Banck
Versioned Build-Depends libhts-dev >= 1.0
Fix synopsis and vcs-browser
Add lintian-override to document that the language extensions are used internally
Fix spelling
Mark as team upload since I do not intend to become Uploader for samtools
Fix Mayhem issues caused by unlimited reads of gz input
Provide some more manpages
Upload to unstable
Please use UNRELEASED as long as a package is not uploaded
Remove wrong debian-changes patch
Merge tag '1.4' into debian/unstable
Replaced Dominique Belhachemi by my own ID as Uploader
Adapt patches
Bump versioned Depends: libhts-dev (>= 1.4), upload to experimental
Rebuild against properly named libhts which had a soname change
Merge tag '1.4.1' into debian/unstable
New upstream version
Close bug, upload to unstable
New upstream version 1.5
Updated version 1.5 from '1.5'
New upstream version
debhelper 10
Standards-Version: 4.0.0 (no changes needed)
Bump versioned Build-Depends: libhts-dev (>= 1.5)
Add recommends to cwl-tool and fix shebang line of cwl scripts
Do not warn about cwl-runner , upload to unstable
New upstream version 1.6
Anton Khodak (3):
Add CWL tools to the package
Add CWL tools
minor fixes
Charles Plessy (190):
Imported Upstream version 0.1.5c
Imported Debian patch 0.1.5c-1
Imported Debian patch 0.1.5c-2
Merge branch 'upstream'
Imported Upstream version 0.1.6~dfsg
Imported Debian patch 0.1.6~dfsg-1
Merge commit 'upstream/0.1.7.dfsg'
Imported Upstream version 0.1.7~dfsg
Update in preparation for new upstream release.
Converted to the source format ‘3.0 (quilt)’.
Imported Upstream version 0.1.7a~dfsg
Merge commit 'upstream/0.1.7a.dfsg'
Minor upstream update correcting a build failure.
Simple manpage created with help2man.
Tidied the minimalistic razip.1 manual page.
Uploaded package after misc. improvements.
In version 1.8, there are no binary files to remove from the upstream tarball.
Imported Upstream version 0.1.8
Merge commit 'upstream/0.1.8'
The 1.8 tarball does not contain Windows binaries anymore.
Copyright notice bureaucracy.
This source package is managed with Git since upstream version 1.7~dfsg.
Copied from SVN revision 4710 and adapted to Git.
New upstream release, with among many changes a new python script.
Added notes on how the package is tested.
Merge commit 'upstream/0.1.9'
Imported Upstream version 0.1.9
# New files in the new upstream release.
# Updated and reformatted debian/copyright according to latest DEP-5 draft.
# Incremented Standards-Version to reflect conformance with Policy 3.9.1.
# Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.
# New upstream release, and new program: bcftools.
Imported Upstream version 0.1.10
Merge commit 'upstream/0.1.10'
# New upstream release.
Imported Upstream version 0.1.11
Merge commit 'upstream/0.1.11'
Imported Upstream version 0.1.12a
Merge commit 'upstream/0.1.12a'
# New usptream release; no change for licenses or copyrights.
# Use bzip2 compression for the binary packages and raised DH compat level.
# Uploaded 0.1.12a-1 to Debian.
# Install the manual page of bcftools.
Merge commit 'upstream/0.1.13'
Imported Upstream version 0.1.13
# Copyright review of the diff between 0.1.12 and 0.1.13.
# bcftools/bcf-fix.pl removed upstream.
# Uploaded 0.1.13 to Sid.
Merge commit 'upstream/0.1.14'
Imported Upstream version 0.1.14
# New upstream release (new copyright notices and licenses proofchecked).
# Uploaded samtools version 0.1.14-1.
Merge commit 'upstream/0.1.15'
Imported Upstream version 0.1.15
New upstream release (no new copyright notices).
Uploaded 0.1.15-1 to Sid.
Imported Upstream version 0.1.16
Merge commit 'upstream/0.1.16'
New upstream release, introducing two files with new copyright statements.
Added a configuration file to make it obvious git-buildpackage is used.
Distribute transiently sam.h in /usr/include.
Move the headers to /usr/include/samtools.
Uploaded samtools_0.1.16-1_amd64.changes.
Imported Upstream version 0.1.17
Merge commit 'upstream/0.1.17'
New upstream release (no new copyright holder nor license statement).
bcftools.1 and samtools.1 were merged in upstream release 0.1.17.
Patched the example makefile to not use samtools pileup, deprecated.
Uploading samtools_0.1.17-1_amd64.changes.
Imported Upstream version 0.1.18
Merge commit 'upstream/0.1.18'
New upstream release.
Compress binary packages with xz.
Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Uploading 0.1.18-1 to unstable.
Starting the work on next package update.
Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt-cache.
Do not compress the example binary alignment file.
Renamed debian/upstream-metadata.yaml to debian/upstream.
Moved DOI and PubMed to the Reference namespace.
Pass build flaggs set by dpkg-buildflags via Debhelper.
Build-depend on Debhelper 9 (see e6882df5b3e4a66100acf69c8f0f213208d16c92).
Bash completion, see https://github.com/arq5x/bash_completion.
Normalised with config-model.
Include 7 digits of the commit id in the changelog entry.
Imported Upstream version 0.1.19
Merge tag 'upstream/0.1.19'
New upstream release, no new license nor copyright statements.
Binary files (re-)introduced by the update.
Collapsed copyright notices from main holders.
Normalised with cme (from the libconfig-model-perl package).
Deleted DM-Upload-Allowed field.
Conforms to Policy version 3.9.4.
Removed fix_float_tag.patch, corrected upstream.
Refreshed patches.
Rename no-pileup-tests.patch fix_example_makefile.patch.
Pass -lpthread when compiling calDepth.
Harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
Moved to GitHub.
New tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua and vcfutils.lua.
URL to the latest upstream changelog.
Normalised VCS URLs.
Use NEWS as upstream changelog.
samtools (0.1.19-1) unstable; urgency=low
Also track release candidates.
This package uses pristine-tar, and does not follow the canonical layout of git-buildpackage.
Merge branch 'develop' into debian/unstable
New upstream release candidate.
Disable patches for the moment.
Stop depending on CDBS and quilt.
Use the single-debian-patch option.
Stop providing the static libbam, replaced by the dynamic libhts.
razip was removed from samtools.
Breaks and replace tabix for the bgzip program.
Rely on the new upstream Makefile.
Merge branch 'develop' into debian/unstable
Updated changelog.
Merge branch 'master' into debian/unstable
Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
Build-depend on tabix for the regression tests, that use bgzip.
Adjust for dynamic linking.
Indicate path to packaged bgzip.
Mimick Makefile's CPPFLAGS.
Create a test package for the test data.
Current changelog.
Close #544976, about libbam being built with -fPIC, since libbam is dropped.
Move back Homepage field where it belongs.
Adjust install file for two-package build.
No new copyright nor license notice.
Conforms to Policy 3.9.5.
Opened https://github.com/samtools/samtools/issues/284
Refreshed for upstream version 1.0.
Re-enable fix_coverage_cap.patch.
Drop patch for file that was dropped.
Refreshed to for upstream version 1.0.
Sent pull request.
New homepage.
Re-enable fix_segfault_with_small_ref.patch after refreshing it.
Temporary patch to build dynamically samtools.
Allow parallel building.
Clean before installing test files (this removes compiled files).
Recommend python since samtools installs a python script in /usr/bin.
One more small patch that I hope removing at the next upstream release.
Current changelog.
Branch to build packages for Experimental.
samtools (1.0-1~experimental) experimental; urgency=low
Merge branch 'debian/experimental' into debian/unstable
Prevent Makefile from including local copy of the HTSlib.
Build for Unstable.
Build-depend on libhts-dev...
Current changelog.
Conforms with Policy 3.5.6.
samtools (1.0-1) unstable; urgency=low
Add autopkg tests.
Current changelog.
Merge tag '1.1' into debian/unstable
Merge branch 'develop' into debian/unstable
Removed python-wrong-path-for-interpreter.patch, solved upstream.
Removed sed command redundant with patch dynamic-build.patch.
samtools (1.1-1) unstable; urgency=medium
Build-depend and recommend libio-pty-perl for the regression tests.
Current changelog.
Make autopkg test depend on tabix.
Merge tag '1.2' into debian/unstable
New upstream release ; no new copyright notice nor license term.
Corrected syntax.
Removed fix_coverage_cap.patch, obsoleted by -d option.
Refreshed fuzzy patches.
Build-depend on libhts-dev 1.2.
Current changelog.
Revert last commit, that included patched files by mistake.
Current changelog.
samtools (1.2-1) unstable; urgency=medium
Revert "Remove source files not present in upstream tarball"
Note that this source package is managed like htslib.
samtools (1.2-2) unstable; urgency=medium
Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
Merge tag '1.3' into debian/unstable
New upstream release; no new copyright nor license notice.
Replace LDLIBS by LIBS, following upstream changelog.
Removed patch; issue solved upstream.
Removed patch; issue solved upstream.
Merge tag '1.3.1' into debian/unstable
New upstream release; no new copyright nor license notice.
Conforms with Policy version 3.9.8.
Remove legacy statement on the libbam.
samtools (1.3.1-1) unstable; urgency=medium
Needs htslib 1.3.1.
Current changelog.
samtools (1.3.1-2) unstable; urgency=medium
Dominique Belhachemi (1):
added 3 bug fixes
James McCoy (1):
Move debian/upstream to debian/upstream/metadata
Sascha Steinbiss (15):
adapt to new build system
use secure Vcs-Git
patch configure.in to not call make in m4_esyscmd_s()
add Build-Dep to automake
cleanup copyright
add patch header
patch spelling
update d/changelog
add NEWS for 1.3 commandline API changes
dch -r
fix FTBFS
use John Marshall's patch to address test pty issue
fall back to working ax_with_curses.m4
adjust d/changelog
dch -r
Steffen Moeller (1):
Added references to registries
-----------------------------------------------------------------------
This annotated tag includes the following new commits:
new 8abd692 New upstream version 1.6
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
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