Tags

samtools (1.3.1-2~bpo8+1) jessie-backports; urgency=medium

  * Team upload.
  * Rebuild for jessie-backports.

 -- Afif Elghraoui <afif@debian.org>  Fri, 05 Aug 2016 21:03:54 -0700

samtools (1.3.1-2) unstable; urgency=medium

  952da10 Build-depends on htslib 1.3.1. (Closes: #822701)

 -- Charles Plessy <plessy@debian.org>  Sun, 08 May 2016 21:11:12 +0900

samtools (1.3.1-1) unstable; urgency=medium

  0c961b2 Merge tag '1.3.1' into debian/unstable
  3666b08 Conforms with Policy version 3.9.8.

 -- Charles Plessy <plessy@debian.org>  Tue, 26 Apr 2016 21:12:05 +0900

Samtools release 1.3.1: bug fixes, notably sort temporary files

* The sort command creates any needed temporary files alongside the final
  output file (similarly to the pre-1.3 behaviour), and now aborts when
  it detects a collision with another sort invocation's temporary files.

  When the -T PREFIX option specified is a directory (or when sorting to
  standard output), a random component is now added to temporary filenames
  to try to avoid collisions (#432, #523, #529, #535, PR #530).

* All samtools commands now check for I/O errors more carefully, especially
  when writing output files (#111, #253, #470, PR #467).

* Build fixes for 32-bit systems; be sure to run configure on such systems
  to enable large file support and access to 2GiB+ files.

* The fasta/fastq/bam2fq command no longer ignores reads when the -s option
  is used (#532).

* The fastq -O option no longer crashes on reads that do not have an OQ tag
  field (#517).

* The merge and sort commands now handle (unusual) BAM files that have no
  textual @SQ headers (#548, #550).

* Sorting files containing @CO headers no longer duplicates the comment
  headers, which previously happened on large sorts for which temporary
  files were needed (#563).

* The rmdup and view -l commands no longer crash on @RG headers that do not
  have a LB field (#538).

* Fixed miscellaneous issues #128, #130, #131, #489, and #514.

samtools (1.3-1~bpo8+1) jessie-backports; urgency=medium

  * Rebuild for jessie-backports.

 -- Charles Plessy <plessy@debian.org>  Fri, 12 Feb 2016 12:54:03 +0900

Samtools release 1.3: many improvements, fixes, new commands

* The obsolete "samtools sort in.bam out.prefix" usage has been removed.
  If you are still using -f, -o, or out.prefix, convert to use -T PREFIX
  and/or -o FILE instead.  (#295, #349, #356, #418, PR #441; see also
  discussions in #171, #213.)

* The "bamshuf" command has been renamed to "collate" (hence the term
  bamshuf no longer appears in the documentation, though it still works
  on the command line for compatibility with existing scripts).

* The mpileup command now outputs the unseen allele in VCF/BCF as <*>
  rather than X or <X> as previously, and now has AD, ADF, ADR, INFO/AD,
  INFO/ADF, INFO/ADR --output-tags annotations that largely supersede
  the existing DV, DP4, DPR annotations.

* The mpileup command now applies BAQ calculations at all base positions,
  regardless of which -l or -r options are used (previously with -l it was
  not applied to the first few tens of bases of each chromosome, leading
  to different mpileup results with -l vs. -r; #79, #125, #286, #407).

* Samtools now has a configure script which checks your build environment
  and facilitates choosing which HTSlib to build against.  See INSTALL
  for details.

* Samtools's Makefile now fully supports the standard convention of
  allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed.
  Previously it listened to $(LDLIBS) instead; if you were overriding
  that, you should now override LIBS rather than LDLIBS.

* A new addreplacerg command that adds or alters @RG headers and RG:Z
  record tags has been added.

* The rmdup command no longer immediately aborts (previously it always
  aborted with "bam_get_library() not yet implemented"), but remains
  not recommended for most use (#159, #252, #291, #393).

* Merging files with millions of headers now completes in a reasonable
  amount of time (#337, #373, #419, #453; thanks to Nathan Weeks,
  Chris Smowton, Martin Pollard, Rob Davies).

* Samtools index's optional index output path argument works again (#199).

* Fixed calmd, targetcut, and potential mpileup segfaults when given broken
  alignments with POS far beyond the end of their reference sequences.

* If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(),
  or bam_prob_realn_core() functions, note that these now take an additional
  ref_len parameter.  (The versions named without "_core" are unchanged.)

* The tview command's colour scheme has been altered to be more suitable
  for users with colour blindness (#457).

* Samtools depad command now handles CIGAR N operators and accepts
  CRAM files (#201, #404).

* Samtools stats now outputs separate "N" and "other" columns in the
  ACGT content per cycle section (#376).

* Added -a option to samtools depth to show all locations, including
  zero depth sites (#374).

* New samtools dict command, which creates a sequence dictionary
  (as used by Picard) from a FASTA reference file.

* Samtools stats --target-regions option works again.

* Added legacy API sam.h functions sam_index_load() and samfetch() providing
  bam_fetch()-style iteration over either BAM or CRAM files.  (In general
  we recommend recoding against the htslib API directly, but this addition
  may help existing libbam-using programs to be CRAM-enabled easily.)

* Fixed legacy API's samopen() to write headers only with "wh" when writing
  SAM files.  Plain "w" suppresses headers for SAM file output, but this
  was broken in 1.2.

* "samtools fixmate - -" works in pipelines again; with 1.0 to 1.2,
  this failed with "[bam_mating] cannot determine output format".

* Restored previous "samtools calmd -u" behaviour of writing compression
  level 0 BAM files.  Samtools 1.0 to 1.2 incorrectly wrote raw non-BGZF
  BAM files, which cannot be read by most other tools.  (Samtools commands
  other than calmd were unaffected by this bug.)

* Restored bam_nt16_nt4_table[] to legacy API header bam.h.

* Fixed bugs #269, #305, #320, #328, #346, #353, #365, #392, #410, #445,
  #462, #475, and #495.

samtools (1.2-3~bpo8+1) jessie-backports; urgency=medium

  * Team upload.
  * Rebuild for jessie-backports.

 -- Afif Elghraoui <afif@ghraoui.name>  Sun, 04 Oct 2015 18:22:30 -0700

samtools (1.2-2) unstable; urgency=medium

  [ Afif Elghraoui ]
  eb56918 Add patch to fix building on i386
  702d289 Remove source files not present in upstream tarball
  7afd302 Allow all scripts to be called without language extensions

  [ Charles Plessy ]
  876f680 Document the update workflow of the source package's repository.

 -- Charles Plessy <plessy@debian.org>  Thu, 17 Sep 2015 20:21:15 +0900

samtools (1.2-1) unstable; urgency=medium

  a5f28a0 Merge tag '1.2' into debian/unstable
  c542e84 Build-depend on libhts-dev 1.2.
  6c2d9cd Build-depend and recommend libio-pty-perl.
          (Needed for the regression tests.)
  23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
  1091aab Refreshed fuzzy patches.

 -- Charles Plessy <plessy@debian.org>  Tue, 16 Jun 2015 06:12:12 +0900

Bug fix release

samtools (1.1-1) unstable; urgency=medium

  c448d48 Merge tag '1.1' into debian/unstable
  d12ab1e Merge branch 'develop' into debian/unstable to solve issue
          with regression tests needing a pseudo-terminal.
          See https://github.com/samtools/samtools/issues/300
  c87f8ce Add autopkg tests.
  7c50b7b Removed python-wrong-path-for-interpreter.patch
          (issue solved upstream).

 -- Charles Plessy <plessy@debian.org>  Thu, 25 Sep 2014 09:04:20 +0900

samtools (1.0-1) unstable; urgency=low

  [ Charles Plessy ]
  54ca0c1 Merge with upstream's develop branch.
  241a731 razip was removed from samtools.
  dc25b81 debian/watch: also track release candidates.
  07aaf71 Indicate repository layout in git-buildpackage conf. file.

  * debian/control

  8bc0fb7 Stop depending on CDBS and quilt.
  e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
  b5f284c Build-depend on tabix for the regression tests, that use bgzip.
  9febad6 Recommend python since samtools installs a python script in /usr/bin.
  0446ed7 Conforms with Policy 3.5.6.

  * New package samtools-test

  7293cca Create a test package for the test data.
  6bd7b89 Adjust install file for two-package build.
  caff5f5 Clean before installing test files (this removes compiled files).

  * debian/rules

  c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
  845581d Adjust for dynamic linking.
  d859052 Indicate path to packaged bgzip.
  cb23517 Mimick Makefile's CPPFLAGS.
  aee1c6c Allow parallel building.
  edc09e4 Prevent Makefile from including local copy of the HTSlib.

  * debian/patches

  f73d764 d062687 Refreshed patches.
  2c52f6a 61ac2c5 Forwarded patches on GitHub.
  b8eb378 Dropped fix_example_makefile.patch, obsolete.
  66079b9 Correct path to python interpreter.
  218c1c1 Modify Makefile to facilitate dynamic linking.

  [ Andreas Tille ]
  f69f412 Versioned Build-Depends libhts-dev >= 1.0

 -- Charles Plessy <plessy@debian.org>  Tue, 23 Sep 2014 09:36:27 +0900

Bug fix release

samtools (1.0-1~experimental) experimental; urgency=low

  54ca0c1 Merge with upstream's develop branch.
  241a731 razip was removed from samtools.
  dc25b81 debian/watch: also track release candidates.
  07aaf71 Indicate repository layout in git-buildpackage conf. file.

  * debian/control

  8bc0fb7 Stop depending on CDBS and quilt.
  e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
  b5f284c Build-depend on tabix for the regression tests, that use bgzip.
  9febad6 Recommend python since samtools installs a python script in /usr/bin.
  e6ad97f Conforms to Policy 3.9.5.

  * New package samtools-test

  7293cca Create a test package for the test data.
  6bd7b89 Adjust install file for two-package build.
  caff5f5 Clean before installing test files (this removes compiled files).

  * debian/rules

  c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
  845581d Adjust for dynamic linking.
  d859052 Indicate path to packaged bgzip.
  cb23517 Mimick Makefile's CPPFLAGS.
  aee1c6c Allow parallel building.

  * debian/patches

  f73d764 d062687 Refreshed patches.
  2c52f6a 61ac2c5 Forwarded patches on GitHub.
  b8eb378 Dropped fix_example_makefile.patch, obsolete.
  66079b9 Correct path to python interpreter.
  218c1c1 Modify Makefile to facilitate dynamic linking.

 -- Charles Plessy <plessy@debian.org>  Sat, 23 Aug 2014 16:02:12 +0900

First HTSlib-based Samtools release

Final standalone non-htslib samtools release

Test release RC12

Test release RC11

Test release RC10

Test release RC9