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Commits on Jul 13, 2023

• fix various typos caught by lintian parsers

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  emollier

  authored and

  whitwham

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  28c5243

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Commits on Jan 24, 2023

• Improve samtools collate consistency with sort - re: temp file handling.

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  jkbonfield

  authored and

  daviesrob

  committed
  6102753

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• Use TMPDIR environment variable, when looking for a temporary folder.

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  2 peopleauthored and

  daviesrob

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Commits on Oct 13, 2022

• Revise collate to require an input filename.

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  jkbonfield

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  daviesrob

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  ac44b4c

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• Fix SEGV in samtoools collate when no filename given.

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  jkbonfield

  authored and

  daviesrob

  committed
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Commits on Nov 12, 2019

• Updates copyright message for 2019.

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  whitwham

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  daviesrob

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Commits on Oct 16, 2019

• Add --verbosity INT global option for setting hts_verbose

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  jmarshall

  authored and

  jkbonfield

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Commits on Aug 20, 2019

• Add a PG line when producing a new file.

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  valeriuo

  authored and

  daviesrob

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Commits on Aug 19, 2019

• Change `bam_hdr*` to `sam_hdr*`, with the exception of `bam_hdr_read` and `bam_hdr_write`.

  

  valeriuo

  authored and

  daviesrob

  committed
  8a52b07

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• Switch to new header API.

  

  valeriuo

  authored and

  daviesrob

  committed
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Commits on May 3, 2018

• Add a fast paired collate option.

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  whitwham

  authored and

  daviesrob

  committed
  e6c3114

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Commits on Mar 2, 2018

• Improve collate interface and add tests

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  daviesrob

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Commits on Jan 17, 2018

• Use the update HD function from HTSlib in sort and collate.

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  valeriuo

  authored and

  daviesrob

  committed
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Commits on Feb 9, 2017

• Improved multi-threading support for many more samtools commands.

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  jkbonfield

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Commits on Nov 4, 2016

• Fix usage description of bamshuf/collate

  

  kdm9

  authored and

  jmarshall

  committed
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Commits on Apr 14, 2016

• Merge error checking improvements (PR #467)

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  jmarshall

  committed
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• Various tidying up and segfault fixes

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  jmarshall

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Commits on Apr 13, 2016

• Use print_error_errno() where appropriate

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  jmarshall

  committed
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Commits on Mar 8, 2016

• Fix warnings from adding HTS_RESULT_USED to htslib prototypes.

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  daviesrob

  authored and

  jmarshall

  committed
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Commits on Jan 28, 2016

• Add #include <config.h> to all *.c source files [minor]

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  jmarshall

  committed
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Commits on Dec 8, 2015

• Rename bamshuf to collate

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  mp15

  authored and

  jmarshall

  committed
  97c9883

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Commits on Aug 20, 2015

• Prefix errors with "samtools <subcmd>:" rather than "samtools:"

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  jmarshall

  committed
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Commits on Aug 13, 2015

• Merge --output-fmt-option etc global option handling (PR #395)

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  jmarshall

  committed
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Commits on Aug 6, 2015

• Replace assign_short_opts() so struct options can be const

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  jmarshall

  committed
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Commits on Jun 10, 2015

• Add checks for bam_hdr_read and sam_hdr_read returning NULL.

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  daviesrob

  committed
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Commits on May 20, 2015

• More long option handling.

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  jkbonfield

  committed
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Commits on May 15, 2015

• Fixed bamshuf to use BAM level 1 for temp files and .%s for final output file.

  jkbonfield

  committed
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• Updated to keep in sync with htslib changes (hts_open_format et al).

  jkbonfield

  committed
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• More --output-fmt-options: fixmate and bamshuf.

  jkbonfield

  committed
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Commits on May 14, 2015

• Changed bamshuf to use sam_open instead of bgzf_open so it can handle all formats.

  jkbonfield

  committed
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Commits on Sep 9, 2014

• Merge abort/assert reduction (PR #290)

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  jmarshall

  committed
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Commits on Aug 28, 2014

• Reduce use of abort, remove assert(fp), pass one string to fprintf not multicall

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  mp15

  committed
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Commits on Aug 1, 2014

• Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

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  jmarshall

  committed
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• Add copyright notices and licensing boilerplate

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  jmarshall

  committed
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Commits on Dec 4, 2013

• Usage message tweaks to satisfy test/test.pl's test_usage()

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  jmarshall

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