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Commits on Oct 30, 2019

• Mostly ref length changes.

  

  whitwham

  authored and

  valeriuo

  committed
  3ccd329

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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

  committed
  f9e1caf

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Commits on Sep 24, 2019

• Prepare for 64-bit positions

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  daviesrob

  authored and

  valeriuo

  committed
  cbe1246

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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

  committed
  7eb338f

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Commits on Aug 19, 2019

• Remove the direct use of header stuct fields.

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  valeriuo

  authored and

  daviesrob

  committed
  0cff5ab

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• Switch to the new header API methods for reference name and length.

  

  valeriuo

  authored and

  daviesrob

  committed
  4e76835

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• 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
  b44ffdf

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Commits on Jul 3, 2019

• Add global --write-index option.

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  jkbonfield

  authored and

  valeriuo

  committed
  23a0e42

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Commits on Aug 30, 2018

• Fixed very minor memory leaks.

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  jkbonfield

  authored and

  daviesrob

  committed
  284feed

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Commits on Sep 27, 2017

• Remove trailing whitespace and tabs

  daviesrob

  committed
  d47faf0

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Commits on Jun 28, 2017

• Limited the number of LN tag reads to one, inside a SQ line.

  

  valeriuo

  authored and

  daviesrob

  committed
  8eff6e8

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Commits on Feb 9, 2017

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

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  jkbonfield

  committed
  24971ad

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Commits on Apr 14, 2016

• Merge error checking improvements (PR samtools#467)

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  jmarshall

  committed
  f6db782

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• Various tidying up and segfault fixes

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  jmarshall

  committed
  1152881

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Commits on Apr 13, 2016

• Use print_error_errno() where appropriate

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  jmarshall

  committed
  24d3235

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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
  de96bfb

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Commits on Feb 22, 2016

• Reformat "Notes" in long -? usage output

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  jmarshall

  committed
  d49c73b

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Commits on Jan 28, 2016

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

  Show description for 74a3e0a
  jmarshall

  committed
  74a3e0a

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Commits on Sep 9, 2015

• Merge --output-fmt-option etc followup (PR samtools#461)

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  jmarshall

  committed
  caea801

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Commits on Aug 26, 2015

• Added calls to sam_open_mode() to auto-detect file format by name.

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  jkbonfield

  committed
  25bee0e

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Commits on Aug 25, 2015

• Added global i/o options to "samtools depad".

  jkbonfield

  committed
  cf18e41

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Commits on Jun 18, 2015

• Merge depad improvements and conversion to htslib API (PR samtools#404)

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  jmarshall

  committed
  29d6b58

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Commits on Jun 3, 2015

• Further CRAM fixes.

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  jkbonfield

  committed
  63c060d

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• Fixes samtools#201 - thanks Peter.

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  jkbonfield

  committed
  f85deba

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Commits on Jun 2, 2015

• Switched to using htslib instead of bam.h. Plus CRAM support.

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  jkbonfield

  committed
  9c2461e

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• Samtools depad fixes (part 1).

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  jkbonfield

  committed
  7802db3

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Commits on Nov 4, 2014

• Prevent warnings when compiling on a 32-bit host [minor]

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  jmarshall

  committed
  a25229a

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Commits on Sep 9, 2014

• Merge abort/assert reduction (PR samtools#290)

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  jmarshall

  committed
  20817a8

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• Recanonicalise padding.c whitespace -- USE -b/-w TO DIFF/BLAME

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  jmarshall

  committed
  1f8267d

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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
  7b5a9ea

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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
  fcb8af0

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• Add copyright notices and licensing boilerplate

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  jmarshall

  committed
  8da9ef2

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Commits on May 14, 2014

• Prevent segfault when input file could not be opened

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  jmarshall

  committed
  8bd7048

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• Prevent segfault when input file could not be opened

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  jmarshall

  committed
  971d0e8

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