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Commits on Oct 14, 2021

• NEWS update

  

  daviesrob

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  whitwham

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  260b6b8

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• Rationalise expected empty output files for tests

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  daviesrob

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  whitwham

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  8768fb6

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• Fix missing test_cmd() out parameter

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  daviesrob

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  whitwham

  committed
  305c7a4

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Commits on Oct 13, 2021

• NEWS tweak [minor]

  daviesrob

  committed
  5fa5ac2

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Commits on Oct 12, 2021

• NEWS updates for autumn 2021 (PR #1516)

  jkbonfield

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  db9f5bb

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Commits on Oct 7, 2021

• Autumn 2021 Release Copyright Updates

  

  whitwham

  authored and

  daviesrob

  committed
  a4ea156

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• Unmap filtered alignments in samtools view (PR #1512)

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  whitwham

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  fee11de

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Commits on Oct 6, 2021

• Add view --rf option

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  jkbonfield

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  whitwham

  committed
  568b5ea

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• Use sam.gz for temporaries when sorting files with long references

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  daviesrob

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  whitwham

  committed
  401e254

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• Strip index name from prefix used for sort temporary files

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  daviesrob

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  whitwham

  committed
  4487d83

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• Make sort better handle temporary file collisions

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  daviesrob

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  whitwham

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Commits on Oct 1, 2021

• Replace Curses mvprintw() with va_list-based equivalent

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  jmarshall

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Commits on Sep 27, 2021

• Fix clang-13 unused variable message.

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  whitwham

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Commits on Sep 22, 2021

• Add support for the SRA "@RUN.1234 proper:name:100:200" FASTQ syntax

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  jkbonfield

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  daviesrob

  committed
  a765ee0

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Commits on Sep 9, 2021

• Flush standard output samFiles before printing error messages

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  jmarshall

  authored and

  valeriuo

  committed
  a78376c

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Commits on Sep 8, 2021

• Exit with error from `init_group_id` in case of unrecoverable failure.

  valeriuo

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  5b56865

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Commits on Sep 7, 2021

• Fix a bug: qsort was called on an empty array.

  valeriuo

  committed
  02baa80

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• Implement filtering by read group or sample name in stats.

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  valeriuo

  committed
  447aff2

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Commits on Sep 3, 2021

• Use `getopt_long` instead of `getopt`, to allow for flexible ordering of the

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  valeriuo

  committed
  f6ab19d

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• remove trailing space for test/maintainer/check_spaces.pl

  

  lindenb

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  valeriuo

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  2c58425

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• answer to https://github.com/samtools/samtools/pull/1432

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  lindenb

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  valeriuo

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  4addf47

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• Fix styling.

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  valeriuo

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• Added support for custom index files.

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  lindenb

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  valeriuo

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• Remove blank spaces.

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  valeriuo

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• New Tool "samtools samples" . See https://github.com/samtools/samtools/pull/1432

  

  lindenb

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  valeriuo

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Commits on Aug 31, 2021

• Add mpileup --output-BP-5 option.

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  jkbonfield

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  valeriuo

  committed
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Commits on Aug 27, 2021

• Removed code prematurely setting optical state.

  Show description for c8095d7
  whitwham

  committed
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Commits on Aug 25, 2021

• Remove the legacy samtools API

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  jmarshall

  authored and

  valeriuo

  committed
  7751ae3

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Commits on Aug 24, 2021

• Protect against out of order headers for samtools merge.

  Show description for 589b8d2
  

  jkbonfield

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  valeriuo

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  589b8d2

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• Make samtools merge and pileup use CRAM_OPT_SHARED_REF to share

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  jkbonfield

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  valeriuo

  committed
  0e4de41

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Commits on Aug 19, 2021

• Make inplace samtools reheader use maximum compression on CRAM.

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  jkbonfield

  authored and

  daviesrob

  committed
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Commits on Aug 18, 2021

• Make the filter expression language apply before modifying records.

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  jkbonfield

  authored and

  whitwham

  committed
  1cb068a

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Commits on Aug 11, 2021

• Bug fix writing dual index records on single-ended input.

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  jkbonfield

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  whitwham

  committed
  c33ca91

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Commits on Aug 10, 2021

• Add the missing mod1.sam test file

  

  jkbonfield

  authored and

  whitwham

  committed
  0fd47ff

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• Add base modification mpileup tests, plus bug fixes.

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  jkbonfield

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  whitwham

  committed
  70e7b10

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