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Commits on Aug 31, 2022

• Limit the number of sort temporary files by merging if too many

  

  daviesrob

  authored and

  jkbonfield

  committed
  145b1ee

• Use the thread pool when reading temporary files

  

  daviesrob

  authored and

  jkbonfield

  committed
  1a0367d

• Use the same thread pool for reading and writing in sort

  

  daviesrob

  authored and

  jkbonfield

  committed
  707b1fe

• Ensure searching NEWS for /empty/ finds this "zero-length file" entry

  

  jmarshall

  authored and

  jkbonfield

  committed
  23e803e

Commits on Aug 26, 2022

• bug fix: samtools merge --template-coordinate

  

  nh13

  authored and

  whitwham

  committed
  3571c32

• Also add a --min-BQ option to samtools consensus.

  

  jkbonfield

  authored and

  daviesrob

  committed
  5627e9d

• Make consensus -m simple use a more usual definition of min_depth.

  

  jkbonfield

  authored and

  daviesrob

  committed
  537667d

• bug fix: template coordinate sort when merging in memory

  

  nh13

  authored and

  whitwham

  committed
  454a397

• Revision to sort -n name comparison function strnum_cmp.

  

  jkbonfield

  authored and

  whitwham

  committed
  4eee171

• Improve samtools sort on lustre.

  

  jkbonfield

  authored and

  whitwham

  committed
  9844c5b

• Make sort merge in memory before writing temporary files

  

  daviesrob

  authored and

  whitwham

  committed
  038cde8

Commits on Aug 24, 2022

• Added tests and documentation.

  

  whitwham

  authored and

  daviesrob

  committed
  629fb5e

• Changed error handling to use print_error.

  

  whitwham

  authored and

  daviesrob

  committed
  360db61

• Added json formatted stats.

  

  whitwham

  authored and

  daviesrob

  committed
  81e5af3

• Enable the use of read groups in duplicate marking.

  

  whitwham

  authored and

  daviesrob

  committed
  8a802e1

Commits on Aug 23, 2022

• Change stats to use a single structure.

  

  whitwham

  authored and

  daviesrob

  committed
  0ebd2bd

• add mapq histogram to samtools stats (PR samtools#1684)

  lindenb

  authored
  0ec8128

Commits on Aug 19, 2022

• Minor formatting fix to samtools-reference man page

  jkbonfield

  committed
  116f0ed

Commits on Aug 18, 2022

• Merge version number bump and NEWS file from master

  daviesrob

  committed
  f1b26f3

• Release 1.16

  daviesrob

  committed
  41a6dd6

Commits on Aug 16, 2022

• Add NEWS item on samtools reference fix.

  

  daviesrob

  authored and

  jkbonfield

  committed
  58b9303

• Fix unaligned access in dump_ref()

  

  daviesrob

  authored and

  jkbonfield

  committed
  a60ce3d

• Add reference and head to the list of known usage/tty failures on MINGW

  

  jkbonfield

  authored and

  daviesrob

  committed
  434242e

Commits on Aug 12, 2022

• NEWS Additions for Summer 2022 Release. (PR samtools#1673)

  

  whitwham

  and

  daviesrob

  authored
  08cb48b

Commits on Aug 10, 2022

• Ensure test output files are ignored and cleaned

  jmarshall

  committed
  9082f4c

Commits on Aug 8, 2022

• Extend FILTER EXPRESSION man page section.

  

  jkbonfield

  authored and

  daviesrob

  committed
  9a2ca07

Commits on Aug 1, 2022

• Summer 2022 copyright corrections.

  

  whitwham

  authored and

  daviesrob

  committed
  c9c1722

Commits on Jul 28, 2022

• Merge Enable samtools index on multiple alignment files (PR samtools#1674)

  daviesrob

  committed
  90b3649

• Add -M option required to activate multiple input file indexing

  jmarshall

  committed
  1df722b

• Be explicit about earlier Samtools versions in the man page

  jmarshall

  committed
  f7acaf2

• Allow multiple alignment files to be indexed at once

  jmarshall

  committed
  7f17c43

Commits on Jul 25, 2022

• Merge Allow '*' for -T to write all tags to fastq (PR samtools#1679)

  daviesrob

  committed
  c7acf84

• Fix missing @rg headers when using 'samtools merge -r'

  

  daviesrob

  authored and

  whitwham

  committed
  1c5fbed

Commits on Jul 21, 2022

• Document -T '*' in the samtools-fasta man page

  daviesrob

  committed
  d302dbb

• Make fastq -T '' work, and add fastq -T '*' tests

  daviesrob

  committed
  40ce26f

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