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Commits on Feb 12, 2020

• Added the ability to sort unmapped data by minhash.

  Show description for 6e6d5f9
  

  jkbonfield

  authored and

  whitwham

  committed
  6e6d5f9

• Fix documentation and help string for addreplacerg.

  valeriuo

  committed
  4fc76fe

Commits on Feb 5, 2020

• Add more explanation on remote fasta files to samtools view docs

  daviesrob

  committed
  a6a160b

• Use the new method fai_path to retrieve the name of a FAI file.

  Show description for 451834d
  

  valeriuo

  authored and

  daviesrob

  committed
  451834d

• Delete the "samtools import" subcommand.

  Show description for 616f2c3
  

  jkbonfield

  authored and

  daviesrob

  committed
  616f2c3

Commits on Feb 4, 2020

• Convert remaining samtools code to use HTSlib API directly

  Show description for f4346b1
  jmarshall

  committed
  f4346b1

Commits on Jan 30, 2020

• Spelling corrections [minor]

  Show description for 20c72f1
  

  jmarshall

  authored and

  jkbonfield

  committed
  20c72f1

Commits on Jan 23, 2020

• Fix target_count size and value. (PR samtools#1174)

  Show description for 383a31b
  

  valeriuo

  authored and

  daviesrob

  committed
  383a31b

• Make hts_with_curses.m4 test if -ltinfo is needed for linking

  Show description for db7681c
  

  daviesrob

  authored and

  whitwham

  committed
  db7681c

• Add #ifdef check for KEY_RESIZE

  Show description for 8d70534
  

  daviesrob

  authored and

  whitwham

  committed
  8d70534

• Add location for ncursesw-compatible header on Illumos

  Show description for 0c4c43c
  

  daviesrob

  authored and

  whitwham

  committed
  0c4c43c

• Improve autoconf curses tests

  Show description for 2a8d57b
  

  daviesrob

  authored and

  whitwham

  committed
  2a8d57b

• Rename AX_WITH_CURSES to HTS_WITH_CURSES

  Show description for 0a00cbd
  

  daviesrob

  authored and

  whitwham

  committed
  0a00cbd

Commits on Jan 21, 2020

• Ensure tview test prints the correct number of columns

  Show description for acf411a
  

  daviesrob

  authored and

  jkbonfield

  committed
  acf411a

Commits on Jan 15, 2020

• Fix Illumos build: autoconfiscate @awk@, other miscellanea (PR samtools#1165)

  Show description for dcb0b2a
  

  jmarshall

  authored and

  daviesrob

  committed
  dcb0b2a

• Add dict -A/--alias option to add AN by adding/removing 'chr' (PR samtools#1164)

  Show description for c245ae4
  

  jmarshall

  authored and

  daviesrob

  committed
  c245ae4

• Add option (-J) to include deletions in depth computation. (PR samtools#1163)

  

  valeriuo

  authored and

  daviesrob

  committed
  b034693

Commits on Jan 14, 2020

• Document that fixmate / markdup need name collated, not name sorted data.

  

  jkbonfield

  authored and

  whitwham

  committed
  5ca6ee2

Commits on Jan 8, 2020

• Updated SAM.gz indexing documentation.

  jkbonfield

  committed
  a2916aa

• Update man page introduction to reflect modern samtools

  

  jmarshall

  authored and

  jkbonfield

  committed
  2dd125d

• Added -@, --threads option to various manual pages.

  jkbonfield

  committed
  d1bc74a

• Added man page for samtools coverage sub-command.

  jkbonfield

  committed
  b6097a3

• Reshuffle main man page ordering.

  Show description for 9813dbf
  jkbonfield

  committed
  9813dbf

Commits on Jan 7, 2020

• Better length estimation. (PR samtools#1161)

  Show description for 80395dc
  

  whitwham

  authored and

  daviesrob

  committed
  80395dc

• Add unit test for merging with a BED file.

  

  valeriuo

  authored and

  daviesrob

  committed
  519e90d

• Add BED file interface for merge.

  

  valeriuo

  authored and

  daviesrob

  committed
  5b27a0c

Commits on Jan 3, 2020

• Limit memory use on sort tests

  Show description for 7f446ca
  daviesrob

  committed
  7f446ca

• Use hts_srand48() rather than srand48()

  Show description for 77a4a01
  

  jmarshall

  authored and

  daviesrob

  committed
  77a4a01

• Prevent shell brace expansion in this complex awk expression

  Show description for a42029e
  

  jmarshall

  authored and

  daviesrob

  committed
  a42029e

Commits on Dec 10, 2019

• Added new tests for optical duplicates.

  Show description for c62a0f1
  

  whitwham

  authored and

  jkbonfield

  committed
  c62a0f1

Commits on Dec 6, 2019

• Merge version number bump and NEWS file from master

  daviesrob

  committed
  c5b7134

• Release 1.10

  daviesrob

  committed
  76877ea

• Fix invalid memory access in tv_win_goto()

  Show description for 79eecf6
  daviesrob

  committed
  79eecf6

• Fix header file for strcasecmp.

  valeriuo

  committed
  6fe0285

Commits on Dec 2, 2019

• Add on-the-fly indexing for samtools sort

  Show description for 064361a
  

  daviesrob

  authored and

  whitwham

  committed
  064361a

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