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Commits on Dec 14, 2021

• Add the header line to the output SAM

  Show description for 6b18630
  nh13

  authored
  6b18630

Commits on Feb 23, 2021

• debug flag to measure memory

  lh3

  committed
  b9accf9

Commits on Jul 2, 2020

• added MIT license to some non-GPL source files

  lh3

  committed
  436aceb

Commits on Jul 30, 2017

• Merge pull request lh3#84 from jblachly/readgroupfix

  Show description for 1eee77a
  lh3

  authored
  1eee77a

Commits on Jun 30, 2017

• Copy the whole kstring_t even if it contains NULs

  Show description for 6906498
  jmarshall

  committed
  6906498

Commits on Jun 26, 2017

• Prevent Clang warnings on abs() and fabs() calls

  Show description for ab3a92b
  jmarshall

  committed
  ab3a92b

Commits on Aug 9, 2016

• Forbid literal TAB control characters in @rg line

  jblachly

  committed
  8cc02ba

Commits on May 3, 2016

• r1134: use AH:* instead of AH:Y

  lh3

  committed
  7ec3261

Commits on Apr 28, 2016

• r1130: changed "ah" to "AH"

  lh3

  committed
  3c03825

Commits on Dec 12, 2014

• r1027: segfault caused by the last commit

  lh3

  committed
  c561759

Commits on Dec 11, 2014

• r1025: accept file with -H; allow to replace @sq

  lh3

  committed
  925ddfb

Commits on Nov 19, 2014

• r1005: insert arbitrary header lines

  lh3

  committed
  b5f6ed3

Commits on Nov 18, 2014

• r998: smart pairing; allow mixture of SE/PE reads

  lh3

  committed
  80e4ecf

Commits on Oct 17, 2014

• r915: fixed broken example.c

  lh3

  committed
  a066464

Commits on Oct 16, 2014

• r905: lower peak RAM for "shm -f"

  lh3

  committed
  e318d8e

Commits on Oct 15, 2014

• shm works on small files, but not large ones

  Show description for bfd5e18
  lh3

  committed
  bfd5e18

• shared memory

  lh3

  committed
  6a09529

• r898: read the index into a single memory block

  Show description for c5e859b
  lh3

  committed
  c5e859b

• r896: more flexible ALT reading

  lh3

  committed
  71277f0

Commits on May 1, 2014

• r741: fixed segfault in rare cases

  lh3

  committed
  7954e77

Commits on Apr 16, 2014

• r723: merge adjacent hits

  lh3

  committed
  b93fca2

Commits on Apr 11, 2014

• dev-472: get rid of bwa_fix_xref()

  Show description for 8638cfa
  lh3

  committed
  8638cfa

Commits on Apr 10, 2014

• dev-470: don't stop on bwa_fix_xref2() failures

  Show description for ccbbe48
  lh3

  committed
  ccbbe48

Commits on Mar 28, 2014

• dev-450: support diff ins/del penalties. NO TEST!!

  lh3

  committed
  9ce50a4

Commits on Mar 17, 2014

• r444: more debugging output in CIGAR generation

  Show description for 7d63e76
  lh3

  committed
  7d63e76

Commits on Feb 20, 2014

• r440: a condition not work due to a typo

  lh3

  committed
  e879817

Commits on Feb 19, 2014

• r438: still an issue in MD

  Show description for 17fb85a
  lh3

  committed
  17fb85a

• r436: fix rare MD/NM-CIGAR inconsistencies

  lh3

  committed
  bdd14d2

Commits on Feb 18, 2014

• r435: bugfix - base not complemented on the rev

  lh3

  committed
  4adc34e

Commits on Jan 31, 2014

• Release bwa-0.7.6a-r433

  lh3

  committed
  7c50bad

Commits on Jan 29, 2014

• r431: added the MD tag to bwa-mem

  lh3

  committed
  f524c7d

Commits on Nov 19, 2013

• r419: print the @pg line

  lh3

  committed
  ff6faf8

Commits on May 22, 2013

• conform to the latest (unpublished) SAM spec

  Show description for 9735d7a
  lh3

  committed
  9735d7a

• r391: better method to resolve xref alignment

  Show description for 9a6abe5
  lh3

  committed
  9a6abe5

Commits on May 2, 2013

• Reduce dependency on utils.h - new malloc wrapping scheme.

  Show description for 96e445d
  

  Rob Davies

  committed
  96e445d

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