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Commits on Apr 2, 2018

• Merge branch 'dev' into XB

  lh3

  committed
  11d53b0

• optionally write XB to include alignment score

  Show description for eb7dbc1
  lh3

  committed
  eb7dbc1

Commits on Sep 26, 2017

• r1187: a typo in command line help

  lh3

  committed
  b582816

Commits on Jul 31, 2017

• Release 0.7.16-r1180

  lh3

  committed
  47d9fb2

Commits on Jul 4, 2017

• Several trivial Debian patches

  Show description for c56c2e4
  

  tillea

  authored and

  jmarshall

  committed
  c56c2e4

Commits on Jun 27, 2017

• Add "bwa mem -o FILE" synonym and documentation

  Show description for bc58bf2
  jmarshall

  committed
  bc58bf2

• Added option to write output to file

  

  José Manuel Abuín Mosquera

  authored and

  jmarshall

  committed
  d28da05

Commits on May 31, 2016

• r1142: added option -5 for Hi-C data

  lh3

  committed
  f123871

Commits on Feb 1, 2016

• a typo in fastmap command-line prompt

  lh3

  committed
  1e6a10c

Commits on Jan 27, 2016

• removed the pbread mode

  Show description for 1247dc2
  lh3

  committed
  1247dc2

Commits on Dec 21, 2014

• updated documentations

  Show description for ed95769
  lh3

  committed
  ed95769

Commits on Dec 11, 2014

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

  lh3

  committed
  925ddfb

Commits on Nov 26, 2014

• r1017: process I/O in a separate thread

  Show description for 9d8c906
  lh3

  committed
  9d8c906

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 30, 2014

• r963: expose mask_level

  lh3

  committed
  9bf898f

Commits on Oct 21, 2014

• r933: with bwa-postalt ready, drop option -g

  lh3

  committed
  76a15ea

Commits on Oct 20, 2014

• r930: use 3rd round seeding by default

  Show description for a6b5a30
  lh3

  committed
  a6b5a30

Commits on Oct 15, 2014

• shm works on small files, but not large ones

  Show description for bfd5e18
  lh3

  committed
  bfd5e18

Commits on Sep 28, 2014

• r876: optionally ignore idxbase.alt file

  lh3

  committed
  0a2cf98

Commits on Sep 19, 2014

• r867: fixed a few bugs; added ALT hits to XA

  lh3

  committed
  9af3606

Commits on Sep 17, 2014

• r854: improved the calculation of pa

  Show description for c982443
  lh3

  committed
  c982443

Commits on Sep 16, 2014

• r844: added intra-species contig mapping mode

  lh3

  committed
  92bc684

• r843: presetting for ONT 2d reads

  Show description for 90518f1
  lh3

  committed
  90518f1

• r830: optionally fixed chunk size

  lh3

  committed
  4b6eeb3

• r828: changed the default scoring for pacbio

  lh3

  committed
  5d26ab0

Commits on Aug 29, 2014

• r815: optionally output ref fasta header

  Show description for 35ac99b
  lh3

  committed
  35ac99b

Commits on Aug 25, 2014

• r809: new strategy for the -a mode

  lh3

  committed
  b5cba25

Commits on May 13, 2014

• r764: changed -c in "-x pacbio" to 500

  lh3

  committed
  08517ac

Commits on May 12, 2014

• updated maual page

  lh3

  committed
  a35a6c2

Commits on May 11, 2014

• r762: cleanup for the new release; unfinished

  Show description for 39a6cd5
  lh3

  committed
  39a6cd5

Commits on May 6, 2014

• r754: added command msg for -h

  lh3

  committed
  6ac8dd5

Commits on May 4, 2014

• r749: max_hits tunable on CMD; default to 5

  lh3

  committed
  ce3c198

Commits on Apr 30, 2014

• r735: fixed a bug caused by merge

  lh3

  committed
  11698fc

Commits on Apr 24, 2014

• r729: halved band width; doubled patch band width

  lh3

  committed
  76bb49e

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