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Commits on May 19, 2022

• Document that the XB tag now contains the mapping quality too

  clintval

  committed
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Commits on Mar 6, 2022

• Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option

  lh3

  committed
  58e3ed2

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• Merge pull request lh3#292 from nh13/patch-1

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  lh3

  authored
  cb7e5df

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• Merge pull request lh3#297 from nh13/patch-3

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  lh3

  authored
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Commits on Feb 23, 2021

• debug flag to measure memory

  lh3

  committed
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Commits on Aug 19, 2020

• Clarify bwa mem -5 option

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  nh13

  authored
  84b2abb

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Commits on Aug 12, 2020

• allow the user to specify the XA drop ratio via the -z option

  nh13

  committed
  50122be

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• Update fastmap.c

  nh13

  authored
  ab9e0e0

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Commits on Aug 6, 2020

• Document "-u"

  nh13

  authored
  e598572

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Commits on Jul 2, 2020

• added MIT license to some non-GPL source files

  lh3

  committed
  436aceb

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Commits on Apr 2, 2018

• Merge branch 'dev' into XB

  lh3

  committed
  11d53b0

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• optionally write XB to include alignment score

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  lh3

  committed
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Commits on Sep 26, 2017

• r1187: a typo in command line help

  lh3

  committed
  b582816

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Commits on Jul 31, 2017

• Release 0.7.16-r1180

  lh3

  committed
  47d9fb2

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Commits on Jul 4, 2017

• Several trivial Debian patches

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  tillea

  authored and

  jmarshall

  committed
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Commits on Jun 27, 2017

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

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  jmarshall

  committed
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• Added option to write output to file

  

  José Manuel Abuín Mosquera

  authored and

  jmarshall

  committed
  d28da05

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Commits on May 31, 2016

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

  lh3

  committed
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Commits on Feb 1, 2016

• a typo in fastmap command-line prompt

  lh3

  committed
  1e6a10c

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Commits on Jan 27, 2016

• removed the pbread mode

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  lh3

  committed
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Commits on Dec 21, 2014

• updated documentations

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  lh3

  committed
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Commits on Dec 11, 2014

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

  lh3

  committed
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Commits on Nov 26, 2014

• r1017: process I/O in a separate thread

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  lh3

  committed
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Commits on Nov 19, 2014

• r1005: insert arbitrary header lines

  lh3

  committed
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Commits on Nov 18, 2014

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

  lh3

  committed
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Commits on Oct 30, 2014

• r963: expose mask_level

  lh3

  committed
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Commits on Oct 21, 2014

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

  lh3

  committed
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Commits on Oct 20, 2014

• r930: use 3rd round seeding by default

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  lh3

  committed
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Commits on Oct 15, 2014

• shm works on small files, but not large ones

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  lh3

  committed
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Commits on Sep 28, 2014

• r876: optionally ignore idxbase.alt file

  lh3

  committed
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Commits on Sep 19, 2014

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

  lh3

  committed
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Commits on Sep 17, 2014

• r854: improved the calculation of pa

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  lh3

  committed
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Commits on Sep 16, 2014

• r844: added intra-species contig mapping mode

  lh3

  committed
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• r843: presetting for ONT 2d reads

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  lh3

  committed
  90518f1

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• r830: optionally fixed chunk size

  lh3

  committed
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