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Commits on Jul 2, 2020

• added MIT license to some non-GPL source files

  lh3

  committed
  436aceb

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 Sep 11, 2017

• r1185: don't lower supp mapq with -5

  lh3

  committed
  340babd

Commits on Jul 31, 2017

• r1181: fixed a segfault (lh3#145) due to (lh3#138)

  lh3

  committed
  a9c688a

Commits on Jul 3, 2017

• Mem should set the mate cigar tag.

  nh13

  committed
  3b96dce

Commits on May 31, 2016

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

  lh3

  committed
  f123871

Commits on Jan 27, 2016

• removed the pbread mode

  Show description for 1247dc2
  lh3

  committed
  1247dc2

Commits on Oct 22, 2014

• r943: change the default -y to 20, but ...

  Show description for 3d129be
  lh3

  committed
  3d129be

• r942: ignore ALT hits when counting n_sub for ...

  Show description for 4177d6c
  lh3

  committed
  4177d6c

Commits on Oct 21, 2014

• r941: set a min length for 3rd-round seeding

  lh3

  committed
  60b7284

• r940: fixed a bug - missing primary hit

  lh3

  committed
  282130a

• 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

• r929: added simplified LAST-like seeding

  lh3

  committed
  038af2a

• r926: prepare to move -g to bwa-postalt.js

  lh3

  committed
  3370ae9

Commits on Oct 16, 2014

• r907: revert to -g.8 by default

  lh3

  committed
  76a365a

• r906: don't reduce non-ALT mapQ by default

  lh3

  committed
  d8d8b23

Commits on Oct 14, 2014

• r895: increase the default max_XA_hits_alt to 200

  Show description for 2a18fa1
  lh3

  committed
  2a18fa1

Commits on Sep 30, 2014

• r878: XA is given to the best alignment

  Show description for a03d01f
  lh3

  committed
  a03d01f

Commits on Sep 26, 2014

• r875: invalid SAM output for ALT hits

  lh3

  committed
  dae4ca3

Commits on Sep 19, 2014

• r868: use soft clip for ALT hits

  lh3

  committed
  7426a75

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

  lh3

  committed
  9af3606

Commits on Sep 18, 2014

• These files were committed on a wrong branch

  lh3

  committed
  a41afe4

Commits on Sep 17, 2014

• r854: improved the calculation of pa

  Show description for c982443
  lh3

  committed
  c982443

• r849: the pa tag now gives a number

  Show description for 825ae92
  lh3

  committed
  825ae92

Commits on Sep 16, 2014

• r848: tag alignments with primary ALT

  lh3

  committed
  6f37c14

• r830: optionally fixed chunk size

  lh3

  committed
  4b6eeb3

• r829: killed a harmless gcc warning

  lh3

  committed
  624687b

Commits on Sep 15, 2014

• r827: an alt hit as good as a pri hit as supp

  lh3

  committed
  b07587f

• r824: ALT mapping seems working

  lh3

  committed
  aee53f1

Commits on Sep 14, 2014

• r823: towards ALT support

  lh3

  committed
  015ab3f

• Merge branch 'dev' into alt

  lh3

  committed
  8116bcc

Commits on Sep 12, 2014

• r821: more relax on containing seeds

  lh3

  committed
  8d2b931

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