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Commits on Apr 21, 2023

• r1171: add operator priority explicit with ()

  lh3

  committedApr 21, 2023
  180faa3

• An option to output SEQ field for secondary alignment (lh3#687)

  

  mikolmogorov

  and

  lh3

  committedApr 21, 2023
  704fbc6

Commits on Feb 14, 2023

• Add HD header ilne to SAM output

  

  nh13

  authored and

  lh3

  committedFeb 14, 2023
  1d3c3ee

Commits on Jul 19, 2021

• dev-r1084: fixed flag integer overflow

  lh3

  committedJul 19, 2021
  83a535f

• dev-r1079: per-read error rate

  lh3

  committedJul 19, 2021
  161ae7f

Commits on Jul 16, 2021

• fixed potential integer overflows

  lh3

  committedJul 16, 2021
  5f449c5

• Merge branch 'master' into utec

  lh3

  committedJul 16, 2021
  b046052

Commits on Jul 2, 2021

• Use #defines for CIGAR operators in C code

  

  jmarshall

  authored and

  lh3

  committedJul 2, 2021
  260a68d

• Use the full MIDNSHP=X string whenever printing CIGAR strings

  

  jmarshall

  authored and

  lh3

  committedJul 2, 2021
  177eef2

Commits on Apr 5, 2021

• r1009: fixed a compiler warning

  lh3

  committedApr 5, 2021
  0b41dd2

Commits on Apr 22, 2020

• r987: position on for strand wrongly outputted

  lh3

  committedApr 22, 2020
  cd2b190

Commits on Apr 21, 2020

• r985: optionally report cs/cg on the query strand

  lh3

  committedApr 21, 2020
  da7109f

Commits on Jan 21, 2020

• r972: fixed negative de:f caused by ambiguous base

  lh3

  committedJan 21, 2020
  7996f04

Commits on Jan 7, 2020

• r962: abort given wrong RG line; resolves lh3#541

  lh3

  committedJan 7, 2020
  3c0d05d

Commits on Apr 5, 2019

• SAM TLEN should be 0 when either read is unmapped

  

  jmarshall

  authored and

  lh3

  committedApr 5, 2019
  371bc95

Commits on Feb 27, 2019

• r921: output unmapped reads in full PAF

  lh3

  committedFeb 27, 2019
  55e39c2

Commits on Feb 5, 2019

• r913: output tag "rl", length of unseedable regs

  lh3

  committedFeb 5, 2019
  1739a26

Commits on Jan 23, 2019

• r908: added an assertion to detect a potential bug

  lh3

  committedJan 23, 2019
  597212b

Commits on Jan 12, 2019

• r906: de tag is wrongly calculated given "N"

  lh3

  committedJan 12, 2019
  48e230f

Commits on Nov 25, 2018

• r892: avoid de:f:0.0000

  lh3

  committedNov 25, 2018
  2c52364

• r891: compute gap-compressed divergence

  lh3

  committedNov 25, 2018
  128476e

Commits on Nov 5, 2018

• r873: comforming to C99/C11; resolves lh3#261

  lh3

  committedNov 5, 2018
  a8ee48c

Commits on Oct 27, 2018

• r860: MD/cs not working with --eqx

  lh3

  committedOct 27, 2018
  9ed56b4

Commits on Sep 15, 2018

• r832: fixed outdated -L. Resolved lh3#231 and lh3#233

  lh3

  committedSep 15, 2018
  7d80d6d

Commits on Aug 22, 2018

• r828: --MD to support spliced alignment

  lh3

  committedAug 22, 2018
  3a119d6

Commits on Jul 25, 2018

• r819: mappy to support cs/MD

  lh3

  committedJul 25, 2018
  ff9917a

Commits on Jul 7, 2018

• optionally output unmapped query in PAF

  lh3

  committedJul 7, 2018
  a609a07

Commits on Jun 19, 2018

• r792: fixed -Wextra warnings and resolved lh3#184

  lh3

  committedJun 19, 2018
  7e6e8ca

Commits on May 30, 2018

• r784: support the =/X CIGAR operators (lh3#156)

  lh3

  committedMay 30, 2018
  154d2ca

Commits on Mar 23, 2018

• r752: option to copy comments to output (lh3#136)

  lh3

  committedMar 23, 2018
  08bd212

Commits on Mar 22, 2018

• r751: optionally output MD (lh3#118)

  lh3

  committedMar 22, 2018
  8766d28

• r750: check puts() return (lh3#132 & lh3#103)

  lh3

  committedMar 22, 2018
  623b5d9

Commits on Dec 8, 2017

• r611: document --idx-no-seq; better inv aln

  lh3

  committedDec 8, 2017
  0e42628

Commits on Dec 6, 2017

• r607: estimate sequence divergence

  lh3

  committedDec 6, 2017
  704ff9f

Commits on Nov 10, 2017

• r567: minor change to lh3#56

  lh3

  committedNov 10, 2017
  99a2709

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