Commits · 1c5ab2a12e6880e80832fdeb8817ce8d5b949d71 · github_fork / Chromap

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Jan 24, 2021
- Fix bugs in generating SAM · 1c5ab2a1
  Haowen Zhang authored Jan 14, 2021
  
  1c5ab2a1
- A painful implementation of split alignment with ed · d552d9ab
  Haowen Zhang authored Jan 12, 2021
  
  d552d9ab
- Generate SAM with ksw for single end read mapping · 053df9bb
  Haowen Zhang authored Jan 11, 2021
  
  053df9bb
- Formatting debug output · 68db07b4
  Haowen Zhang authored Dec 15, 2020
  
  68db07b4
Nov 25, 2020
- Tune parameters · df39e2a9
  Haowen Zhang authored Nov 25, 2020
  
  df39e2a9
Nov 19, 2020
- Avoid too many supplement operations · ccd90a8d
  Li authored Nov 18, 2020
  
  ccd90a8d
Nov 18, 2020
- Merge branch 'li_dev' · bfae352b
  Haowen Zhang authored Nov 18, 2020
  bfae352b
- Supplement more · 26d51a3c
  Haowen Zhang authored Nov 18, 2020
  
  26d51a3c
- Do not supplement if too many best mates. · d37ad5da
  Li authored Nov 17, 2020
  
  d37ad5da
- Limit the supplement of best candidates · ab48f22d
  Haowen Zhang authored Nov 17, 2020
  
  ab48f22d
- Avoid repeated candidate add in supplementary · f0db86e2
  Li authored Nov 17, 2020
  
  f0db86e2
- Get back singletons · 93a80914
  Haowen Zhang authored Nov 17, 2020
  
  93a80914
- Fix multiple bugs · b1120d68
  Haowen Zhang authored Nov 17, 2020
  
  b1120d68
Nov 10, 2020
- Merge branch 'master' into refactor · 31a02b34
  Haowen Zhang authored Nov 10, 2020
  
  31a02b34
- Code refactor and same results · da883d90
  Haowen Zhang authored Nov 10, 2020
  
  da883d90
Nov 08, 2020
- Reduce the memory usage of cache. Fix an issue of a situation similar to palindrome. · 67b62cd5
  Li authored Nov 08, 2020
  
  67b62cd5
Oct 12, 2020
- Merge remote-tracking branch 'origin/li_dev' · 5c533895
  Haowen Zhang authored Oct 11, 2020
  5c533895
Sep 16, 2020
- Tune MAPQ · 9a3b3eb0
  Haowen Zhang authored Sep 15, 2020
  
  9a3b3eb0
- Reduce the stored history size · 6d71babd
  Li authored Sep 15, 2020
  
  6d71babd
Sep 09, 2020
- Improve barcode correction · ac2692de
  Haowen Zhang authored Sep 09, 2020
  
  ac2692de
- Don't use mapq to update candidate count · 4a00cfa5
  Haowen Zhang authored Sep 08, 2020
  
  4a00cfa5
Sep 08, 2020
- Fix an issue of underflowing cause heap sort failure · ef049267
  Li authored Sep 08, 2020
  
  ef049267
- Fix several issues with computing repetitive_seed_length · 8419f917
  Li authored Sep 07, 2020
  
  8419f917
- Better handling the coordinate when there is tandem repeats · 624b80dc
  Li authored Sep 07, 2020
  
  624b80dc
Sep 05, 2020
- Do not trigger repetitive second round if there are too few minimizers to start with · 05a446c7
  Li authored Sep 04, 2020
  
  05a446c7
- Augment the candidates with mate information, which is more general than rescuing from mate · 8aa7ed94
  Li authored Sep 04, 2020
  
  8aa7ed94
- Rescue the mate if there is unique best candidate. Use less seed requirement when rescuing · 1625797f
  Li authored Sep 04, 2020
  
  1625797f
Sep 01, 2020
- Fix an issue of early stopping · e6cb2e89
  Li authored Sep 01, 2020
  
  e6cb2e89
Aug 24, 2020
- Better rule for stop early heuristic. Try to redo the collect seeds if too many repetitive seeds · 8b31bade
  Li authored Aug 24, 2020
  
  8b31bade
Aug 20, 2020
- Refactor and fix a bug in early stop · 914ab5de
  Haowen Zhang authored Aug 19, 2020
  
  914ab5de
Aug 16, 2020
- Merge branch 'master' of github.com:haowenz/chromap · 560a488f
  Haowen Zhang authored Aug 16, 2020
  560a488f
- Merge remote-tracking branch 'origin/li_dev' · c5b7eb3e
  Haowen Zhang authored Aug 16, 2020
  c5b7eb3e
Aug 11, 2020
- Tune mapq. Stop early if mapq already 0. · bf415ed1
  Li authored Aug 10, 2020
  
  bf415ed1
Aug 08, 2020
- Merge · a0d91b7b
  Li authored Aug 07, 2020
  
  a0d91b7b
Aug 05, 2020
- Fix an issue of unsigned underflow issue in binary search. · 881b28a1
  Li authored Aug 04, 2020
  
  881b28a1
- Tune mapq · b219427b
  Haowen Zhang authored Aug 04, 2020
  
  b219427b
- Rescue the extreme repetitve read whose mate is very unqiue. · d5bdd97c
  Li authored Aug 04, 2020
  
  d5bdd97c
Jul 29, 2020
- Tune mapq · 61b8fd1b
  Haowen Zhang authored Jul 28, 2020
  
  61b8fd1b
Jul 24, 2020
- Fix a bug on second best mappings of paired-end reads and tune mapq · 932e13c2
  Haowen Zhang authored Jul 24, 2020
  
  932e13c2
- Tune mapq · 75e7722d
  Haowen Zhang authored Jul 23, 2020
  
  75e7722d

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Commits · 1c5ab2a12e6880e80832fdeb8817ce8d5b949d71