Commits · ff50bd20273e11818d209afcfb7a9de9d98121a2 · github_fork / Chromap

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Apr 28, 2021
- Support barcode filtering by whitelist · ff50bd20
  Haowen Zhang authored Apr 27, 2021
  
  ff50bd20
- Use all barcodes to compute barcode abundance · 07cb578d
  Haowen Zhang authored Apr 27, 2021
  
  07cb578d
Apr 27, 2021
- Fix a bug in bulk dedup · d32678df
  Haowen Zhang authored Apr 27, 2021
  
  d32678df
- Fix a bug in bulk dedup · 0999cc45
  Haowen Zhang authored Apr 26, 2021
  
  0999cc45
- Improved barcode correction · a95474e3
  Haowen Zhang authored Apr 26, 2021
  
  a95474e3
- Bulk dedup for low mem mode · 53a9a9f1
  Haowen Zhang authored Apr 26, 2021
  
  53a9a9f1
Apr 26, 2021
- Fix a potential overflow · 617ef157
  Haowen Zhang authored Apr 25, 2021
  
  617ef157
Apr 24, 2021
- Scale up MAPQ · e9e5680c
  Haowen Zhang authored Apr 24, 2021
  
  e9e5680c
Apr 23, 2021
- Improve MAPQ · f0152318
  Haowen Zhang authored Apr 23, 2021
  
  f0152318
Apr 19, 2021
- Tune MAPQ · b04fe5de
  Haowen Zhang authored Apr 19, 2021
  
  b04fe5de
- Fix a data type issue. · e836e2c2
  Li authored Apr 18, 2021
  
  e836e2c2
- Tune MAPQ · cace2324
  Haowen Zhang authored Apr 18, 2021
  
  cace2324
Apr 18, 2021
- Fix sam mapping positions · 8edb2a56
  Haowen Zhang authored Apr 17, 2021
  
  8edb2a56
Apr 17, 2021
- Use MAPQ to filter untrustworhty mate pair rescue instead of hard removing. · 84643789
  Li authored Apr 16, 2021
  
  84643789
- Relax the criterion for cancelling supplement candidate · 8e586bd1
  Li authored Apr 16, 2021
  
  8e586bd1
Apr 16, 2021
- Fix an strand bias issue when supplementing mate pairs · 685da8b0
  Li authored Apr 15, 2021
  
  685da8b0
- Merge branch 'master' of github.com:haowenz/chromap · 4caa2dda
  Haowen Zhang authored Apr 15, 2021
  
  4caa2dda
- Improve MAPQ · b5da1f21
  Haowen Zhang authored Apr 15, 2021
  
  b5da1f21
- Stable SAM sorting · d62cc773
  Haowen Zhang authored Apr 15, 2021
  
  d62cc773
Apr 14, 2021
- Fix issues in PAF low mem mode · 67395f8e
  Haowen Zhang authored Apr 14, 2021
  
  67395f8e
- Low mem mode for PAF · d7c561f0
  Haowen Zhang authored Apr 14, 2021
  
  d7c561f0
Apr 09, 2021
- Add build test on travis · 2332f589
  Haowen authored Apr 08, 2021
  
  2332f589
- Update command line parsing · 4e11850a
  Haowen Zhang authored Apr 08, 2021
  
  4e11850a
Mar 31, 2021
- Fix SAM sorting issue · 34f5545f
  Haowen Zhang authored Mar 31, 2021
  
  34f5545f
- Merge branch 'master' of github.com:haowenz/chromap · 7730851c
  Haowen Zhang authored Mar 31, 2021
  
  7730851c
- Fix issues in low mem for SAM and pairs · e07fa3d0
  Haowen Zhang authored Mar 31, 2021
  
  e07fa3d0
Mar 19, 2021
- Filter repetitive alignments more in split alignment · d8e3009e
  Li authored Mar 18, 2021
  
  d8e3009e
- Dedupe can be turned off in low mem mode · 8bbbb83f
  Haowen Zhang authored Mar 18, 2021
  
  8bbbb83f
Mar 09, 2021
- Add a heuristic mapq filter for split alignment · c201171f
  Li authored Mar 08, 2021
  
  c201171f
- Fix a bug of outputing pairs header when no natural order given · 3a29a378
  Li authored Mar 08, 2021
  
  3a29a378
Mar 03, 2021
- Add the option for specifying global chrom order. · 68a95f0e
  Li authored Mar 02, 2021
  
  68a95f0e
Mar 02, 2021
- Fix a small issue for splitalignment mapq · 2a10ed91
  Li authored Mar 01, 2021
  
  2a10ed91
Mar 01, 2021
- Only apply the user provided chr order for pairs flipping · 90b41ee0
  Li authored Feb 28, 2021
  
  90b41ee0
Feb 26, 2021
- Sort pairs format prioritizing chrom. Allow user to provide chromsome order for the output. · 36eddda4
  Li authored Feb 25, 2021
  
  36eddda4
Feb 24, 2021
- Finalize the split alignment without end fixing · d8ec11ec
  Li authored Feb 23, 2021
  
  d8ec11ec
Feb 05, 2021
- Merge branch 'li_dev' into haowen_dev · a99e6272
  Haowen Zhang authored Feb 04, 2021
  a99e6272
- Reformat code · 60efd798
  Haowen Zhang authored Feb 04, 2021
  
  60efd798
Feb 04, 2021
- Fix a bug of misplacing two lines · 34a6ec8d
  Li authored Feb 04, 2021
  
  34a6ec8d
Feb 02, 2021
- Do not use mapq_pe when split alignment · e5c6c213
  Li authored Feb 01, 2021
  
  e5c6c213
Feb 01, 2021
- Fix a bug of adjusting read end for pairs format · 075caeb8
  Li authored Jan 31, 2021
  
  075caeb8

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Commits · ff50bd20273e11818d209afcfb7a9de9d98121a2