Commits · 67395f8e6cf021652038bcc6d27a2f3dc8004cf0 · github_fork / Chromap

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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
Jan 31, 2021
- Support the F1F2,R1R2 case for split alignment. Fix several bugs regarding... · 690d97d0
  Li authored Jan 30, 2021
  690d97d0
Jan 28, 2021
- Use ksw for pairs format mapping · 8f3f1fc2
  Li authored Jan 28, 2021
  
  8f3f1fc2
- Add the format pairs for hic data analysis · e4645bae
  Li authored Jan 28, 2021
  
  e4645bae
Jan 26, 2021
- Support paired-end mode for SAM format. Fix several potential bugs. · 63e039ce
  Li authored Jan 26, 2021
  
  63e039ce
- Fix a possible bug of using out range reference sequence · 4024369b
  Li authored Jan 25, 2021
  
  4024369b
- Prepare to add the support for paired-end split alignment · 2fe280ee
  Li authored Jan 25, 2021
  
  2fe280ee
Jan 25, 2021
- Fix a bug of using wrong map_end_position · 826c238d
  Li authored Jan 25, 2021
  
  826c238d
- Support the split alignment starting with gap · 50e87713
  Li authored Jan 24, 2021
  
  50e87713
- Merge branch 'li_dev' of https://github.com/haowenz/chromap into li_dev · 93366593
  Li authored Jan 24, 2021
  
  93366593
Jan 24, 2021
- Merge branch 'li_dev' of https://github.com/haowenz/chromap into li_dev · d1e8d108
  Li authored Jan 24, 2021
  
  d1e8d108
- Fix cigar and position bugs · d5836636
  Haowen Zhang authored Jan 17, 2021
  
  d5836636
- Add MD tag for debug · b7354d2a
  Haowen Zhang authored Jan 17, 2021
  
  b7354d2a
- Fix some bugs for split alignments and get ready for a big change · 30026dfb
  Haowen Zhang authored Jan 16, 2021
  
  30026dfb
- 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
Jan 18, 2021
- Add SAM header · f85025ae
  Haowen Zhang authored Jan 18, 2021
  
  f85025ae
- Fix cigar and position bugs · c3f8e555
  Haowen Zhang authored Jan 17, 2021
  
  c3f8e555

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Commits · 67395f8e6cf021652038bcc6d27a2f3dc8004cf0