Commits · b543bb7ab9818c01ac6eeaf2d842b7f04c6a412c · Chaos / chaos.juicer

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Mar 31, 2021
- remove KR · b543bb7a
  Muhammad S Shamim authored Mar 30, 2021
  
  b543bb7a
Mar 30, 2021
- update slurm parameters · ee86244b
  Muhammad S Shamim authored Mar 30, 2021
  
  ee86244b
- update default parameter · 05a0ddfc
  Muhammad S Shamim authored Mar 30, 2021
  
  05a0ddfc
- handle new usage · 41b01f5d
  Muhammad S Shamim authored Mar 29, 2021
  
  41b01f5d
Mar 27, 2021
- Merge pull request #217 from eernst/encode · 43af6757
  nchernia authored Mar 26, 2021
  43af6757
Mar 26, 2021
- Resolves #216 · 80eca072
  eernst authored Mar 26, 2021
  
  80eca072
- Making final stage work in SLURM, permission update to index by chr · 9f609f05
  nchernia authored Mar 25, 2021
  
  9f609f05
Mar 25, 2021
- Some issues corrected around fragment assignment (MT circular chromosome issue) · b4c36542
  nchernia authored Mar 25, 2021
  
  b4c36542
Mar 23, 2021
- Count unique reads correctly · 4e58e70f
  nchernia authored Mar 23, 2021
  
  4e58e70f
- write bam · 5e57f89d
  nchernia authored Mar 23, 2021
  
  5e57f89d
- Major update to Juicer 2.0. Now operates on SAM files · 3c62cd63
  nchernia authored Mar 23, 2021
  
  3c62cd63
- Major update to Juicer 2.0. Now operates on SAM files · 428b55e6
  nchernia authored Mar 23, 2021
  
  428b55e6
Jul 03, 2020
- adding header to mapq0 files · f4cc8e46
  nchernia authored Jul 02, 2020
  
  f4cc8e46
May 12, 2020
- Pulling in master to encode branch · da9b3322
  nchernia authored May 11, 2020
  
  da9b3322
- updating usage. note that none is now the default · d4906482
  nchernia authored May 11, 2020
  
  d4906482
- Change log · 0ecc10e1
  nchernia authored May 11, 2020
  0ecc10e1
May 01, 2020
- Files from @suhas-rao · cab7978b
  Muhammad Saad Shamim authored Apr 30, 2020
  
  cab7978b
Apr 18, 2020
- Update juicer.sh · df12164b
  nchernia authored Apr 17, 2020
  
  View commits for tag 1.5.7 1.5.7
  
  df12164b
Dec 11, 2019
- Last rollback removed a lot of changes in the Juicer 2.0 CPU scripts. Rolling... · 07992b14
  nchernia authored Dec 10, 2019
  07992b14
Nov 25, 2019
- removing repetitive script; the one in misc/ is what should be used · 6403a279
  nchernia authored Nov 25, 2019
  
  6403a279
Nov 13, 2019
- Update custom.md · edbe00da
  Muhammad Saad Shamim authored Nov 13, 2019
  
  edbe00da
- Update bug_report.md · 52847a6a
  Muhammad Saad Shamim authored Nov 13, 2019
  
  52847a6a
Sep 19, 2019
- fixing problem in generate site positions when using Python 3.7 · 8f7177a6
  nchernia authored Sep 19, 2019
  
  8f7177a6
Aug 27, 2019
- Now properly handle quadruple reads. Also eliminated MT check, which was not doing the right thing · c9de8924
  nchernia authored Aug 26, 2019
  
  c9de8924
- added new handling of four way reads to END block · 66e9807c
  nchernia authored Aug 26, 2019
  
  66e9807c
Aug 24, 2019
- Changed chimeric blacklist to handle quadruple reads and eliminate MT exception · a55bfe32
  nchernia authored Aug 23, 2019
  
  a55bfe32
Aug 23, 2019
- merging master into encode branch · 6deb1ee3
  nchernia authored Aug 22, 2019
  
  6deb1ee3
- Major change to chimeric blacklist handling of chimeric reads (3 alignments)... · 2fff94b9
  nchernia authored Aug 22, 2019
  2fff94b9
Aug 09, 2019
- Merge pull request #88 from ecsedi/enhanced-patterns · 7bfdb99a
  nchernia authored Aug 09, 2019
  7bfdb99a
- Merge branch 'master' into enhanced-patterns · 0ff45931
  nchernia authored Aug 09, 2019
  
  0ff45931
- Merge pull request #128 from cErikson/master · 3c6609e1
  nchernia authored Aug 08, 2019
  3c6609e1
- Fixed hardcode core count · 0217ee98
  Christian Erikson authored Aug 08, 2019
  
  0217ee98
- forgot then fi · 50ef1cec
  Christian Erikson authored Aug 08, 2019
  
  50ef1cec
- Added ligation regex quote check · fd760622
  Christian Erikson authored Aug 08, 2019
  fd760622
- Add Arima Ligation · 72de0431
  Christian Erikson authored Aug 08, 2019
  72de0431
- Quote ligation regex · bc2c9117
  Christian Erikson authored Aug 08, 2019
  bc2c9117
- Adding options for ligation junction and setting scripts directory; fixing bug... · 8891985c
  nchernia authored Aug 08, 2019
  8891985c
- deleting separate LibraryComplexity class · beaa79e1
  nchernia authored Aug 08, 2019
  
  beaa79e1
- Got rid of LibraryComplexity class; moved statistics into things that happen with early exit · 74a70ed8
  nchernia authored Aug 08, 2019
  
  74a70ed8
- changing email address · 217a5e5f
  nchernia authored Aug 08, 2019
  
  217a5e5f

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Commits · b543bb7ab9818c01ac6eeaf2d842b7f04c6a412c