Commits · eebab126a20caa960a3e40ef490793aa801a78a5 · Mirrors / biopet.biopet

Jan 27, 2016
- Pindel update wrapper, specifing the output files (pindel generates more files) · eebab126
  Wai Yi Leung authored 9 years ago
  
  eebab126
Jan 26, 2016
- Some fixes with boolean in the pindelvcf wrapper · 314d4942
  Wai Yi Leung authored 9 years ago
  
  314d4942
Jan 25, 2016
- Adding sampleBamInsertSize (with some error, too be fixed later) · 5827c070
  Wai Yi Leung authored 9 years ago
  
  5827c070
Jan 20, 2016
- Add pindel2vcf to pipeline · d4901714
  Wai Yi Leung authored 9 years ago
  
  d4901714
- PindelVCF wrapper · 2e9fffdb
  Wai Yi Leung authored 9 years ago
  
  2e9fffdb
Jan 19, 2016
- Style refactor of PindelCaller wrapper · 674e3168
  Wai Yi Leung authored 9 years ago
  
  674e3168
- Remove pindel from the list of default callers · 225b0cae
  Wai Yi Leung authored 9 years ago
  
  225b0cae
Jan 18, 2016
- Refactor style · 262ad5ef
  Wai Yi Leung authored 9 years ago
  
  262ad5ef
- Pindel outputpath fix. · ef29ace5
  Wai Yi Leung authored 9 years ago
  
  ef29ace5
Jan 15, 2016
- Fix output path for pindel (pindel outputs to certain dir with prefix_) · 8867a510
  Wai Yi Leung authored 9 years ago
  
  8867a510
- Fix output path for pindel (pindel outputs to certain dir with prefix_) · 102aa9e7
  Wai Yi Leung authored 9 years ago
  
  102aa9e7
- Our option couln't be -l (due to biopet debug flag) · 216b8df6
  Wai Yi Leung authored 9 years ago
  
  216b8df6
- Changed defaults and fix the pindelconfig script. · bdca6a2d
  Wai Yi Leung authored 9 years ago
  
  bdca6a2d
- Fix major error, things in beforeCmd was intended to do in beforeGraph · 9db6c09d
  Wai Yi Leung authored 9 years ago
  
  9db6c09d
- Fix pindel caller (fixing null error with Option[File] = None instead of _) · de250d3f
  Wai Yi Leung authored 9 years ago
  
  de250d3f
- Fix input of bams to svcalling tools.. · 8af58a0b
  Wai Yi Leung authored 9 years ago
  
  8af58a0b
Jan 14, 2016
- Fix compile errors · e42f7355
  Wai Yi Leung authored 9 years ago
  
  e42f7355
- Adding Pindel to ShivaSVCalling · d1384de8
  Wai Yi Leung authored 9 years ago
  
  d1384de8
Jan 12, 2016
- Adding the pindel wrapper to the extensions. Updated to support v0.2.5b8 · 7213a031
  Wai Yi Leung authored 9 years ago
  
  7213a031
- Fix short name · d46354a7
  Peter van 't Hof authored 9 years ago
  
  d46354a7
Jan 11, 2016
- fix tiny setting · 9fbc2376
  Sander Bollen authored 9 years ago
  
  9fbc2376
- Change gvcf input · 6ebf4f39
  Peter van 't Hof authored 9 years ago
  
  6ebf4f39
- Merge bed records · 7bedb39b
  Peter van 't Hof authored 9 years ago
  
  7bedb39b
- Improved logging · 798f296b
  Peter van 't Hof authored 9 years ago
  
  798f296b
- Disable report · 621ccaf4
  Peter van 't Hof authored 9 years ago
  
  621ccaf4
- Style fix · 203a0c98
  Peter van 't Hof authored 9 years ago
  
  203a0c98
Jan 10, 2016
- Fixed type · bf11fd13
  Peter van 't Hof authored 9 years ago
  
  bf11fd13
Jan 08, 2016
- Code improvement · 26f84c6a
  Peter van 't Hof authored 9 years ago
  
  26f84c6a
- Style changes · 96efe61e
  Peter van 't Hof authored 9 years ago
  
  96efe61e
- Fix output file for tophat step · e3fd97af
  Peter van 't Hof authored 9 years ago
  
  e3fd97af
- Style fix · a2c4d7bc
  Peter van 't Hof authored 9 years ago
  
  a2c4d7bc
- Fixed rna metrics · 565f3979
  Peter van 't Hof authored 9 years ago
  
  565f3979
Jan 06, 2016
- Switch to multisample mapping · d9c88772
  Peter van 't Hof authored 9 years ago
  
  d9c88772
- fix merge request issues · a161a802
  Sander Bollen authored 9 years ago
  
  a161a802
- Fixed typo · fa4b60f8
  Peter van 't Hof authored 9 years ago
  
  fa4b60f8
- Moved summaryFile · 4143a145
  Peter van 't Hof authored 9 years ago
  
  4143a145
Jan 05, 2016
- Fix temp files in mapping · 748dd6c2
  Peter van 't Hof authored 9 years ago
  
  748dd6c2
- Fix scoverage aggregate · e21646ad
  Peter van 't Hof authored 9 years ago
  
  e21646ad
- Fixed executable in test · 9e4144e8
  Peter van 't Hof authored 9 years ago
  
  9e4144e8
- merge bed file to prevent massive files · 29ddfee6
  Sander Bollen authored 9 years ago
  
  29ddfee6