Commits · 9812237cbb27f5e86a8bcb64eefd8eb4f0995d0c · Mirrors / biopet.biopet

Jul 01, 2015
- Optimize imports · 9812237c
  Peter van 't Hof authored 9 years ago
  
  9812237c
- Fixing code warning from ide · 7f2580f2
  Peter van 't Hof authored 9 years ago
  
  7f2580f2
Jun 30, 2015
- Fix code style warnings by IDE · b563034b
  Peter van 't Hof authored 9 years ago
  
  b563034b
- possible to override defaultVmemFactor now · 483fe407
  Peter van 't Hof authored 9 years ago
  
  483fe407
- Adding more information for each executable to summary · ee5ed3c8
  Peter van 't Hof authored 9 years ago
  
  ee5ed3c8
- Change template · 0733d2fe
  Peter van 't Hof authored 9 years ago
  
  0733d2fe
Jun 29, 2015
- front page message · 7b9e2e8e
  Sander Bollen authored 9 years ago
  
  7b9e2e8e
- flexiprep base messages · c93b5637
  Sander Bollen authored 9 years ago
  
  c93b5637
- flexiprep read messages · 660e1416
  Sander Bollen authored 9 years ago
  
  660e1416
- Add more stats to summary from flexiprep · 0833e74c
  bow authored 9 years ago
  
  0833e74c
- Set default config for CollectRnaSeqMetrics RefFlat value · 84b4fbf2
  bow authored 9 years ago
  
  84b4fbf2
- Rename num_qual_gte on reads to num_avg_qual_gte · 8df7adf6
  bow authored 9 years ago
  
  8df7adf6
Jun 28, 2015
- Add CollectRnaSeqMetrics histogram to summary file · 85f91910
  bow authored 9 years ago
  
  85f91910
- Use absolute path for tophat fix output · 657d8684
  bow authored 9 years ago
  
  657d8684
- Update default memory settings · a0e4262d
  bow authored 9 years ago
  
  a0e4262d
- Update Gentrap test for compatibility with new reference · 10363d74
  bow authored 9 years ago
  
  10363d74
- Update BamMetrics RNA mode and its tests · 5301853f
  bow authored 9 years ago
  
  5301853f
- Style updates · a8a816b5
  bow authored 9 years ago
  
  a8a816b5
Jun 27, 2015
- Rename SeqStat in summary for consistency · ce4db038
  bow authored 9 years ago
  
  ce4db038
- Update 'num_qual_gte' to 'num_qual' array · 42334159
  bow authored 9 years ago
  
  42334159
- Remove 'num_n' in base stats since we already have 'nucleotides.N' · 0a07f02f
  bow authored 9 years ago
  
  0a07f02f
- Rename Seqstat -> SeqStat · 58102415
  bow authored 9 years ago
  
  58102415
- Cleanup + style updates · e4b0834e
  bow authored 9 years ago
  
  e4b0834e
- Add step for merging unmapped and mapped tophat alignment files · 2db37a64
  bow authored 9 years ago
  
  2db37a64
- Add missing stats display in Gentrap report · a9beb867
  bow authored 9 years ago
  
  a9beb867
Jun 26, 2015
- variant messages · ae450d22
  Sander Bollen authored 9 years ago
  
  ae450d22
- insert size messages · 3fe23d90
  Sander Bollen authored 9 years ago
  
  3fe23d90
- Initial Gentrap update to use new Metrics module · d6acc80f
  bow authored 9 years ago
  
  d6acc80f
- proper alignment summaries · 3ca1e994
  Sander Bollen authored 9 years ago
  
  3ca1e994
Jun 25, 2015
- Fix for NullPointer exception error in #156 · eb9c02c0
  bow authored 9 years ago
  
  eb9c02c0
- Revert phase change in Maven since we use the correct Option now · 77360126
  bow authored 9 years ago
  
  77360126
- Revert phase change in Maven since we use the correct Option now · 2efc1a6d
  bow authored 9 years ago
  
  2efc1a6d
- Wrap Picard dependency list fetch in Option · e5d886e4
  bow authored 9 years ago
  
  e5d886e4
- Use 'compile' phase for pulling Picard version · f78ea918
  bow authored 9 years ago
  
  f78ea918
- Use new reference module in Gentrap · ea23733f
  bow authored 9 years ago
  
  ea23733f
- Wrap Picard dependency list fetch in Option · 92b003d5
  bow authored 9 years ago
  
  92b003d5
- Use 'compile' phase for pulling Picard version · c6e433e2
  bow authored 9 years ago
  
  c6e433e2
- Bump version to 0.3.2 · b77d7b4c
  bow authored 9 years ago
  
  View commits for tag v0.3.2 v0.3.2
  
  b77d7b4c
- Fix bug causing missing fragment count row · ad91759b
  bow authored 9 years ago
  
  ad91759b
- Make numHeaderLines default to 0 in tool and be explicit in Gentrap · 15b8ad49
  bow authored 9 years ago
  
  15b8ad49