Commits · 672a25a85c0d6b09909981f3ab851235da58f24f · Mirrors / biopet.biopet

03 Mar, 2015 11 commits
- Add -f and -F flags to samtools view wrapper · 672a25a8
  bow authored Mar 03, 2015
  
  672a25a8
- Use proper repeat argument creation · 2b26dc69
  bow authored Mar 03, 2015
  
  2b26dc69
- Add check for input file and input labels size · 3ed4b2e0
  bow authored Mar 03, 2015
  
  3ed4b2e0
- Check that gene and/or exon output is set for base count aggregation script · a30614f7
  bow authored Mar 03, 2015
  
  a30614f7
- Update hist2count script wrapper · a7905322
  bow authored Mar 03, 2015
  
  a7905322
- Update base count aggregator script wrapper · a461849e
  bow authored Mar 03, 2015
  
  a461849e
- Move Gentrap-specific scripts and their wrappers to the Gentrap package · 82437aa9
  bow authored Mar 03, 2015
  
  82437aa9
- Update makeMergeTableFunction to return the created job · a517be04
  bow authored Mar 03, 2015
  
  a517be04
- Fix optional MergeTables flag errors · 93cda8b8
  bow authored Mar 03, 2015
  
  93cda8b8
- Add merge jobs for cufflinks outputs · dfc0d6d9
  bow authored Mar 03, 2015
  
  dfc0d6d9
- Add symlink jobs for cufflinks outputs · beb6cf00
  bow authored Mar 03, 2015
  
  beb6cf00
02 Mar, 2015 11 commits
- Add MergeTable jobs for gene and exon fragment counts · c15f56d4
  bow authored Mar 02, 2015
  
  c15f56d4
- Update exon fragment count extension · eb7e2d34
  bow authored Mar 02, 2015
  
  eb7e2d34
- Add biopet wrapper for MergeTables · 59c4a795
  bow authored Mar 02, 2015
  
  59c4a795
- Update Gentrap with new Summarizable Sample and Library · 70332617
  bow authored Mar 02, 2015
  
  70332617
- Formatting fix · d85f6941
  bow authored Mar 02, 2015
  
  d85f6941
- Add MergeTables to main tool executables list · 335563b9
  bow authored Mar 02, 2015
  
  335563b9
- Merge branch 'develop' into feature-gentrap · 2a14fb0e
  bow authored Mar 02, 2015
  
  2a14fb0e
- Merge branch 'patch-mutisample_summary' into 'develop' · 1571f046
  bow authored Mar 02, 2015
```
Patch mutisample summary

See merge request !112
```
  1571f046
- Change in scala docs · ca8089a0
  Peter van 't Hof authored Mar 02, 2015
  
  ca8089a0
- Format change · 5109976c
  Peter van 't Hof authored Mar 02, 2015
  
  5109976c
- Format change · a1f5260d
  Peter van 't Hof authored Mar 02, 2015
  
  a1f5260d
01 Mar, 2015 6 commits
- Add MergeTables unit testing · 62fac67a
  bow authored Mar 01, 2015
  
  62fac67a
- Update input prep function and main function · bd97bdb6
  bow authored Mar 01, 2015
  
  bd97bdb6
- Remove extension stripping from mergeTables · 45469451
  bow authored Mar 01, 2015
  
  45469451
- Add checks for feature ID and value index when parsing · 1336161d
  bow authored Mar 01, 2015
  
  1336161d
- Initial working version of table merging tool · e0367dba
  bow authored Mar 01, 2015
  
  e0367dba
- Update scopt dependency · 2c08a258
  bow authored Mar 01, 2015
  
  2c08a258
27 Feb, 2015 12 commits
- Add todo's · e3b3e129
  Peter van 't Hof authored Feb 27, 2015
  
  e3b3e129
- Add default function to add summarizable · 53c4ba81
  Peter van 't Hof authored Feb 27, 2015
  
  53c4ba81
- Fix summary cufflink FPKMs pointing to the same object · cfeef2cc
  bow authored Feb 27, 2015
  
  cfeef2cc
- Make samples and libraries Summarizable · 21182480
  Peter van 't Hof authored Feb 27, 2015
  
  21182480
- Remove Config · 8cdbba34
  Peter van 't Hof authored Feb 27, 2015
  
  8cdbba34
- Use proper names for read counting (=> fragment counting) · 04de5c96
  bow authored Feb 27, 2015
  
  04de5c96
- Fix typo in Gsnap wrapper · db64713f
  bow authored Feb 27, 2015
  
  db64713f
- Use defs for Gentrap sample and library instead of lazy vals · c8445516
  bow authored Feb 27, 2015
  
  c8445516
- Refactor library mapping job · 4e754471
  bow authored Feb 27, 2015
  
  4e754471
- Merge branch 'develop' into feature-gentrap · 0e79aad1
  bow authored Feb 27, 2015
  
  0e79aad1
- Make Gentrap's Sample and Library summarizable · 8a28906a
  bow authored Feb 27, 2015
  
  8a28906a
- Add proper settings map to Gentrap · fe52d7cb
  bow authored Feb 27, 2015
  
  fe52d7cb