Commits · 49a122e853fb83fd21a57be625c71aa4c6dcbb08 · Mirrors / biopet.biopet

04 Mar, 2015 11 commits
- Use correct flag repetition for SamtoolsView · 49a122e8
  bow authored Mar 04, 2015
  
  49a122e8
- Add strand-specific jobs · 87141e4a
  bow authored Mar 04, 2015
  
  87141e4a
- Properly enclose outputs in RawBaseCounter · 77a04b4b
  bow authored Mar 04, 2015
  
  77a04b4b
- Rename Ln.out => Ln.output and Ln.in => Ln.input · 7eae47d3
  bow authored Mar 04, 2015
  
  7eae47d3
- Add isoforms output to summary · a3e87679
  bow authored Mar 04, 2015
  
  a3e87679
- Add wrapper for bgzip · ba3e1de5
  bow authored Mar 04, 2015
  
  ba3e1de5
- Remove default value from expressionMeasures option · 0b6eb747
  bow authored Mar 04, 2015
  
  0b6eb747
- Use '0' as fallback character when merging tables of counts · 4764854d
  bow authored Mar 04, 2015
  
  4764854d
- Refactor Ln-or-MergeSamFiles job into a single factory function · b1665acf
  bow authored Mar 04, 2015
  
  b1665acf
- Use symlink for strand-separation jobs for single-strand samples · 8ae89b1b
  bow authored Mar 04, 2015
  
  8ae89b1b
- Formatting updates and `add` function call update · 33295ff4
  bow authored Mar 04, 2015
  
  33295ff4
03 Mar, 2015 29 commits
- Add optional WipeReads job · 1d119f17
  bow authored Mar 03, 2015
  
  1d119f17
- Update WipeReads wrapper · 2d230d3b
  bow authored Mar 03, 2015
  
  2d230d3b
- Initial flag and validation for rRNA removal · 98ef4383
  bow authored Mar 03, 2015
  
  98ef4383
- Use structural typing to unify Ln and MergeSamFiles output access · 7b69ab04
  bow authored Mar 03, 2015
  
  7b69ab04
- Add option to supply rRNA intervals · 50aac08f
  bow authored Mar 03, 2015
  
  50aac08f
- Specify correct strand options in cufflinks · c9844261
  bow authored Mar 03, 2015
  
  c9844261
- Add strand separation jobs · 2918b2ee
  bow authored Mar 03, 2015
  
  2918b2ee
- Supply default arguments to samtools view wrapper · 566bfacd
  bow authored Mar 03, 2015
  
  566bfacd
- Require sample libraries to have all single-end or paired-end · d205c898
  bow authored Mar 03, 2015
  
  d205c898
- Formatting updates · 768ac623
  bow authored Mar 03, 2015
  
  768ac623
- Reorganize imports · 4d676d03
  bow authored Mar 03, 2015
  
  4d676d03
- Add base counts per-sample output to summary · b3269f0e
  bow authored Mar 03, 2015
  
  b3269f0e
- Expose merge jobs outside of multi sample jobs function · ad31d8a9
  bow authored Mar 03, 2015
  
  ad31d8a9
- Add base count table merge jobs · a19f5ef3
  bow authored Mar 03, 2015
  
  a19f5ef3
- Add conditional installation of required packages in aggr_base_count.R · ffacca84
  bow authored Mar 03, 2015
  
  ffacca84
- Add jobs for base counting on gene and exon · edc53ef9
  bow authored Mar 03, 2015
  
  edc53ef9
- Update base count aggregator for easier use in the pipeline · ca772e5b
  bow authored Mar 03, 2015
  
  ca772e5b
- Initial jobs for base counting · ed444315
  bow authored Mar 03, 2015
  
  ed444315
- 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