Commits · c093c17cfe76553fbee83a6b1c488d68a2c022b4 · Mirrors / biopet.biopet

Apr 22, 2016
- Fixed unit tests · c093c17c
  Peter van 't Hof authored 8 years ago
  
  c093c17c
Apr 21, 2016
- Force reference dict in vcf to check on unknown contigs · adf7f321
  Peter van 't Hof authored 8 years ago
  
  adf7f321
Apr 12, 2016

Merge branch 'feature-sortvcf-picard' into 'develop' · 4caab1f4

bow authored 8 years ago

Adding SortVcf extension

This wrapper can be used to sort VCF files, whenever they have to be sorted (some variant callers generate non-sorted VCF).

See merge request !372

4caab1f4

Apr 11, 2016
- Merge branch 'fix-bamutils-insertsize' into 'develop' · 998687b1
  Peter van 't Hof authored 8 years ago
  
  BamUtils Insertsize estimation is more acurate by sampling from all over the contig. Updated BamUtils to fix the insertsize estimation used in the PindelConfig tool. See merge request !371
  998687b1
- Refactored code to avoid collection.Breakout. (With help from Peter) · 26d14d83
  Wai Yi Leung authored 8 years ago
  
  26d14d83
- Merge branch 'fix-vcffilter' into 'develop' · d7177565
  bow authored 8 years ago
  
  Fixed bug See merge request !375
  d7177565
- Fixed bug · 9c002013
  Peter van 't Hof authored 8 years ago
  
  9c002013
- Merge branch 'develop' into fix-bamutils-insertsize · d2d52a5a
  Wai Yi Leung authored 8 years ago
  
  d2d52a5a
Apr 10, 2016
- Merge branch 'feature-seq_error_test' into 'develop' · 180bb97e
  bow authored 8 years ago
  
  Added binominal test Added this for project 168 See merge request !367
  180bb97e
Apr 08, 2016
- Merge branch 'feature-confignamespace' into 'develop' · 3637e383
  Peter van 't Hof authored 8 years ago
  
  Feature configNamespace See #163. See merge request !348
  3637e383
- Change description · 99a7f2e0
  Peter van 't Hof authored 8 years ago
  
  99a7f2e0
- no more failing tests :-) · 7d00bf07
  Sander Bollen authored 8 years ago
  
  7d00bf07
- well.. it compiles · 6e5f1478
  Sander Bollen authored 8 years ago
  
  6e5f1478
- Merge branch 'develop' into feature-confignamespace · c2e8dbba
  Sander Bollen authored 8 years ago
  
  Conflicts: public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
  c2e8dbba
Apr 06, 2016
- Merge branch 'fix-basecounter' into 'develop' · 6623805f
  bow authored 8 years ago
  
  Fix basecounter Some small fixes See merge request !373
  6623805f
- Fixed typo's · 5a7743d9
  Peter van 't Hof authored 8 years ago
  
  5a7743d9
- Added more status logging · 3297f0bf
  Peter van 't Hof authored 8 years ago
  
  3297f0bf
- Raise default memory · 99ba29c3
  Peter van 't Hof authored 8 years ago
  
  99ba29c3
- Added bam index as depency · c2473edb
  Peter van 't Hof authored 8 years ago
  
  c2473edb
Apr 05, 2016
- set dictRequired to true for this tool · efb74852
  Wai Yi Leung authored 8 years ago
  
  efb74852
- Add file so remove output from testing · 06bc8e4e
  Peter van 't Hof authored 8 years ago
  
  06bc8e4e
- Fix style · de6f2bdc
  Peter van 't Hof authored 8 years ago
  
  de6f2bdc
- Let SortVcf also use Reference trait · dd163178
  Peter van 't Hof authored 8 years ago
  
  dd163178
- Refactor Reference so dict and fai file becomes accessable as a method · 2af46d82
  Peter van 't Hof authored 8 years ago
  
  2af46d82
Apr 04, 2016
- Style changes · 2759a09f
  Peter van 't Hof authored 8 years ago
  
  2759a09f
- Style changes · 40de3b9b
  Peter van 't Hof authored 8 years ago
  
  40de3b9b
- Set required argument to Input · b8b1779f
  Wai Yi Leung authored 8 years ago
  
  b8b1779f
- sequenceDictionary is a File... fixed · f5ffdbb4
  Wai Yi Leung authored 8 years ago
  
  f5ffdbb4
- Adding SortVcf extension · ec9a7972
  Wai Yi Leung authored 8 years ago
  
  ec9a7972
- A bit refactoring on the variable names · b1c4e031
  Wai Yi Leung authored 8 years ago
  
  b1c4e031
- BamUtils Insertsize estimation is more acurate by sampling from all over the contig. · eea29773
  Wai Yi Leung authored 8 years ago
  
  eea29773
- Added MA-SEQ-ERR value · 6656e37d
  Peter van 't Hof authored 8 years ago
  
  6656e37d
Apr 01, 2016
- Merge branch 'fix-vcf_filter' into 'develop' · 34ffaaf0
  bow authored 8 years ago
  
  Fixed bug in vcffilter Fixes #313 See merge request !370
  34ffaaf0
Mar 31, 2016
- Added option to keep raw ref calls · 792650ee
  Peter van 't Hof authored 8 years ago
  
  792650ee
- Remove unused import · d3324d2d
  Peter van 't Hof authored 8 years ago
  
  d3324d2d
- Fixed bug in vcffilter · d66701ba
  Peter van 't Hof authored 8 years ago
  
  (cherry picked from commit f5f2787f)
  d66701ba
- Fixed bug in vcffilter · f5f2787f
  Peter van 't Hof authored 8 years ago
  
  f5f2787f
- Invert to pValue · 6035d15b
  Peter van 't Hof authored 8 years ago
  
  6035d15b
Mar 30, 2016
- Fixed pysvtools · 38824296
  Peter van 't Hof authored 8 years ago
  
  38824296
- Switch back to vcf 4.1 · a5afc3e5
  Peter van 't Hof authored 8 years ago
  
  a5afc3e5