Commits · a0c297b349f422e201077cb1a772863c5bb356f5 · Mirrors / biopet.biopet

04 Dec, 2014 12 commits
- Merge remote-tracking branch 'remotes/origin/feature-documentation' into release-0.2.0 · a0c297b3
  Peter van 't Hof authored Dec 04, 2014
  
  a0c297b3
- added start up sage docs · 731d6089
  sajvanderzeeuw authored Dec 04, 2014
  
  731d6089
- Merge branch 'feature-genotype_filter' into 'develop' · 610e9ad5
  bow authored Dec 04, 2014
```
Feature genotype filter

For #92

See merge request !62
```
  610e9ad5
- Added Qual filter option · 4a4fa9be
  Peter van 't Hof authored Dec 04, 2014
  
  4a4fa9be
- Fix compile error · 54d50322
  Peter van 't Hof authored Dec 04, 2014
  
  54d50322
- Merge branch 'feature-prerelease_fixes' into 'develop' · 110b16b0
  Peter van 't Hof authored Dec 04, 2014
```
Feature prerelease fixes

Commit messages should be clear enough :).

See merge request !61
```
  110b16b0
- Split every filter option into functions · a5030119
  Peter van 't Hof authored Dec 04, 2014
  
  a5030119
- Added text to args · a190d233
  Peter van 't Hof authored Dec 04, 2014
  
  a190d233
- Pattern match refactor in ExtractAlignedFastq · b83f5736
  bow authored Dec 04, 2014
  
  b83f5736
- Documentation updates · 10518502
  bow authored Dec 04, 2014
  
  10518502
- Test refactors · 846acd6c
  bow authored Dec 04, 2014
  
  846acd6c
- No default limitation on variantcalling when target_bed is given · 09bf4a36
  Peter van 't Hof authored Dec 04, 2014
  
  09bf4a36
03 Dec, 2014 2 commits
- Changes in documentation · 1a209ea0
  sajvanderzeeuw authored Dec 03, 2014
  
  1a209ea0
- Added 4 new options for vcfFilter · ecff240c
  Peter van 't Hof authored Dec 03, 2014
  
  ecff240c
02 Dec, 2014 11 commits
- Fix bug on gubbins · d057ab01
  Peter van 't Hof authored Dec 02, 2014
  
  d057ab01
- Changes in documentation of GATK BASTY adn BastyGenerateFasta · 72936783
  sajvanderzeeuw authored Dec 02, 2014
  
  72936783
- Fix bug on gubbins · fbdd632c
  Peter van 't Hof authored Dec 02, 2014
  
  fbdd632c
- Changes in help screen GatkPipeline · 026b2015
  sajvanderzeeuw authored Dec 02, 2014
  
  026b2015
- Merge branch 'feature-gubbins' into 'develop' · deab689c
  bow authored Dec 02, 2014
```
Feature gubbins

For #30

See merge request !60
```
  deab689c
- Fix bug on indel tree · 7e8cd038
  Peter van 't Hof authored Dec 02, 2014
  
  7e8cd038
- Changes in help screen tool BastyGenerateFasta · 9581d328
  sajvanderzeeuw authored Dec 02, 2014
  
  9581d328
- Fix on outputDir · 09c25863
  Peter van 't Hof authored Dec 02, 2014
  
  09c25863
- Added snp + indels tree · 98db90f1
  Peter van 't Hof authored Dec 02, 2014
  
  98db90f1
- fix bug on mpileup · 1b9ceb90
  Peter van 't Hof authored Dec 02, 2014
  
  1b9ceb90
- Fix bug on output name · e995516a
  Peter van 't Hof authored Dec 02, 2014
  
  e995516a
01 Dec, 2014 13 commits
- Changes in docs · 1c537b84
  sajvanderzeeuw authored Dec 01, 2014
  
  1c537b84
- Added gubbins to the pipeline · f35b7861
  Peter van 't Hof authored Dec 01, 2014
  
  f35b7861
- Added getBipartitionsFile function · b32bc6cc
  Peter van 't Hof authored Dec 01, 2014
  
  b32bc6cc
- Added workdirectory · 82a8a2b6
  Peter van 't Hof authored Dec 01, 2014
  
  82a8a2b6
- Added extension for gubbins script · 2127bf05
  Peter van 't Hof authored Dec 01, 2014
  
  2127bf05
- Merge branch 'feature-license' into 'develop' · 801b72ed
  bow authored Dec 01, 2014
```
Feature license

Issue: #47
Added license to the project. Bash script to check and reformat if needed.

Also fix for #90 and #91

See merge request !59
```
  801b72ed
- Merge branch 'develop' into feature-documentation · 0613bc7e
  Zeeuw authored Dec 01, 2014
  
  0613bc7e
- Changes in docs · 4b60e366
  sajvanderzeeuw authored Dec 01, 2014
  
  4b60e366
- Added license bash script · d8189966
  Peter van 't Hof authored Dec 01, 2014
  
  d8189966
- Added protected license · 17319c63
  Peter van 't Hof authored Dec 01, 2014
  
  17319c63
- Exclude public License from protected package · ac8326b8
  Peter van 't Hof authored Dec 01, 2014
  
  ac8326b8
- Fix dirty build warning · 4a83920e
  Peter van 't Hof authored Dec 01, 2014
  
  4a83920e
- Fix for #90 · 5750c33e
  Peter van 't Hof authored Dec 01, 2014
  
  5750c33e
28 Nov, 2014 1 commit
- changes in docs · eb74d901
  sajvanderzeeuw authored Nov 28, 2014
  
  eb74d901
27 Nov, 2014 1 commit
- Fix for #91 · 016ba380
  Peter van 't Hof authored Nov 27, 2014
  
  016ba380