Commits · ba36a06aa3842d4fba58b0352dba636306f94194 · Mirrors / biopet.biopet

19 May, 2016 1 commit
- Fix tabix step · ba36a06a
  Peter van 't Hof authored May 19, 2016
  
  ba36a06a
18 May, 2016 6 commits
- Remove deps on intermediates · fa41ea50
  Peter van 't Hof authored May 18, 2016
  
  fa41ea50
- Added contig map for dbsnp · 8ecb7f41
  Peter van 't Hof authored May 18, 2016
  
  8ecb7f41
- Merge branch 'feature-check_unused_keys' into 'develop' · 6ae5046c
  bow authored May 18, 2016
```
Added check on unused config values

Fixes #327 

See merge request !400
```
  6ae5046c
- Merge branch 'feature-singletons_flagstat' into 'develop' · 4df69c64
  bow authored May 18, 2016
```
Added singletons to summary



See merge request !404
```
  4df69c64
- Fixed test · e37fd3ac
  Peter van 't Hof authored May 18, 2016
  
  e37fd3ac
- Merge branch 'feature-index_generation' into 'develop' · e11ff161
  bow authored May 18, 2016
```
Reference index generation



See merge request !396
```
  e11ff161
17 May, 2016 29 commits
- Added singletons to summary · e49f81e3
  Peter van 't Hof authored May 17, 2016
  
  e49f81e3
- Style fixes · ee5c73f8
  Peter van 't Hof authored May 17, 2016
  
  ee5c73f8
- Added test to write config · b8a26250
  Peter van 't Hof authored May 17, 2016
  
  b8a26250
- Added test for gtf down · 01d3e5d8
  Peter van 't Hof authored May 17, 2016
  
  01d3e5d8
- Fixed output · a3c21103
  Peter van 't Hof authored May 17, 2016
  
  a3c21103
- Fix extension · 9bc45be2
  Peter van 't Hof authored May 17, 2016
  
  9bc45be2
- style changes · f7937990
  Peter van 't Hof authored May 17, 2016
  
  f7937990
- Add gtf to refflat · 9cb010e9
  Peter van 't Hof authored May 17, 2016
  
  9cb010e9
- Merge branch 'feature-more_unit_tests' into 'develop' · 11c11c41
  bow authored May 17, 2016
```
More unit tests



See merge request !403
```
  11c11c41
- Fixed input error · f297526c
  Peter van 't Hof authored May 17, 2016
  
  f297526c
- Add input annotation · 006e38a7
  Peter van 't Hof authored May 17, 2016
  
  006e38a7
- Fixed type · a2cba5e1
  Peter van 't Hof authored May 17, 2016
  
  a2cba5e1
- Style fixes · 26a7681c
  Peter van 't Hof authored May 17, 2016
  
  26a7681c
- Merge remote-tracking branch 'remotes/origin/develop' into feature-more_unit_tests · 10bbbbda
  Peter van 't Hof authored May 17, 2016
  
  10bbbbda
- Added gtf to star index generation · 315f5230
  Peter van 't Hof authored May 17, 2016
  
  315f5230
- Fix config · 53cc5101
  Peter van 't Hof authored May 17, 2016
  
  53cc5101
- Style changes · 80de022e
  Peter van 't Hof authored May 17, 2016
  
  80de022e
- Extract gtf when needed · 88389008
  Peter van 't Hof authored May 17, 2016
  
  88389008
- Make curl pipable · d03b8be7
  Peter van 't Hof authored May 17, 2016
  
  d03b8be7
- Adding gtf download · 0d14a49a
  Peter van 't Hof authored May 17, 2016
  
  0d14a49a
- Merge remote-tracking branch 'remotes/origin/develop' into feature-index_generation · 142c815a
  Peter van 't Hof authored May 17, 2016
  
  142c815a
- Added mapping to gears testing · 052f9e11
  Peter van 't Hof authored May 17, 2016
  
  052f9e11
- Fixed typo · 8b93a99d
  Peter van 't Hof authored May 17, 2016
  
  8b93a99d
- Merge branch 'feature-bed_check' into 'develop' · 7eb9af74
  bow authored May 17, 2016
```
Init bed check

fixes #298 

See merge request !401
```
  7eb9af74
- Fixed test · f4e420a9
  Peter van 't Hof authored May 17, 2016
  
  f4e420a9
- Fix format · d08b6c72
  Peter van 't Hof authored May 17, 2016
  
  d08b6c72
- Merge branch 'fix-exit_calls' into 'develop' · 09fa0b3f
  bow authored May 17, 2016
```
Changes arg parser with getOrElse(throw new IllegalArgumentException)

Fixes #342 

See merge request !402
```
  09fa0b3f
- Merge branch 'fix-fifo_job_name' into 'develop' · 29a84a74
  bow authored May 17, 2016
```
Fixed fifo job names

Fixes #334 

See merge request !399
```
  29a84a74
- Added testing for start from bam · 75f13b0e
  Peter van 't Hof authored May 17, 2016
  
  75f13b0e
15 May, 2016 4 commits
- Style fixes · ec4eb7de
  Peter van 't Hof authored May 15, 2016
  
  ec4eb7de
- Remove old comment · 03360822
  Peter van 't Hof authored May 15, 2016
  
  03360822
- switch to trait · 5eb775cb
  Peter van 't Hof authored May 15, 2016
  
  5eb775cb
- Added basic testing · 1ac97254
  Peter van 't Hof authored May 15, 2016
  
  1ac97254