Commits · a50e42cc7ec75a3a262993c0ad45c35365c1b390 · Mirrors / biopet.biopet

01 Jun, 2016 2 commits
- remove gvf method · a50e42cc
  Peter van 't Hof authored Jun 01, 2016
  
  a50e42cc
- fixed a config value · 95f8441a
  Peter van 't Hof authored Jun 01, 2016
  
  95f8441a
30 May, 2016 2 commits
- Merge branch 'fix-mapping_precentage' into 'develop' · bfdad518
  bow authored May 30, 2016
```
Fix mapping precentage

Fixes #349 

See merge request !412
```
  bfdad518
- Merge branch 'feature-autodetect_paired' into 'develop' · 912cab31
  bow authored May 30, 2016
```
Added autodetect fileformat paired

Fixed #350 

See merge request !414
```
  912cab31
29 May, 2016 1 commit
- Merge branch 'feature-unique_sample_filter' into 'develop' · 6a965b1c
  bow authored May 29, 2016
```
Added more filter options

fixes #316 

See merge request !410
```
  6a965b1c
27 May, 2016 2 commits
- Added autodetect fileformat paired · 500d864f
  Peter van 't Hof authored May 27, 2016
  
  500d864f
- Merge branch 'fix-gatk-license' into 'develop' · ece09a76
  Peter van 't Hof authored May 27, 2016
```
remove gatk-specific parts from license

Fixes #343 

@h.mei @p.j.van_t_hof Could you check this? Thanks :-). 

See merge request !406
```
  ece09a76
25 May, 2016 10 commits
- change ALL licenses across all files. · 55b1b7dd
  Sander Bollen authored May 25, 2016
  
  55b1b7dd
- also change docs to reflect new license · 556229a0
  Sander Bollen authored May 25, 2016
  
  556229a0
- Correct duplicate precentage for secondary reads · ad02205f
  Peter van 't Hof authored May 25, 2016
  
  ad02205f
- Correct mapping precentage for secondary reads · 3425ce2f
  Peter van 't Hof authored May 25, 2016
  
  3425ce2f
- Fix compile error · 02936179
  Peter van 't Hof authored May 25, 2016
  
  02936179
- Code improvement · 0e6920a2
  Peter van 't Hof authored May 25, 2016
  
  0e6920a2
- Filter references calls · 43006ba6
  Peter van 't Hof authored May 25, 2016
  
  43006ba6
- Fix compile error · afb31099
  Peter van 't Hof authored May 25, 2016
  
  afb31099
- Fixed denovo filter · db6b6ffa
  Peter van 't Hof authored May 25, 2016
  
  db6b6ffa
- Style fix · 37ae7b76
  Peter van 't Hof authored May 25, 2016
  
  37ae7b76
24 May, 2016 1 commit
- Merge branch 'fix-mapping_plot' into 'develop' · cb93552e
  bow authored May 24, 2016
```
Fix mapping plot in report

Fixes #349 

See merge request !411
```
  cb93552e
23 May, 2016 5 commits
- Fix mapping plot in report · 00bf2bf3
  Peter van 't Hof authored May 23, 2016
  
  00bf2bf3
- Style fix · 4982a72c
  Peter van 't Hof authored May 23, 2016
  
  4982a72c
- Merge branch 'fix-report' into 'develop' · 160ed2d3
  bow authored May 23, 2016
```
Somehow the rootpath was broken

fixes #347 

See merge request !408
```
  160ed2d3
- Added more filter options · 9b8ddc12
  Peter van 't Hof authored May 23, 2016
  
  9b8ddc12
- Somehow the rootpath was broken · 10c34a57
  Peter van 't Hof authored May 23, 2016
  
  10c34a57
19 May, 2016 2 commits

remove gatk-specific parts from license · c61544e9
Sander Bollen authored May 19, 2016

c61544e9

Merge branch 'fix-svcallers-vcf' into 'develop' · 9139289c

Peter van 't Hof authored May 19, 2016

Fix vcf files from SV calling output to contain samplename

The SV callers in our pipeline name the samples 'default', ideally all of these 'default' should be named to the sample called accordingly. Otherwise we have issues later on in the SV merging.

fixes #321

See merge request !365

9139289c

18 May, 2016 4 commits
- 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 11 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