Commits · 4c3c746b0e9b0a886f027df31edea4232c641108 · Mirrors / biopet.biopet

02 Jun, 2016 1 commit
- Merge branch 'fix-haplotypercaller' into 'develop' · 4c3c746b
  bow authored Jun 02, 2016
```
fixed a config value



See merge request !417
```
  4c3c746b
01 Jun, 2016 3 commits
- Merge branch 'fix-star-mapping-keep-unmapped' into 'develop' · baa5ab44
  Peter van 't Hof authored Jun 01, 2016
```
Fix star mapping keep unmapped reads in bamfile

An addition of a config value to the `Mapping` pipeline. Let Star output unmapped reads.

See merge request !416
```
  baa5ab44
- 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
31 May, 2016 3 commits
- Fix lowercase · 5665f7e9
  Wai Yi Leung authored May 31, 2016
  
  5665f7e9
- Set default star to output unmapped reads also in the bamfile · cf99b25d
  Wai Yi Leung authored May 31, 2016
  
  cf99b25d
- Merge remote-tracking branch 'origin/develop' into develop · a4c324e1
  Wai Yi Leung authored May 31, 2016
  
  a4c324e1
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 11 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
- Merge remote-tracking branch 'origin/develop' into develop · ee32217c
  Wai Yi Leung authored May 25, 2016
  
  ee32217c
- 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
20 May, 2016 1 commit
- Merge remote-tracking branch 'origin/develop' into develop · 7116efe9
  Wai Yi Leung authored May 20, 2016
  
  7116efe9
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 6 commits
- Merge remote-tracking branch 'origin/develop' into develop · c23b5306
  Wai Yi Leung authored May 18, 2016
  
  c23b5306
- 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
- Merge remote-tracking branch 'origin/develop' into develop · 8e07f7fe
  Wai Yi Leung authored May 18, 2016
  
  8e07f7fe
17 May, 2016 2 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