Commits · 4caab1f440d693c728de042d812d5d1e6a7575d5 · Mirrors / biopet.biopet

12 Apr, 2016 1 commit

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

bow authored Apr 12, 2016

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

11 Apr, 2016 5 commits
- Merge branch 'fix-bamutils-insertsize' into 'develop' · 998687b1
  Peter van 't Hof authored Apr 11, 2016
```
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 Apr 11, 2016
  
  26d14d83
- Merge branch 'fix-vcffilter' into 'develop' · d7177565
  bow authored Apr 11, 2016
```
Fixed bug



See merge request !375
```
  d7177565
- Fixed bug · 9c002013
  Peter van 't Hof authored Apr 11, 2016
  
  9c002013
- Merge branch 'develop' into fix-bamutils-insertsize · d2d52a5a
  Wai Yi Leung authored Apr 11, 2016
  
  d2d52a5a
10 Apr, 2016 1 commit
- Merge branch 'feature-seq_error_test' into 'develop' · 180bb97e
  bow authored Apr 10, 2016
```
Added binominal test

Added this for project 168

See merge request !367
```
  180bb97e
08 Apr, 2016 5 commits
- Merge branch 'feature-confignamespace' into 'develop' · 3637e383
  Peter van 't Hof authored Apr 08, 2016
```
Feature configNamespace

See #163.  

See merge request !348
```
  3637e383
- Change description · 99a7f2e0
  Peter van 't Hof authored Apr 08, 2016
  
  99a7f2e0
- no more failing tests :-) · 7d00bf07
  Sander Bollen authored Apr 08, 2016
  
  7d00bf07
- well.. it compiles · 6e5f1478
  Sander Bollen authored Apr 08, 2016
  
  6e5f1478
- Merge branch 'develop' into feature-confignamespace · c2e8dbba
  Sander Bollen authored Apr 08, 2016
```
Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
```
  c2e8dbba
06 Apr, 2016 5 commits
- Merge branch 'fix-basecounter' into 'develop' · 6623805f
  bow authored Apr 06, 2016
```
Fix basecounter

Some small fixes

See merge request !373
```
  6623805f
- Fixed typo's · 5a7743d9
  Peter van 't Hof authored Apr 06, 2016
  
  5a7743d9
- Added more status logging · 3297f0bf
  Peter van 't Hof authored Apr 06, 2016
  
  3297f0bf
- Raise default memory · 99ba29c3
  Peter van 't Hof authored Apr 06, 2016
  
  99ba29c3
- Added bam index as depency · c2473edb
  Peter van 't Hof authored Apr 06, 2016
  
  c2473edb
05 Apr, 2016 5 commits
- set dictRequired to true for this tool · efb74852
  Wai Yi Leung authored Apr 05, 2016
  
  efb74852
- Add file so remove output from testing · 06bc8e4e
  Peter van 't Hof authored Apr 05, 2016
  
  06bc8e4e
- Fix style · de6f2bdc
  Peter van 't Hof authored Apr 05, 2016
  
  de6f2bdc
- Let SortVcf also use Reference trait · dd163178
  Peter van 't Hof authored Apr 05, 2016
  
  dd163178
- Refactor Reference so dict and fai file becomes accessable as a method · 2af46d82
  Peter van 't Hof authored Apr 05, 2016
  
  2af46d82
04 Apr, 2016 8 commits
- Style changes · 2759a09f
  Peter van 't Hof authored Apr 04, 2016
  
  2759a09f
- Style changes · 40de3b9b
  Peter van 't Hof authored Apr 04, 2016
  
  40de3b9b
- Set required argument to Input · b8b1779f
  Wai Yi Leung authored Apr 04, 2016
  
  b8b1779f
- sequenceDictionary is a File... fixed · f5ffdbb4
  Wai Yi Leung authored Apr 04, 2016
  
  f5ffdbb4
- Adding SortVcf extension · ec9a7972
  Wai Yi Leung authored Apr 04, 2016
  
  ec9a7972
- A bit refactoring on the variable names · b1c4e031
  Wai Yi Leung authored Apr 04, 2016
  
  b1c4e031
- BamUtils Insertsize estimation is more acurate by sampling from all over the contig. · eea29773
  Wai Yi Leung authored Apr 04, 2016
  
  eea29773
- Added MA-SEQ-ERR value · 6656e37d
  Peter van 't Hof authored Apr 04, 2016
  
  6656e37d
01 Apr, 2016 1 commit
- Merge branch 'fix-vcf_filter' into 'develop' · 34ffaaf0
  bow authored Apr 01, 2016
```
Fixed bug in vcffilter

Fixes #313 

See merge request !370
```
  34ffaaf0
31 Mar, 2016 5 commits
- Added option to keep raw ref calls · 792650ee
  Peter van 't Hof authored Mar 31, 2016
  
  792650ee
- Remove unused import · d3324d2d
  Peter van 't Hof authored Mar 31, 2016
  
  d3324d2d
- Fixed bug in vcffilter · d66701ba
  Peter van 't Hof authored Mar 31, 2016
```
(cherry picked from commit f5f2787f)
```
  d66701ba
- Fixed bug in vcffilter · f5f2787f
  Peter van 't Hof authored Mar 31, 2016
  
  f5f2787f
- Invert to pValue · 6035d15b
  Peter van 't Hof authored Mar 31, 2016
  
  6035d15b
30 Mar, 2016 4 commits
- Fixed pysvtools · 38824296
  Peter van 't Hof authored Mar 30, 2016
  
  38824296
- Switch back to vcf 4.1 · a5afc3e5
  Peter van 't Hof authored Mar 30, 2016
  
  a5afc3e5
- Fix compile error · fbba2eb3
  Peter van 't Hof authored Mar 30, 2016
  
  fbba2eb3
- Added binominal test · 05bf28b2
  Peter van 't Hof authored Mar 30, 2016
  
  05bf28b2