Commits · 97803088a677dd48fc5b8cc54ed40cd11c31d09f · Mirrors / biopet.biopet

24 Aug, 2016 1 commit
- Merge remote-tracking branch 'remotes/origin/develop' into fix-extractAlignedFastq · 97803088
  Peter van 't Hof authored Aug 24, 2016
  
  97803088
22 Aug, 2016 3 commits
- Merge branch 'feature-raise_memory' into 'develop' · e5384fc2
  bow authored Aug 22, 2016
```
Raised default residental memory for java jobs



See merge request !447
```
  e5384fc2
- Merge branch 'fix-varscan_threads' into 'develop' · f26c4004
  bow authored Aug 22, 2016
```
Reduce threads for varscan

Reduce over scheduling of threads for varscan

See merge request !446
```
  f26c4004
- Raised picard default memory · 04038e39
  Peter van 't Hof authored Aug 22, 2016
  
  04038e39
21 Aug, 2016 1 commit
- Raised default residental memory for java jobs · cfd88812
  Peter van 't Hof authored Aug 21, 2016
  
  cfd88812
18 Aug, 2016 1 commit
- Merge branch 'fix-toucan_summary' into 'develop' · 9ed130e8
  bow authored Aug 18, 2016
```
Fix toucan summary

Fix #381 

See merge request !443
```
  9ed130e8
17 Aug, 2016 4 commits
- Fixed whitespace · f5c50326
  Peter van 't Hof authored Aug 17, 2016
  
  f5c50326
- Adding more testing for vep summary parsing · bb72a164
  Peter van 't Hof authored Aug 17, 2016
  
  bb72a164
- Skip empty values · 77d657ac
  Peter van 't Hof authored Aug 17, 2016
  
  77d657ac
- Fix default 0 · e5e47f6c
  Peter van 't Hof authored Aug 17, 2016
  
  e5e47f6c
15 Aug, 2016 1 commit
- Reduce threads for varscan · ca53b210
  Peter van 't Hof authored Aug 15, 2016
  
  ca53b210
11 Aug, 2016 1 commit
- Fixing bug with freebayes · 79b42eea
  Peter van 't Hof authored Aug 11, 2016
  
  79b42eea
10 Aug, 2016 2 commits
- Merge branch 'feature-shiva_report_trait' into 'develop' · 33d98997
  bow authored Aug 10, 2016
```
Moved report to a trait so it can be extended by magpie2



See merge request !444
```
  33d98997
- Fixed type · cdc1f3c6
  Peter van 't Hof authored Aug 10, 2016
  
  cdc1f3c6
09 Aug, 2016 3 commits
- Force no flexiprep in gears · c2fdfed6
  Peter van 't Hof authored Aug 09, 2016
  
  c2fdfed6
- Format fix · 72bfc405
  Peter van 't Hof authored Aug 09, 2016
  
  72bfc405
- Moved report to a trait so it can be extended by magpie2 · f249177a
  Peter van 't Hof authored Aug 09, 2016
  
  f249177a
05 Aug, 2016 1 commit
- Change key sets · fcecdf0c
  Peter van 't Hof authored Aug 05, 2016
  
  fcecdf0c
04 Aug, 2016 1 commit
- Build in check for passing correct interval to the tool. · f0cccdd0
  Sander van der Zeeuw authored Aug 04, 2016
  
  f0cccdd0
01 Aug, 2016 1 commit
- Merge branch 'docs-carp-broadpeaks' into 'develop' · 8eb7deef
  Peter van 't Hof authored Aug 01, 2016
```
ATAC seq config

@s.a.j.van_der_zeeuw kun je even kijken of er nog iets mist?

See merge request !425
```
  8eb7deef
29 Jul, 2016 1 commit

Merge branch 'feature-bamstats' into 'develop' · 196fc34e

bow authored Jul 29, 2016

Feature bamstats

Fixes #308 

- [x] Multi sample base with scala futures
- [x] Base stats like total number of reads
- [x] mapping quality histogram
- [x] insertsize histogram
- [x] Clipping stats

- [x] Add unit testing

See merge request !435

196fc34e

28 Jul, 2016 1 commit
- Changed to Future.sequence · 351508ec
  Peter van 't Hof authored Jul 28, 2016
  
  351508ec
26 Jul, 2016 1 commit
- Merge branch 'fix-basecounter' into 'develop' · 4ddb5a93
  bow authored Jul 26, 2016
```
Fix basecounter

Fixes #377 and #378 

See merge request !440
```
  4ddb5a93
25 Jul, 2016 1 commit
- Added index check · cdc3eea0
  Peter van 't Hof authored Jul 25, 2016
  
  cdc3eea0
22 Jul, 2016 1 commit
- Added check for outputDir · 2f23e353
  Peter van 't Hof authored Jul 22, 2016
  
  2f23e353
21 Jul, 2016 15 commits
- Format fix · 50bb1535
  Peter van 't Hof authored Jul 21, 2016
  
  50bb1535
- Split methods · 1579a88b
  Peter van 't Hof authored Jul 21, 2016
  
  1579a88b
- Merge branch 'fix-core_memory' into 'develop' · a16e109d
  bow authored Jul 21, 2016
```
Added option to correct memory for threads

Fixes #376 

See merge request !439
```
  a16e109d
- Added simple test on main · 30633108
  Peter van 't Hof authored Jul 21, 2016
  
  30633108
- Fixed number of bins · 99b31701
  Peter van 't Hof authored Jul 21, 2016
  
  99b31701
- Fixed test · 6d39308c
  Peter van 't Hof authored Jul 21, 2016
  
  6d39308c
- Added bamstats to executable · fb7b5d5d
  Peter van 't Hof authored Jul 21, 2016
  
  fb7b5d5d
- Merge remote-tracking branch 'remotes/origin/develop' into feature-bamstats · 74091f0f
  Peter van 't Hof authored Jul 21, 2016
```
# Conflicts:
#	biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
```
  74091f0f
- Remove duplicated stats · ed129189
  Peter van 't Hof authored Jul 21, 2016
  
  ed129189
- Added flagstats to bamstats · 99f13260
  Peter van 't Hof authored Jul 21, 2016
  
  99f13260
- Format fix · 4cab61ef
  Peter van 't Hof authored Jul 21, 2016
  
  4cab61ef
- Fixed memory correction · 78b45798
  Peter van 't Hof authored Jul 21, 2016
  
  78b45798
- Added contig stats to files · 498358c5
  Peter van 't Hof authored Jul 21, 2016
  
  498358c5
- Added test to Stats class · fbe97ce0
  Peter van 't Hof authored Jul 21, 2016
  
  fbe97ce0
- Added option to correct memory for threads · cd532363
  Peter van 't Hof authored Jul 21, 2016
  
  cd532363