Commits · d81585cad6576bda47b2492bc79c6bb40aaeae2f · Mirrors / biopet.biopet

07 Mar, 2015 1 commit
- Adding scala docs · d81585ca
  Peter van 't Hof authored Mar 07, 2015
  
  d81585ca
05 Mar, 2015 4 commits
- Merge branch 'develop' into feature-shiva · 7908eb1d
  Peter van 't Hof authored Mar 05, 2015
  
  7908eb1d
- Merge branch 'patch-executable_check' into 'develop' · 8fbf2803
  bow authored Mar 05, 2015
```
Patch executable check

See merge request !114
```
  8fbf2803
- Possible to not convert executable to CanonicalPath · 043874a8
  Peter van 't Hof authored Mar 05, 2015
  
  043874a8
- Merge branch 'patch-carp' into 'develop' · 27035485
  bow authored Mar 05, 2015
```
Patch carp

Merge to fix the wrong directory of MACS2 single samples runs

See merge request !113
```
  27035485
04 Mar, 2015 21 commits
- Fix version · f160fd61
  Peter van 't Hof authored Mar 04, 2015
  
  f160fd61
- Version · 70d19f85
  Peter van 't Hof authored Mar 04, 2015
  
  70d19f85
- fix on missing AD field · 439da30a
  Peter van 't Hof authored Mar 04, 2015
  
  439da30a
- Fix chromosome stats · 50b908db
  Peter van 't Hof authored Mar 04, 2015
  
  50b908db
- Added todo · 9f604dce
  Peter van 't Hof authored Mar 04, 2015
  
  9f604dce
- fix version · c6682896
  Peter van 't Hof authored Mar 04, 2015
  
  c6682896
- fix executable · 9b16ee45
  Peter van 't Hof authored Mar 04, 2015
  
  9b16ee45
- added bgzip and tabix to freebayes · fb53f990
  Peter van 't Hof authored Mar 04, 2015
  
  fb53f990
- Added index as input file · e12f0f66
  Peter van 't Hof authored Mar 04, 2015
  
  e12f0f66
- Added tabix · f0954114
  Peter van 't Hof authored Mar 04, 2015
  
  f0954114
- Add wrapper for bgzip · 551e3812
  bow authored Mar 04, 2015 and Peter van 't Hof committed Mar 04, 2015
```
(cherry picked from commit ba3e1de5)
```
  551e3812
- changes in output folder of MACS single sample runs · 09103695
  Sander van der Zeeuw authored Mar 04, 2015
  
  09103695
- Switched Basty to Shiva · c0a2280c
  Peter van 't Hof authored Mar 04, 2015
  
  c0a2280c
- fix bug · aab08ec8
  Peter van 't Hof authored Mar 04, 2015
  
  aab08ec8
- fix bug on single sample calling · 96c33eab
  Peter van 't Hof authored Mar 04, 2015
  
  96c33eab
- remove unused import · 5e7634c1
  Peter van 't Hof authored Mar 04, 2015
  
  5e7634c1
- Switch Basty to Shiva · ab50cd4f
  Peter van 't Hof authored Mar 04, 2015
  
  ab50cd4f
- Make variantcaller public · 04b80825
  Peter van 't Hof authored Mar 04, 2015
  
  04b80825
- Rename pipelines · 99f18f74
  Peter van 't Hof authored Mar 04, 2015
  
  99f18f74
- Remove non gatk version of shiva from the protected exe · 9c83fc47
  Peter van 't Hof authored Mar 04, 2015
  
  9c83fc47
- Added haplotypeLength option · 48f85cd4
  Peter van 't Hof authored Mar 04, 2015
  
  48f85cd4
03 Mar, 2015 14 commits
- Added freebayes · 1621e5cd
  Peter van 't Hof authored Mar 03, 2015
  
  1621e5cd
- Fix default tags · e7aa783e
  Peter van 't Hof authored Mar 03, 2015
  
  e7aa783e
- Minor changes to options · 6264c8cd
  Peter van 't Hof authored Mar 03, 2015
  
  6264c8cd
- Added args to queue extension · 7825fcdf
  Peter van 't Hof authored Mar 03, 2015
  
  7825fcdf
- Added excludeNonVariants · f4b0b185
  Peter van 't Hof authored Mar 03, 2015
  
  f4b0b185
- fix bug · a26063f4
  Peter van 't Hof authored Mar 03, 2015
  
  a26063f4
- Added check for incorrect variantcallers · 77f33770
  Peter van 't Hof authored Mar 03, 2015
  
  77f33770
- Java jobs now show diffrent version output in summary · a332996e
  Peter van 't Hof authored Mar 03, 2015
  
  a332996e
- Skipping header in general stats · ddc6e115
  Peter van 't Hof authored Mar 03, 2015
  
  ddc6e115
- Fix file name · d39b64aa
  Peter van 't Hof authored Mar 03, 2015
  
  d39b64aa
- Adding sample stats from vcfstats to summary · 640496b0
  Peter van 't Hof authored Mar 03, 2015
  
  640496b0
- Added option to add all info and format fields · aa87e2ce
  Peter van 't Hof authored Mar 03, 2015
  
  aa87e2ce
- Fix unit test · 9bca32a9
  Peter van 't Hof authored Mar 03, 2015
  
  9bca32a9
- Added chromosome specific stats · 2cd2e497
  Peter van 't Hof authored Mar 03, 2015
  
  2cd2e497