Commits · 5edfb6af2a2ef3451c19e25e871b4d4839a3f364 · Mirrors / biopet.biopet

13 Oct, 2014 11 commits
- Merge branch 'peter' into 'master' · 5edfb6af
  Wai Yi Leung authored Oct 13, 2014
```
Peter

See merge request !8
```
  5edfb6af
- Fix args · 9e1bc3d0
  Peter van 't Hof authored Oct 13, 2014
  
  9e1bc3d0
- Added CheckAllelesVcfInBam · 1d3bd651
  Peter van 't Hof authored Oct 13, 2014
  
  1d3bd651
- Fix args · 9068a69a
  Peter van 't Hof authored Oct 10, 2014
  
  9068a69a
- Removed unused import · 9467cec8
  Peter van 't Hof authored Oct 10, 2014
  
  9467cec8
- Merge branch 'bow' into 'master' · 2ba13798
  Wai Yi Leung authored Oct 13, 2014
```
Bow

See merge request !7
```
  2ba13798
- Merge branch 'waiyi' into 'master' · a4687aab
  Wai Yi Leung authored Oct 13, 2014
```
Merging branch waiyi back to master

See merge request !6
```
  a4687aab
- Merge from master · 6a83f9d3
  Wai Yi Leung authored Oct 13, 2014
  
  6a83f9d3
- Adding tophat · 2a22fa63
  Wai Yi Leung authored Oct 13, 2014
  
  2a22fa63
- Use TestNGSuite and Matchers in Ln command test · 836eddf1
  bow authored Oct 13, 2014
  
  836eddf1
- Use TestNGSuite and Matchers in WipeReads test · 57478950
  bow authored Oct 13, 2014
  
  57478950
10 Oct, 2014 9 commits
- Use common CLI argument parser for WipeReads · 0ea14304
  bow authored Oct 10, 2014
  
  0ea14304
- Netbeans configurations on formatting using CheckStyle plugin · 85495563
  Wai Yi Leung authored Oct 10, 2014
  
  85495563
- Removing unused dependency · 1c9ffeef
  Wai Yi Leung authored Oct 10, 2014
  
  1c9ffeef
- Merge commit '243fd59a ' · 9cde95b2
  Peter van 't Hof authored Oct 10, 2014
  
  9cde95b2
- Switched to ToolCommand args parsing · af39664b
  Peter van 't Hof authored Oct 10, 2014
  
  af39664b
- Changed name to commandName · b443f31f
  Peter van 't Hof authored Oct 10, 2014
  
  b443f31f
- Update general argument parsing · 8ba5ac3e
  Peter van 't Hof authored Oct 10, 2014
  
  8ba5ac3e
- Set default validation stringency to lenient in WipeReads · 243fd59a
  bow authored Oct 10, 2014
  
  243fd59a
- More unit test for WipeReads · 634364dd
  bow authored Oct 10, 2014
  
  634364dd
09 Oct, 2014 4 commits
- Unused function & comments cleanup in WipeReads · 2f2ba67a
  bow authored Oct 09, 2014
  
  2f2ba67a
- Added scopts library and log4j to ToolCommands · a87a80de
  Peter van 't Hof authored Oct 09, 2014
  
  a87a80de
- Use orestes.bloomfilter instead of com.twitter.algebird for Bloom filter implementation · 2594289d
  bow authored Oct 09, 2014
```
Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
```
  2594289d
- Update returned filter function in WipeReads to use SAMRecords only · e1444972
  bow authored Oct 09, 2014
  
  e1444972
08 Oct, 2014 3 commits
- Automatic class name conversion · 2ce33667
  Peter van 't Hof authored Oct 08, 2014
  
  2ce33667
- Automatic class name conversion · 2c5d1151
  Peter van 't Hof authored Oct 08, 2014
  
  2c5d1151
- Refactor code · 16182a89
  Peter van 't Hof authored Oct 08, 2014
  
  16182a89
07 Oct, 2014 13 commits
- Merge branch 'feat_wipereads' into 'master' · 4e9e3cb6
  Peter van 't Hof authored Oct 07, 2014
```
WipeReads tool

This is the first iteration of the tool (meant) to remove rRNA reads. A few things are still missing: taking into account splicing for region overlap, GTF reading, refFlat reading, and the class wrapper for Queue. However, the main functionalities are all there (mainly paired-end reads removal and optional reads with the same name removal), so I think this is merge-able for now.

See merge request !5
```
  4e9e3cb6
- Update retrieveCommand function · 10c474fa
  bow authored Oct 07, 2014
  
  10c474fa
- Make sure WipeReads also checks for single reads when filtering + writing · 1de25c35
  bow authored Oct 07, 2014
  
  1de25c35
- Update main interface · 84a7f167
  bow authored Oct 07, 2014
  
  84a7f167
- Optimize set building in WipeReads by bypassing mate lookup · 59bb05d8
  bow authored Oct 07, 2014
  
  59bb05d8
- Simplify WipeReads usage message · 940739df
  bow authored Oct 07, 2014
  
  940739df
- Improve mate query to better-disambiguate multiple-mapped reads · 612f9c14
  bow authored Oct 07, 2014
  
  612f9c14
- Merge overlapping intervals prior to making QueryInterval · e96290dc
  bow authored Oct 07, 2014
  
  e96290dc
- Simplify ToolCommand.toolName value · 13da13e9
  bow authored Oct 07, 2014
  
  13da13e9
- Remove strand option in WipeReads · 3a29a0ca
  bow authored Oct 07, 2014
  
  3a29a0ca
- Add explicit system exit points in main jar · 9c612125
  bow authored Oct 07, 2014
  
  9c612125
- Fix typo · e725e48b
  bow authored Oct 07, 2014
  
  e725e48b
- Add WipeReads to main command line interface · 179d9f01
  bow authored Oct 07, 2014
  
  179d9f01