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Merge branch 'feature-wipereads' into 'develop'
Feature wipereads (final) Now we have simple GTF +refFlat support, with more tests + some cleanup :). The feature branch can be deleted afterwards. See merge request !33
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- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala 68 additions, 20 deletions.../src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
- biopet-framework/src/test/resources/rrna01.gtf 10 additions, 0 deletionsbiopet-framework/src/test/resources/rrna01.gtf
- biopet-framework/src/test/resources/rrna01.refFlat 3 additions, 0 deletionsbiopet-framework/src/test/resources/rrna01.refFlat
- biopet-framework/src/test/resources/rrna02.bed 6 additions, 0 deletionsbiopet-framework/src/test/resources/rrna02.bed
- biopet-framework/src/test/resources/single05.bam 0 additions, 0 deletionsbiopet-framework/src/test/resources/single05.bam
- biopet-framework/src/test/resources/single05.bam.bai 0 additions, 0 deletionsbiopet-framework/src/test/resources/single05.bam.bai
- biopet-framework/src/test/resources/single05.sam 9 additions, 0 deletionsbiopet-framework/src/test/resources/single05.sam
- biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala 79 additions, 14 deletions...t/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala
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