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Merge branch 'fix-vcfwriters' into 'develop'
Fix vcfwriters This branch fixes issues #152 and #153, and it includes test cases for #152. See merge request !151
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- docs/tools/VcfFilter.md 1 addition, 1 deletiondocs/tools/VcfFilter.md
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala 7 additions, 3 deletions.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala 3 additions, 2 deletions...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala 4 additions, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala 22 additions, 14 deletions.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala 5 additions, 3 deletions...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala 5 additions, 3 deletions.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
- public/biopet-framework/src/test/resources/README.txt 13 additions, 0 deletionspublic/biopet-framework/src/test/resources/README.txt
- public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz 0 additions, 0 deletions...ic/biopet-framework/src/test/resources/VEP_oneline.vcf.gz
- public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz.tbi 0 additions, 0 deletions...iopet-framework/src/test/resources/VEP_oneline.vcf.gz.tbi
- public/biopet-framework/src/test/resources/chrQ.vcf 85 additions, 0 deletionspublic/biopet-framework/src/test/resources/chrQ.vcf
- public/biopet-framework/src/test/resources/chrQ.vcf.gz 0 additions, 0 deletionspublic/biopet-framework/src/test/resources/chrQ.vcf.gz
- public/biopet-framework/src/test/resources/chrQ.vcf.gz.tbi 0 additions, 0 deletionspublic/biopet-framework/src/test/resources/chrQ.vcf.gz.tbi
- public/biopet-framework/src/test/resources/fake_chrQ.dict 2 additions, 0 deletionspublic/biopet-framework/src/test/resources/fake_chrQ.dict
- public/biopet-framework/src/test/resources/fake_chrQ.fa 2 additions, 0 deletionspublic/biopet-framework/src/test/resources/fake_chrQ.fa
- public/biopet-framework/src/test/resources/fake_chrQ.fa.fai 1 addition, 0 deletionspublic/biopet-framework/src/test/resources/fake_chrQ.fa.fai
- public/biopet-framework/src/test/resources/unvepped.vcf.gz 0 additions, 0 deletionspublic/biopet-framework/src/test/resources/unvepped.vcf.gz
- public/biopet-framework/src/test/resources/unvepped.vcf.gz.tbi 0 additions, 0 deletions...c/biopet-framework/src/test/resources/unvepped.vcf.gz.tbi
- public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala 42 additions, 0 deletions...la/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
- public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala 44 additions, 0 deletions.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
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