Commit b7ae99c2 authored 9 years ago by Wai Yi Leung

Merge branch 'tooltests' into 'develop'

Tooltests

Fixes #188, #196  and #200 

See merge request !224

parents 00ca8854 9c9edf13

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docs/tools/SamplesTsvToJson.md 1 addition, 1 deletion

docs/tools/SamplesTsvToJson.md
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala 36 additions, 11 deletions

.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala 15 additions, 2 deletions

...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala 2 additions, 2 deletions

...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala 2 additions, 2 deletions

.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala 23 additions, 7 deletions

...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala 1 addition, 1 deletion

...main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala 14 additions, 16 deletions

...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala 14 additions, 5 deletions

...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala 47 additions, 32 deletions

...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala 15 additions, 5 deletions

...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala 45 additions, 13 deletions

...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala 2 additions, 2 deletions

.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala 38 additions, 18 deletions

...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala 75 additions, 40 deletions

...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala 1 addition, 1 deletion

.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala 37 additions, 0 deletions

...k/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
public/biopet-framework/src/test/resources/chrQ2.vcf 85 additions, 0 deletions

public/biopet-framework/src/test/resources/chrQ2.vcf
public/biopet-framework/src/test/resources/chrQ2.vcf.gz 0 additions, 0 deletions

public/biopet-framework/src/test/resources/chrQ2.vcf.gz
public/biopet-framework/src/test/resources/chrQ2.vcf.gz.tbi 0 additions, 0 deletions

public/biopet-framework/src/test/resources/chrQ2.vcf.gz.tbi

with 453 additions and 158 deletions

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