Commit e749d3ed authored 9 years ago by Peter van 't Hof

Fix tool extensions

parent 48528ed5

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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala 7 additions, 0 deletions

...n/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala 1 addition, 1 deletion

...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala 1 addition, 1 deletion

.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala 1 addition, 1 deletion

...sc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala 1 addition, 1 deletion

.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala 1 addition, 1 deletion

...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala 1 addition, 1 deletion

...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala 1 addition, 1 deletion

...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala 1 addition, 1 deletion

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala 1 addition, 1 deletion

...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala 1 addition, 1 deletion

...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala 1 addition, 1 deletion

...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala 1 addition, 1 deletion

...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala 1 addition, 1 deletion

.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala 1 addition, 1 deletion

...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala 1 addition, 1 deletion

...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala 1 addition, 1 deletion

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

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

.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala

with 26 additions and 19 deletions

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