Merge branch 'fix-exit_calls' into 'develop'
Changes arg parser with getOrElse(throw new IllegalArgumentException) Fixes #342 See merge request !402
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- biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala 1 addition, 1 deletion...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala 1 addition, 1 deletion.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala 1 addition, 4 deletions...rc/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala 1 addition, 1 deletion.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala 1 addition, 1 deletion.../main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala 1 addition, 1 deletion.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala 1 addition, 1 deletion...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala 1 addition, 1 deletion...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala 1 addition, 1 deletion...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala 1 addition, 1 deletion.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala 1 addition, 1 deletion.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala 1 addition, 1 deletion...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala 1 addition, 1 deletion.../src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala 1 addition, 1 deletion.../scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala 1 addition, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala 1 addition, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala 1 addition, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala 1 addition, 1 deletion.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
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