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Merge branch 'feature-bamstats' into 'develop'
Feature bamstats Fixes #308 - [x] Multi sample base with scala futures - [x] Base stats like total number of reads - [x] mapping quality histogram - [x] insertsize histogram - [x] Clipping stats - [x] Add unit testing See merge request !435
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- biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala 2 additions, 1 deletion...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
- biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala 2 additions, 1 deletion...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala 0 additions, 242 deletions...main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala 201 additions, 0 deletions...n/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala 48 additions, 0 deletions.../scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala 47 additions, 0 deletions...main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala 81 additions, 0 deletions...a/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstat.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala 213 additions, 0 deletions...l/lumc/sasc/biopet/tools/flagstat/FlagstatCollector.scala
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala 39 additions, 0 deletions...ala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala 81 additions, 0 deletions...scala/nl/lumc/sasc/biopet/tools/bamstats/CountsTest.scala
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala 59 additions, 0 deletions...la/nl/lumc/sasc/biopet/tools/bamstats/HistogramTest.scala
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala 49 additions, 0 deletions.../scala/nl/lumc/sasc/biopet/tools/bamstats/StatsTest.scala
- biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala 1 addition, 1 deletion.../lumc/sasc/biopet/tools/flagstat/BiopetFlagstatTest.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala 8 additions, 3 deletions...a/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
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