Merge remote-tracking branch 'upstream/peter'
Conflicts: biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqtk.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/seqtk/SeqtkSeq.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/extensions/fastq/Fastqc.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
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- bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala 3 additions, 3 deletions...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
- bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala 1 addition, 1 deletion...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala 1 addition, 1 deletion...k/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala 1 addition, 1 deletion...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala 34 additions, 0 deletions...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala 1 addition, 1 deletion.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala 1 addition, 1 deletion...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala 1 addition, 1 deletion...et/extensions/picard/CollectAlignmentSummaryMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala 1 addition, 1 deletion.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala 1 addition, 1 deletion...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala 1 addition, 1 deletion...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala 1 addition, 1 deletion.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala 1 addition, 1 deletion...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala 0 additions, 0 deletions...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
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