Merge branch 'develop' into feature-allow-custom-adapters

.gitignore

LICENSE

README.md

bam2wig/.gitignore

bam2wig/pom.xml

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

bam2wig/src/test/resources/log4j.properties

bammetrics/.gitignore

bammetrics/pom.xml

...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

...lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp

...ces/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp

.../sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp

...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp

...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp

...urces/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp

...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

...esources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp

...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp