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Created with Raphaël 2.2.04Dec32128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310987630Sep29262217161512111098532129Aug282726Merge branch 'feature-prerelease_fixes' into 'develop'Split every filter option into functionsAdded text to argsPattern match refactor in ExtractAlignedFastqDocumentation updatesTest refactorsNo default limitation on variantcalling when target_bed is givenChanges in documentation Added 4 new options for vcfFilterFix, remove .toList causing the memory issue. Fix suggested by Peter. #34Fix bug on gubbinsChanges in documentation of GATK BASTY adn BastyGenerateFastaFix bug on gubbinsrefactoringChanges in help screen GatkPipelineMerge branch 'feature-gubbins' into 'develop'Fix bug on indel treeChanges in help screen tool BastyGenerateFastaFix on outputDirAdded snp + indels treefix bug on mpileupFix bug on output nameSeqstat with map reduceFunctional seqstat, but slow, need to refactor out the while loop and dependencies on previous resultsChanges in docsSeqstat ScalaAdded gubbins to the pipelineAdded getBipartitionsFile functionAdded workdirectoryAdded extension for gubbins scriptMerge branch 'feature-license' into 'develop'Merge branch 'develop' into feature-documentationChanges in docsAdded license bash scriptAdded protected licenseExclude public License from protected packageFix dirty build warningFix for #90Update GSNAP version capture testUpdate htseq-count version capture test