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Created with Raphaël 2.2.05Dec432128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310987630Sep29262217161512111098532129AugAdded License to header of all filesChange LicensesFix compile errorMask oncompleted pipelinesChange pom to version 0.2.0-rc1Merge remote-tracking branch 'remotes/origin/feature-documentation' into release-0.2.0Start new implementationadded start up sage docsMerge branch 'feature-genotype_filter' into 'develop'Added Qual filter optionFix compile errorMerge 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 workdirectory