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Created with Raphaël 2.2.02Dec128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310987630Sep29262217161512111098532129Aug28272625Merge 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 testUpdate main pipeline for compatibility with new base classMigrate to new project layoutMerge branch 'develop' into feature-gentrapchanges in docsFixing names of variables and apply sambamba markduplicates on the merged bam of yamsvpFix for #91Merge branch 'develop' into feature-licenseadded licence optionrename filelicense template for file headersAdd link to licenseAdded license-maven-pluginChange licenseMigrate to new project layoutMerge branch 'develop' into feature-fastq_sync