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Created with Raphaël 2.2.019Mar18171615141312111098765432127Feb2624231918171615141312Fix dependency bug in flexiprepFix incorrectly passed java flags for piped VarScan commandMerge branch 'feature-vcfstats' into 'develop'Fix variable and add more docsMerge branch 'patch-varscan' into 'develop'Fix incorrectly passed java flags for piped VarScan commandMerge branch 'patch-flexiprep' into 'develop'adding option to only annotate with exact same alt alleleAdded sample distributionsAlso change dependency for cutadeptFix dependency bug in flexiprepChanges fraction of binsMerge branch 'patch-main_docs' into 'develop'Update main documentationUpdate docs in MergeTablesRemove unused import in MergeTablesDropped sambamba mpileup because of error, might be related to disk quotaBump version to 0.4.0-DEVFall back to samtools mpileupSambamba pileup with pipe to pigzDon't restrict sambamba to be non-freeVarWrapper finetuneMerge branch 'master' into developImprove thread binningMerge branch 'release-0.3.0'v0.3.0v0.3.0Last docs updateAdd documentation for ShivaVariantcallingFir location of count filesChange file extension for better igv supportFix on help info for sample argMore generic pipeline namesConvert docs for shivaThis functions nowUpdate SAGE documentationUpdate GSNAP wrapper memoryFix memory requirementsStats per bin per chrRename VEPNormalizer -> VepNormalizer for consistencyMerge branch 'develop' into feature-vcfwithvcfUpdate main executable pipelines and tool visibility