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Created with Raphaël 2.2.015Oct141312987652130Sep29282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423Fix code warningsdependency graph is now correctadded bcftools_singlesampleFixed version to single end executablesFix picard versionsOutput singleton reads (in case the input bam had dedup with removal turned on)autofixesget sample names from vcf when pipeline is started by itselfcreate config on the flyfix tiny bug and stylevarda in Toucan2varda in ToucanFix MatchErrorAdded version check for pipe jobsAdded version to gatk commandsExtracted version in a traitMerge branch 'fix-chunking' into 'develop' add some tests for gvcftobedadd (g)vcf to bed toolRemove some testingGentypegvcfs added freevar to avoid double annotation flagAdd minimum genome quality to VcfFilterhad to add mockito to biopet extensions pomrefactor (move test and packages to correct folder)Merge branch 'develop' into feature-vardaAdded a thread correction varFixed zipped input filesBcfTools View extensionmpileup_reference_addedFixed numberChunks in summaryFixed default valuesMake name more strictFix zcat for chunkingextensions arround extensions!Fix chunkingMerge branch 'feature-FilterOnMappingQualityCarp' into 'develop' add wait flag to manwe extensionsstyle changes, bamMetrics changed in bammetricsAdded check also to libsFixes #213