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Created with Raphaël 2.2.029Jan28272625232221201918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct30292827262523222120wgs and rna metrics now got config value to enable/disable themFixed units testsOutput strandspecific wiggle/bigwig and TDF filelowering the minimum_length to be keptswitch to core rscript extensionAdded insert size estimation. Fix pindel2vcf dependency (depend on pindel, use beforegraph to set outputpath)fix code warningsAdded meta exon counts to pipelineFixed scopeMerge remote-tracking branch 'remotes/origin/develop' into feature-measure_modulesRemove old unused codeReformatAdded meta exons countsFixed gentrap testschange typo in gentrap docInsertsize estimatoradded fastq extension disclaimer to pipeline docsreorder levelsFix code warningsFixed createMetaExonCounts methodCombine overlapping genes in 1 threadMerge branch 'feature-VarscanIntoShiva' into 'develop' add SHARK config file location.explain 4 level config values Set more specific config for the pipeline. We want to keep the merged bamUpdate some fields of the gentrap docsPindel update wrapper, specifing the output files (pindel generates more files)Give mergeTables a extensionAdded columnName to mergeTablesCode improvementfixed strandProtocolSome fixes with boolean in the pindelvcf wrapperset defaults for mapping pipeline to skipmarkduplicates.Merge remote-tracking branch 'remotes/origin/develop' into feature-measure_modulesFixed single exon transcriptsDisabled countType by defaultFixed htseq-countImplemented LazyCheckFixed config conversionsFixed compile warning