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Created with Raphaël 2.2.028Jan272625232221201918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct3029282726252322212019Insertsize 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 warningSkipped flexiprep stats when flexiprep is not executedFixed bug in reportMerge remote-tracking branch 'remotes/origin/develop' into feature-VarscanIntoShivaChange version commandAdded tables and heatmaps to basecounterAdded tables and heatmaps to summaryRemove extra dot in filenameAdding sampleBamInsertSize (with some error, too be fixed later)Remove old codeImplement baseCounter in pipelineOptimize importsAdded tool extensionAdded transcript countsAdd documentationAdded output files