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Created with Raphaël 2.2.013Apr121098764230Mar2726252423201918171615141312111098765432127Feb262423191817Merge branch 'fix-vcfwriters' into 'develop'adding separator arguments such that one can use a different separator than merely tab-delimitednaming conventions of default fieldsmore spellingconsistency of naming conventions (using VCF names of fields) and spellingMerge branch 'bowtie_extra_option' into 'develop'Added dummy sections for alignmentadd explanation of files to READMEAdding MergeAllelesTest and dependenciesadding checkAllelesVcfInBamTest stub and adding bgzipped and tabixed VCF files for tools that need indexed filesadding Test decoratorsVcfWithVcfTest stubtypos and grammarAnnotateVcfWithBedTest stub and improve argument descriptions in AnnotateVcfWithBedadding VcfFilterTest stubAdding front page for shivaAdded default sample and library liststesting different output modesAdding clipping and trimming statsExtended flexiprep summariesadded extra options to bowtiesetting reference dictionariesAdding plots to flexiprepset sequence dicttionary for vepnormalizercamelCase for arguments in VcfFilter. See issue #153give reference dictionary to writerTry to convert numeric values appropriately in Picard metrics parsingCleanup Picard importsAdd utility function for parsing numbersMerge branch 'patch-meta_in_summary' into 'develop'Merge branch 'patch-extractalignedfastq' into 'develop'Merge branch 'patch-mpileup' into 'develop'Merge branch 'feature-yaml_support' into 'develop'Fix bug in flexiprep tablemake reference specific config valuesAdded reference module to toucanAdded Reference to gentrap testAdding reference stats to summaryChange namingSwitch pipeline to reference module