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Created with Raphaël 2.2.06Feb543230Jan292827262322212019161514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct302928Update HTSeq-count wrapperUpdate GSNAP wrapper testUpdate GSNAP wrapper with correct typesMerge branch 'feature-add_ids_to_filter' into 'develop'Refactor codeAdded inverted output fileMerge branch 'develop' into feature-gentrapAdd --id and --id-file optionAdd missing docsParse module status in Flexiprep FastQC wrapperMerge branch 'feature-fix_raxml' into 'develop'Add --no-bgfs optionAdded igvtoolsFix NullPointerException caused by Option[File] being nullMerge branch 'develop' into feature-bamToBigWigRefactorMerge branch 'patch-flexiprep_mapping_flags' into 'develop'Merge branch 'patch-doc_fixes' into 'develop'Merging develop into branch and fix Mapping.scala and Flexiprep.scala (merging conflicts and typos)Refactor and modified tests, Solexa test still fails (TODO)Remove redundant check on outputDir characterMerge branch 'feature-igvtools' into 'develop'Make setting the tdf/wig less restrictive and no default names anymoreAdded more scala docsMerge branch 'develop' into feature-unittest_coreAdded some scala docsMerge branch 'feature-fix_gatk' into 'develop'Minor code refactoroutput name is now config valueFix bug on vmemMaking the output files Option[File], and use Some() to verify whether it was set or notFix some optionsEnables manual set of jobOutputFileRefactor seqstat and add (few) tests.. wipMerge branch 'feature-vcf_stats' into 'develop'Added basic testingSwitch to case classesFix warning on max colorFix typo bugAdded more general stats