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Created with Raphaël 2.2.016Jan1514131210986517Dec1611985432128Nov272524222120191817141211108765432131Oct30292827252423222120171615141310987Added sampeAdded samseAdded bwa aln extensionMake new package for bwaMove aligners to nl.lumc.sasc.biopet.exetensionsFix unit testingAdding check for database and cache. Removing print statements in normalizer testRemove old reportMake null values in json possible as inputFix RGPI config varFix default sample and libraryRemove unused functionSwitch to config instead of sampleConfig and libraryConfigAdded sub path instead of submoduleFix Path ordersAdded merged input configAdding toucan pipeline stubAdding imls to prevent major headachesMerge remote-tracking branch 'origin/develop' into feature-gentrapMerge branch 'develop' into feature-toucanAdded a null value on NoneAdd new config report to biopetQScriptFirst version of new config reportMerge branch 'develop' into feature-Chipcapfirst step mapping is done, tested and works okeMerge branch 'feature-config_unittest' into 'develop'Added scala docsMerge branch 'feature-fix_contams' into 'develop'Merge branch 'feature-prefix_fastq' into 'develop'Merge branch 'feature-improve_fastqSplitter' into 'develop'Remove old scriptMerge branch 'feature-annotate_bed' into 'develop'Switch to method for adaptersFix for multiple tabs in contams fileAdded getFoundAdapters methodAdded scala docsAdded scala docsAdded scala docsRemove old scriptsSwitch to new tool