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Created with Raphaël 2.2.028Oct27252423222120171615141310987630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun262321191713121096Merge commit '5dd7125a8ea3eef861d5d28807c576923d130a27' into feature-SamToFastqMoved Sage tools to nl.lumc.biopet.toolsBreakdancer, scaliform reformatmake intermediate fastqfix on R2 output namefix on main classUpdate to htsjdk use in GATK 3.3Add unit tests for file writingUpdate write function to accept FASTQ readers and writersAdd more CLI validationAdd mockito dependencyUnit test updatesAdd functions to mainUpdate input and output FASTQs argument flag namesExpose read suffix length argument to command lineAdd logging message when writingFilter on MAPQ instead of read groupsUpdate to use htsjdk from GATK 3.3Switch to Gatk/Queue 3.3Added FastqSplitter to exeAdded MpileupToVcf to exeAdded BedToInterval to exeUpdate main project fileFix argsAdded bam_to_fastq optionMerge branch 'develop' into feature-wipereadsAdd GATK 3.3 IntelliJ fileMerge branch 'feature-gatk_3.3' into 'develop'Added SamToFastqRevert back to JDK 1.7 due to regression in GATK 3.3Merge branch 'develop' into feature-wipereadsSwitch to Gatk/Queue 3.3Changed naming of sage toolsAdded BedtoolsCoverageToCounts to exeAdded CountFastq to exeAdded CreateDeepsageLibrary to exeAdded CreateTagCounts to exeUse DataProvider for testing multiple combinationsMerge branch 'feature-toolcommands' into 'develop'Update tests and filter function name