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Created with Raphaël 2.2.011May1098765432130Apr29282726252221181615141312111087654131Mar3029252423211918171615141311109875432129Feb262524Adding commentsAdded pipeline to agregation and executableFixed testAdded contig check for each recordFixed compile errorFixed file namesAdded cnv to summary settingsAdded test in shiva for cnvcallingAdded cnv calling to shivaStyle fixesRemove old pipeline from executableAdded conifer as methodAdded bedtools sorted flag as defaultAdded summary testAdded basic unit testsStyle fixFix cutadapt test.Merge branch 'develop' into fix-make-rc_trimmingoptionalUpdate testMerge branch 'develop' into fix-svcallers-vcfUse samplename_suffix to change the sample nameMerge branch 'develop' into feature-allow-custom-adaptersAdded summary jobsStyle fixesMake kopisu more modulairRemove empty classMerge remote-tracking branch 'remotes/origin/develop' into feature-cnvpipelineMerge branch 'fix-tagged_files' into 'develop' Fixed tagged filesfix typoAdding compression to all VCF outputs from the SV-callersMerge branch 'feature-more_unit_tests' into 'develop' Style fixesAdded testMerge branch 'fix-gvcfs-extract' into 'develop' Added more testing to shivaFixed summary keysAdded tests for depsattempt to fix cyclic errorsby default report the SVtype in the ALT field