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Created with Raphaël 2.2.025Feb24232221181716151211109875432129Jan28272625232221201918171514121110865430Dec29282625242322211817161514131110764330Nov292726252423201918171612add all ze optionsMerge remote-tracking branch 'remotes/origin/fix-278' into feature-skip_abortForgot to delete tmp file on exitMake test-coverage for BamUtils 100%Add options when starting FreeC from KopisuAdd FreeC wrapper (updated for FreeC 8.7)Merge branch 'develop' into feature-cnvpipelineRemove redundant codeFix readQualHistoMap, reporting wrong number (took counts instead of idx)Fix for issue #258Added option to skip abort stepMerge branch 'feature-report_core_testing' into 'develop' Merge branch 'fix-285' into 'develop' style changesAdded multisampleReport testMerge branch 'feature-gvcftobedtest' into 'develop' Added test to generatePagesAdded test on count methodAdded section render testAdded test on render methodFixed target variant plotChange error to loggerFix intermediatefix el weirdo warningadd the options in the listFix fix_iupacAdd output tests to gvcf2bed.Merge branch 'fix-invalid-sample' into 'develop' Remove correctDictFix dict checkautostyle changesAdd tinycap to aggregate for scoverageFix and test #280Add tinycap to aggregate for scoverageChange tests to accept pindelMerge from developChange default settings. Move min_length of 8 to 15 (advise from Henk Buermans)Fix FastQC test since we now include the reverse complement of a found adapter, the test had to be modified to check the change.Fixed python exeAdded index as output file