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Created with Raphaël 2.2.028Jul26184130Jun2322171630May8Apr18Mar987432125Feb2415141110928Jan27261918171411416Dec1514626Nov1715131211109829Oct28130Sep241723Aug20181029Jul2721201998752130Jun2928252221161514111072131May2825211920Apr1514131230Mar29252322191817118424Feb22211918169428Jan21158628Dec24221615119130Nov272625191712111096543230Oct2827262216151312987652129Sep24232116151411109742126Aug2420191817141312111076529Jul28272322212017161513start adjusting pave commandstart adjusting pave commandMerge remote-tracking branch 'origin' into 5.29_updateMerge pull request #303 from biowdl/sageupdate some tool versionsfix linting issuesagesageupdate changelogMerge branch 'develop' into sagefix typo in star GenomeGenerate parameter_metaMerge pull request #302 from biowdl/gridss_annotateMerge branch 'develop' into gridss_annotateAdd GT to gridss results in AnnotateSvTypesMerge pull request #301 from biowdl/gridss_annotateupdate changelogincrease memory for bcftools sortgive bcftools sort more timefix duoble .bgz and and index to outputdetect if compressedfix output namefix heredocincrease sage memoryperformanceperformanceadjust sage memory and timeadjust some runtime settingsadjust gridss threadsMake sure reportPath directory is createdvariousfixesvariousfixestypocopy paste erroradd task for sv type annotation of gridss resultsMerge pull request #300 from biowdl/fix_gridss_tbiMerge remote-tracking branch 'origin/develop' into fix_gridss_tbiupdate changelogrun tabix if vcf index is missing in gridssRemove duplicate options for markduplicatesfix copy-paste errorfix copy-paste error (orange docker image)fix cupGenerateReportfix CupGenerateReportAdd parameter_meta for Picard UmiAwareMarkDuplicatesWithMateCigarAdd parameter_meta for useSoftclippingforSupplementaryMerge pull request #297 from biowdl/addPicardDedup