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Created with Raphaël 2.2.012Mar1154329Feb26151413106516Jan1122Dec201915429Nov211716141031Oct23101Sep24Aug221814121028Jul272421201728Jun271513217May111021Mar15Feb1413976110Jan15Nov211Oct6520Sep10813Jul29Jun22212083125May2021Apr191576429Mar21151327Feb252317161110743230Jan17320Dec15138724Nov23171612109426Oct252012729Sep17157131Aug20171354330Jul27211413715Jun1498752127May181713103130Apr292814985124Mar22171612119523Feb22108327Jan2522211512117423Dec22151411942125Nov241729Oct141398230Sep2921171632126Aug12106421Jul201413109823Jun2219942128May211815141312628Apr1386330Mar251917161027Feb26212019181514135229Jan272118151419Dec181311928Nov262524201918131287625Oct24221815430Sep2624232019161312111096543130Aug28201915141312107652131Jul2624222019181715121027Jun252120181413115328May2624Reject piped input (/dev/stdin) for BedToIntervalList (#1918)master upstream…master upstream/mastertemporarily turn off deleting files as I suspect race condition is causing errorts_revertsam_le…ts_revertsam_lee upstream/ts_revertsam_leebetter error message for debugging failing cloud testhail maryfasta.gz.failet's try thistry this?restore full testadd cram testsadd a test fileorganize filestests readyFix for order flipping in SortingCollection used for MarkDuplicates (#1945)test draftDirectly compare INPUT to /dev/stdin instead of PicardHtsPath.isOther()can_bed2interva…can_bed2intervallist_stdin_checkMake the VCF option in CollectSamErrorMetrics optional. (#1476)Resolve merge conflictsnh_make_vcf_opt…nh_make_vcf_optional upstream/nh_make_vcf_optionalFix CollectHSMetrics - Don't use Coverage Cap on fold score (#1913)MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read (#1942)Update SamToFastq documentation (#1920)all tests passcloudify revert samAdd the EXT argument to CollectSamErrorMetrics. (#1478)Enable use of cloud reference files (#1804)Fix setting of CommandLineProgram REFERENCE_SEQUENCE.cn_nio_referenc…cn_nio_reference_files_cn upstream/cn_nio_reference_files_cnfix failing testEnable the use of cloud reference files by updating the ReferenceArgumentCollection implementations to use nio paths.cn_nio_referenc…cn_nio_reference_rebase upstream/cn_nio_reference_rebaseUpdate setup_gcloud github action (#1939)Convert to use the java-library plugin (#1934)MarkDuplicates: Add read group ID instead of string "RG" (#1937)Add new argument to allow setting the google requester pays projectlb_requester_pa…lb_requester_pays upstream/lb_requester_paysfixed more failscn_nio_referenc…cn_nio_reference_files_takuto upstream/cn_nio_reference_files_takutosome fixkhalid conflict that was not caughtMerge branch 'master' into cn_nio_reference_filesmanually resolve conflictsproofreadreorganizechris editremove newly disallowed ;lb_update_to_21…lb_update_to_21 upstream/lb_update_to_21