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Created with Raphaël 2.2.011Dec928Nov262524201918131287625Oct24221815430Sep2624232019161312111096543130Aug28201915141312107652131Jul2624222019181715121027Jun252120181413115328May262422212019181413121129Apr272423221512109825Mar221211109827Feb25201411124Jan231817161514107117Dec11754329Nov282018161395231Oct29232219121095427Sep18141211107654229Aug282523222117141376331Jul30252420181310964227Jun2622195131May29252423222118179330Apr27252417141312119429Mar28262219128727Feb26201615131275129Jan26252322191817161312111098654228Dec212019171615141312118520Nov1817161311631Oct3027252322201816133229Sep282725141187531Aug292319161514108754331Jul292827CreateVerifyIDIntensityContaminationMetricsFile handle negative LLK (#1440)2.21.52.21.5Parse Floats from GtcToVcf in VcfToAdpc (#1436)- Cleanupyf_add_Reconstr…yf_add_ReconstructTriosCLPs upstream/yf_add_ReconstructTriosCLPs- Added CLPs for inferring Trio structure and Sex from BAMs and VCFs.Compile and test on 11 (#1410)Generated by gradle-git-publish.CollectRnaSeqMetrics: Made IGNORE_SEQUENCE optional (#1423)2.21.42.21.4- replaced int with long to avoid integer overflow in large files. (#1427)only adding a period if there's not already a period is pathological (#1430)Yf collect duplicate metrics (#1424)eb_make_even_in…eb_make_even_intervals upstream/eb_make_even_intervalsready for prime time?yf_estimate_cov…yf_estimate_coverage_dependence_on_flow upstream/yf_estimate_coverage_dependence_on_flowupdate htsjdk to 2.21.0 (#1422)- test in placeGenerated by gradle-git-publish.-first commitCollectRnaSeqMetrics: Made IGNORE_SEQUENCE optionalmg_collectrnase…mg_collectrnaseqmetrics_make_ignore_sequence_optional upstream/mg_collectrnaseqmetrics_make_ignore_sequence_optionalYf optimize query for independent replicate metrics (#1420)2.21.32.21.3Make CheckIlluminaDirectory log if faking files (#1417)Modified CollectAlignmentSummaryMetric to collect more metrics (#1374)Merge pull request #1415 from broadinstitute/gg_GL-706_BugInVcfToAdpc2.21.22.21.2Fix bug in VcfToAdpcSpeeds up MarkDuplicates on queryname input by using the in memory read-ends map. (#1411)Merge pull request #1414 from broadinstitute/gg_DocumentTwoClpsDocument two CLPsUpdate plugin versions for github-pages documentation (#1405)- removing a spurious newline from the logging output of ReorderSam (#1403)Publish of Github pages from Gradle.Fixing up tests in MarkDuplicates so that tests with duplex UMIs are handled properly (#1404)2.21.12.21.1- trying to fix intermittent failuresyf_fix_intermit…yf_fix_intermittent__STDOUT_failures upstream/yf_fix_intermittent__STDOUT_failuresIncluded support for indel error detection and read filtering in CollectSamErrorMetrics (#1370)Yf add more sample mapping options to crosscheck + make dictionary checking more lenient (#1303)Merge pull request #1376 from broadinstitute/mg_longread_error_reporting_iterationFinal comments addressed.Modified tracking of skipped locimg_longread_err…mg_longread_error_reporting_dev_query upstream/mg_longread_error_reporting_dev_queryCounting skipped bases- Added a test to CollectHsMetrics to harden against future code changes (#1386)optimized importsyf_fix_create_d…yf_fix_create_dictionary upstream/yf_fix_create_dictionary- removed unused code in CreateSequenceDictionaryAddressing comments.Considering variant loci in window around given locus