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  • 266936ed73 添加ProtectedCLGATK类，方便调试protect模块中的代码 main zzh 2026-01-07 18:21:50 +0800
  • 56e0098a71 忽略target子文件夹 zzh 2026-01-05 19:02:51 +0800
  • aa8764d6c3 Update pom versions for the 3.8-1 release Geraldine Van der Auwera 2017-11-09 02:10:43 -0500
  • e4c24188b2 Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2017-11-09 02:09:51 -0500
  • c654e0b9a2 Update pom versions to mark the start of GATK 3.9 development Geraldine Van der Auwera 2017-11-09 02:09:16 -0500
  • a2f45944f3 Serialized GMM no longer depends on command line annotation order (#1632) Samuel Friedman 2017-10-24 11:50:03 -0400
  • 09b4cf70f6 Upgrade GKL to 0.6.0 (#1631) Ernesto Brau 2017-09-29 22:15:43 -0400
  • 76c9902fbf Update GKL to 0.5.9 (#1629) Ernesto Brau 2017-09-06 17:25:23 -0400
  • a9479ee43e Revert "Changed GKL version to 0.5.6 (#1626)" (#1628) Geraldine Van der Auwera 2017-08-29 11:05:04 -0400
  • effaf881b3 Changed GKL version to 0.5.6 (#1626) Ernesto Brau 2017-08-29 10:48:26 -0400
  • aa8b2ab535 Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623) Ernesto Brau 2017-08-18 22:51:33 -0400
  • 3c841eaab5 Merge pull request #1622 from broadinstitute/rhl_vtt_fix_doc_typos Geraldine Van der Auwera 2017-08-07 17:45:06 -0400
  • 9ba104a6e9 Merge pull request #1625 from broadinstitute/ldg_fixPLsubsettingGQproblem Geraldine Van der Auwera 2017-08-07 17:43:49 -0400
  • d28b086862 Update the GQ after PLs get subset Laura Gauthier 2017-08-02 16:05:00 -0400
  • afc257c195 Fix VariantsToTable documentation typos Ron Levine 2017-07-29 08:30:45 -0400
  • 02c8302290 Update pom versions to mark the start of GATK 3.9 development Geraldine Van der Auwera 2017-07-28 10:14:19 -0400
  • 5381dc83b1 Update pom versions for the 3.8 release Geraldine Van der Auwera 2017-07-28 10:01:54 -0400
  • 57929e2a7b Merge remote-tracking branch 'unstable/master' Geraldine Van der Auwera 2017-07-28 10:00:40 -0400
  • 1798afb1f4 Merge pull request #1621 from broadinstitute/gvda_clean_slate Geraldine Van der Auwera 2017-07-28 00:35:00 -0400
  • 04a688f701 Update release scripts Geraldine Van der Auwera 2017-07-27 23:09:10 -0400
  • 8af62576cf Updated gatkdocs template Geraldine Van der Auwera 2017-07-28 00:30:56 -0400
  • be523df1b1 Fix problem filename Geraldine Van der Auwera 2017-07-27 22:40:42 -0400
  • a906e24010 Merge pull request #1615 from broadinstitute/gvda_archive_docs Geraldine Van der Auwera 2017-07-24 02:46:05 +0200
  • 3f3ef608e5 Archive GATK3-specific docs from the forum Geraldine Van der Auwera 2017-07-24 00:57:50 +0200
  • 6de68d556e Merge pull request #1609 from broadinstitute/yf_make_readutils_test_public Geraldine Van der Auwera 2017-07-23 23:18:10 +0200
  • 57588a5661 Make error informative for non-diploid family likelihoods Ron Levine 2017-07-18 23:07:27 -0400
  • e406bb76ea Move htsjdk to ver 2.10.1 and picard to ver 2.10.2 Ron Levine 2017-07-17 22:47:36 -0400
  • 97ed131abd Merge pull request #1610 from broadinstitute/ldg_fixRankSumHistogramOutput2 ldgauthier 2017-07-18 12:51:24 -0400
  • 66f5fe075b Changed ASRankSum single-sample output so it's combine-able single sample gVCF now gets a "histogram" with one entry Laura Gauthier 2017-07-14 12:10:10 -0400
  • 385f06b5cb Merge pull request #1608 from broadinstitute/ldg_renomalizeVQSRdata ldgauthier 2017-06-30 16:44:40 -0400
  • ee39f9141f Normalize input data by same annotation normalization scheme as input model Laura Gauthier 2017-05-05 13:09:49 -0400
  • d535c377b5 - responding to reviewer's comments. Yossi Farjoun 2017-06-28 16:40:55 -0400
  • 741c544fbf Deprecate --allowMissingData, add --errorIfMissingData and print NA for null object in VariantsToTable Ron Levine 2017-06-25 22:02:25 -0400
  • 14e598a401 Merge pull request #1605 from broadinstitute/ldg_updateReference ldgauthier 2017-06-27 08:29:09 -0400
  • 0f8818bc43 Update all the md5s for header reference path changes Laura Gauthier 2017-06-23 17:45:31 -0400
  • 71e361dae9 Merge pull request #1604 from broadinstitute/rhl_close_printstream_1600 ldgauthier 2017-06-26 13:58:52 -0400
  • 312d97d53b Close BQSRGatherer's PrintStream when finished Ron Levine 2017-06-26 13:43:09 -0400
  • fff63bab53 Merge pull request #1595 from broadinstitute/eba_gkl_pairhmm_fpga droazen 2017-06-26 12:06:31 -0400
  • ba7df054f0 Close BQSRGatherer's PrintStream when finished Ron Levine 2017-06-24 13:40:25 -0400
  • 18c9fe41c7 Close SamReader Ron Levine 2017-06-08 10:37:32 -0400
  • 446b11913b Added FPGA support for PairHMM via GKL, and marked as 'experimental' Ernesto Brau 2017-06-07 14:39:11 -0400
  • e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM Ernesto Brau 2017-04-06 10:42:56 -0400
  • 70b2575c29 Move htsjdk to ver 2.10.0 and picard to ver 2.9.2 Ron Levine 2017-06-01 16:36:52 -0400
  • 3de98263f5 Copy Program Records (PG) from input BAM Ron Levine 2017-05-30 15:51:57 -0400
  • 1d6756fbd0 Add assert to testMissingAlleleSpecificAnnotationGroup (#1587) Ron Levine 2017-05-12 17:07:05 -0400
  • 4a0458b2e9 GenotypeGVCFs and CombineGVCFs should error when AS annotations are not present (#1585) Ron Levine 2017-05-11 12:41:51 -0400
  • c855714e10 Merge pull request #1586 from broadinstitute/ldg_turnOffOneMoreTest ldgauthier 2017-05-11 12:17:11 -0400
  • 417d390077 One more stupid fargo bam test to turn off Laura Gauthier 2017-05-11 09:54:38 -0400
  • ae174d3359 Merge pull request #1541 from broadinstitute/ldg_revertToMedianRankSum ldgauthier 2017-05-10 14:43:08 -0400
  • 35d0b72c79 Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess Laura Gauthier 2016-09-28 08:41:20 -0400
  • d512f3f808 Merge pull request #1582 from broadinstitute/SC-input-prior-HC-doc-fix ldgauthier 2017-05-09 14:15:42 -0400
  • 8703642142 Change AC>1 to AC>0 Sheila Chandran 2017-05-09 13:31:58 -0400
  • 00b7135afe Merge pull request #1575 from broadinstitute/snf_ReadGMMReport Samuel Friedman 2017-05-08 14:40:27 -0400
  • ed440f1684 respond to review comments Samuel Friedman 2017-05-05 16:29:01 -0400
  • 68bdb93c8c add annotation mismatch warning and refactor tests Samuel Friedman 2017-05-04 16:48:24 -0400
  • f5d133df87 scientific notation in model report and basic test Samuel Friedman 2017-05-03 18:37:52 -0400
  • e9efd53281 Merge pull request #1581 from broadinstitute/ldg_actuallyFixTests ldgauthier 2017-05-03 09:59:20 -0400
  • c91cacb642 Turn off one more unit test with fargo bam Laura Gauthier 2017-05-03 09:53:08 -0400
  • 67cf29558f Merge pull request #1578 from broadinstitute/ldg_turnOffPicardAggregationTests droazen 2017-05-02 16:20:35 -0400
  • 4df71a3ca1 expect floats in the report Samuel Friedman 2017-05-02 12:05:10 -0400
  • 505383e504 Remove obsolete unmapped reads test for FindCoveredIntervals (#1580) Ron Levine 2017-05-02 08:50:12 -0400
  • 1b4ac51048 move model file parsing to initialize Samuel Friedman 2017-05-01 15:52:45 -0400
  • 2284a69e7c Turn off PicardAggregation tests because they're a pain with all the bams moving to slow storage and because the pipeline utils aren't used anyway Laura Gauthier 2017-04-28 17:16:05 -0400
  • d06a6c7318 string cast bug Samuel Friedman 2017-04-28 17:32:36 -0400
  • 31eee1f2a3 Merge pull request #1576 from broadinstitute/ms_FS_bug meganshand 2017-04-28 17:02:09 -0400
  • ea5efa0b2c Fixes rounding errors in FS using the same solution as R meganshand 2017-04-27 14:12:43 -0400
  • f55b932cfc addressed review comments Samuel Friedman 2017-04-27 17:16:57 -0400
  • 85cb1c2810 dont spam on NaNs Samuel Friedman 2017-04-26 17:33:06 -0400
  • 57c064eaa3 small code cleanup Samuel Friedman 2017-04-26 16:01:16 -0400
  • a8f70c891f Create GMM from model reports in VQSR Samuel Friedman 2016-11-04 15:05:23 -0400
  • 4fe4ace232 minor bug fix in depth of coverage for partitioning by library + test (#1574) skwalker 2017-04-26 10:42:54 -0400
  • 5110b13124 Merge pull request #1572 from broadinstitute/dr_use_gkl_intel_inflater_deflater droazen 2017-04-14 16:22:34 -0400
  • a950d0778f Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default David Roazen 2017-03-31 12:36:53 -0400
  • 728b3db8e0 Merge pull request #1571 from broadinstitute/rhl_vtbp_doc_1570 Ron Levine 2017-03-23 14:22:05 -0400
  • 278985b8bd Update PLINK link and change lines to columns Ron Levine 2017-03-23 11:46:38 -0400
  • 485a090ef6 Merge pull request #1569 from broadinstitute/rhl_vtt_doc_orders_samples_1545 Ron Levine 2017-03-21 18:09:35 -0400
  • 00a434a38b Merge pull request #1568 from broadinstitute/rhl_mutect2_doc_germline_1560 Ron Levine 2017-03-21 18:08:39 -0400
  • 4188745074 Document how VTT orders samples in output table Ron Levine 2017-03-21 12:55:30 -0400
  • c20e682a97 Update MuTect2 documentation about not computing obvious germline variants Ron Levine 2017-03-20 22:41:01 -0400
  • c449b133d0 Merge pull request #1565 from broadinstitute/rhl_fix_cv_merge_1547 Ron Levine 2017-03-14 16:43:33 -0400
  • 687dee22ac Fix CombineVariants merge for different types Ron Levine 2017-03-10 10:44:42 -0500
  • 31315a31c0 Merge pull request #1563 from broadinstitute/rhl_fci_thresholds_1562 Ron Levine 2017-03-07 17:07:45 -0500
  • 49083fc704 Fix FindCoveredIntervals so -minBQ, -minMQ and -cov work as expected Ron Levine 2017-03-02 12:20:36 -0500
  • b3df32047f Merge pull request #1535 from broadinstitute/rhl_clipping_op_align_offset_1447 Ron Levine 2017-03-06 17:53:12 -0500
  • 1e88d849e3 Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test Ron Levine 2016-12-13 13:01:00 -0500
  • faeac6e5a4 Merge pull request #1551 from broadinstitute/rhl_hc_no_dp_ad_1322 Ron Levine 2017-02-28 16:58:21 -0500
  • 8316fa92f3 Set AD and DP to zero if no read coverage Ron Levine 2017-01-26 08:42:25 -0500
  • c0bf07cb78 Merge pull request #1559 from broadinstitute/rhl_htsjdk_2.9.1_picard_2.9.0 Ron Levine 2017-02-23 14:32:44 -0500
  • 91339c12c9 Move htsjdk to ver 2.9.1 and picard to ver 2.9.0 Ron Levine 2017-02-22 19:01:26 -0500
  • 5c178c2a84 Merge pull request #1553 from broadinstitute/rhl_latv_split_nocall_1518 Ron Levine 2017-02-22 18:54:26 -0500
  • 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref Ron Levine 2017-02-14 18:01:48 -0500
  • b9a43cc35e Merge pull request #1557 from broadinstitute/rhl_ggvcfs_input_prior_1532 Ron Levine 2017-02-20 22:21:25 -0500
  • 3c347c1385 Total ploidy does not have to equal to the number of priors Ron Levine 2017-02-20 20:28:41 -0500
  • c55c77ab27 Merge pull request #1555 from broadinstitute/rhl_htsjdk_2.9.0_picard_2.8.3 Ron Levine 2017-02-17 13:54:17 -0500
  • ab75b08ea7 Remove unused compressed_block_size and close BlockCompressedInputStream Ron Levine 2017-02-17 12:21:51 -0500
  • 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 Ron Levine 2017-02-16 10:09:55 -0500
  • 67baa9046c Merge pull request #1550 from broadinstitute/rhl_fix_splitncigarreads_doc_1549 Ron Levine 2017-01-18 17:06:06 -0500
  • dce2e29ade Change ALLOW_N_CIGARS to ALLOW_N_CIGAR_READS in doc Ron Levine 2017-01-18 15:11:52 -0500
  • 7c0e51396f Merge pull request #1539 from broadinstitute/rhl_hc_disable_badmatefilter_1443 Ron Levine 2017-01-18 12:39:22 -0500
  • bfa633a90f Merge pull request #1548 from broadinstitute/rhl_synchonize_upstream_del_1188 Ron Levine 2017-01-13 14:57:05 -0500