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Author SHA1 Message Date
zzh 266936ed73 添加ProtectedCLGATK类，方便调试protect模块中的代码 2026-01-07 18:21:50 +08:00
Geraldine Van der Auwera aa8764d6c3 Update pom versions for the 3.8-1 release 2017-11-09 02:10:43 -05:00
Ernesto Brau 09b4cf70f6 Upgrade GKL to 0.6.0 (#1631) 2017-09-29 22:15:43 -04:00
Ernesto Brau 76c9902fbf Update GKL to 0.5.9 (#1629) 2017-09-06 17:25:23 -04:00
Geraldine Van der Auwera a9479ee43e Revert "Changed GKL version to 0.5.6 (#1626)" (#1628) 
This reverts commit 78acfb95f8672a7fd65c66e0932a0d3b212ec8d8.
 2017-08-29 11:05:04 -04:00
Ernesto Brau effaf881b3 Changed GKL version to 0.5.6 (#1626) 2017-08-29 10:48:26 -04:00
Ernesto Brau aa8b2ab535 Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623) 
Update GKL to version 0.5.5, which fixes a bug in FPGA 'private' mode. Integration test results were updated to reflect different fallback behavior when AVX is not available.
 2017-08-18 22:51:33 -04:00
Geraldine Van der Auwera 3c841eaab5 Merge pull request #1622 from broadinstitute/rhl_vtt_fix_doc_typos 
Fix VariantsToTable documentation typos
 2017-08-07 17:45:06 -04:00
Laura Gauthier d28b086862 Update the GQ after PLs get subset 2017-08-04 09:54:08 -04:00
Ron Levine afc257c195 Fix VariantsToTable documentation typos 2017-07-29 08:33:14 -04:00
Geraldine Van der Auwera 02c8302290 Update pom versions to mark the start of GATK 3.9 development 2017-07-28 10:14:19 -04:00
Geraldine Van der Auwera 6de68d556e Merge pull request #1609 from broadinstitute/yf_make_readutils_test_public 
making a test within readutils-test public
 2017-07-23 23:18:10 +02:00
Ron Levine e406bb76ea Move htsjdk to ver 2.10.1 and picard to ver 2.10.2 2017-07-18 13:16:21 -04:00
Laura Gauthier 66f5fe075b Changed ASRankSum single-sample output so it's combine-able 
single sample gVCF now gets a "histogram" with one entry
 2017-07-18 11:00:59 -04:00
Yossi Farjoun d535c377b5 - responding to reviewer's comments. 2017-06-28 16:40:55 -04:00
Ron Levine 741c544fbf Deprecate --allowMissingData, add --errorIfMissingData and print NA for null object in VariantsToTable 2017-06-28 12:54:07 -04:00
Laura Gauthier 0f8818bc43 Update all the md5s for header reference path changes 2017-06-26 15:53:13 -04:00
Ron Levine 312d97d53b Close BQSRGatherer's PrintStream when finished 2017-06-26 13:47:30 -04:00
droazen fff63bab53 Merge pull request #1595 from broadinstitute/eba_gkl_pairhmm_fpga 
Added FPGA support for PairHMM via GKL, and marked as 'experimental'
 2017-06-26 12:06:31 -04:00
Ron Levine ba7df054f0 Close BQSRGatherer's PrintStream when finished 2017-06-24 15:09:41 -04:00
Ernesto Brau 446b11913b Added FPGA support for PairHMM via GKL, and marked as 'experimental' 2017-06-07 14:39:11 -04:00
Ernesto Brau e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM 
Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code

Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument

Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM

Updae MD5s
 2017-06-07 13:33:32 -04:00
Ron Levine 70b2575c29 Move htsjdk to ver 2.10.0 and picard to ver 2.9.2 2017-06-02 06:52:24 -04:00
Ron Levine 3de98263f5 Copy Program Records (PG) from input BAM 2017-06-01 16:01:20 -04:00
Laura Gauthier 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 2017-05-10 09:04:42 -04:00
Samuel Friedman 00b7135afe Merge pull request #1575 from broadinstitute/snf_ReadGMMReport 
Read model report and reconstruct GMM from it in VQSR
 2017-05-08 14:40:27 -04:00
Samuel Friedman ed440f1684 respond to review comments 2017-05-05 16:29:01 -04:00
Ron Levine 505383e504 Remove obsolete unmapped reads test for FindCoveredIntervals (#1580) 
Remove obsolete unmapped reads test for FindCoveredIntervals
 2017-05-02 08:50:12 -04:00
Samuel Friedman a8f70c891f Create GMM from model reports in VQSR 2017-04-26 16:02:06 -04:00
skwalker 4fe4ace232 minor bug fix in depth of coverage for partitioning by library + test (#1574) 
minor bug fix in depth of coverage for partitioning by library
 2017-04-26 10:42:54 -04:00
David Roazen a950d0778f Add the Intel GKL as a dependency, and turn on the Intel inflater/deflater by default 2017-04-05 12:45:26 -04:00
Ron Levine 278985b8bd Update PLINK link and change lines to columns 2017-03-23 11:46:38 -04:00
Ron Levine 4188745074 Document how VTT orders samples in output table 2017-03-21 18:04:38 -04:00
Ron Levine 687dee22ac Fix CombineVariants merge for different types 2017-03-14 16:42:16 -04:00
Ron Levine 1e88d849e3 Fixed ClippingOP.getNewAlignmentStartOffset() to handle N cases properly and added unit test 2017-03-06 15:40:01 -05:00
Ron Levine 91339c12c9 Move htsjdk to ver 2.9.1 and picard to ver 2.9.0 2017-02-22 19:01:26 -05:00
Ron Levine 61875e4dfa Fix LeftAlignAndTrimVariants -split to not change no-call genotypes to hom-ref 2017-02-22 17:57:59 -05:00
Ron Levine ab75b08ea7 Remove unused compressed_block_size and close BlockCompressedInputStream 2017-02-17 12:22:53 -05:00
Ron Levine 1d36d9fd69 Move htsjdk to ver 2.9.0 and picard to ver 2.8.3 2017-02-17 07:03:03 -05:00
Geraldine Van der Auwera e86da63d04 Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
Geraldine Van der Auwera 56f2c1ac75 Update pom versions for the 3.7 release 2016-12-12 08:49:43 -05:00
Ron Levine 5602095a24 Move htsjdk to ver 2.8.1 and picard to ver 2.7.2 
- Updating VF and tests to match new jexl behavior from htsjdk
     - Use Z instead of DP to test behavior on missing annotation
 2016-12-10 11:50:30 -05:00
Ron Levine 172db666d6 Output files with the vcf.gz extension are gzipped, containing .bcf not as an extension result in VCF" 2016-12-05 22:25:59 -05:00
Geraldine Van der Auwera 234ccdf0c3 Merge pull request #1496 from broadinstitute/db_m2_downsampling 
Expose downsampling parameters as CLI arguments to Mutect2
 2016-12-05 21:53:25 -05:00
David Benjamin b1f2301dd3 Add downsampling arguments to Mutect 
- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
	- maxReadsInMemoryPerSample is an activeRegionWalker arg
 2016-12-05 14:12:22 -05:00
Geraldine Van der Auwera b42dc1624b Documentation fixes 
- Fix missing closing code block tag
	- SOR fix + minor fix to template
	- Minor typo fixes
	- Make no_cmdline_in_header arg visible in docs
	- Caveats for UG-only args that are difficult to move out of common collection
	- Reference -L and -XL in -gvcf documentation
	- Annotation doc fixes (dsde-docs#1289)
	- Unhide some ContEst args and make Advanced
	- Fix inputPrior error message
	- Update web urls
	- Add JEXL doc link
 2016-12-05 14:09:44 -05:00
Ron Levine 68b6f8f638 Replace VariantContextWriterFactory with VariantContextWriterBuilder 2016-11-30 16:04:25 -05:00
Ron Levine 262c08aee3 Make exit system file type message generic 2016-11-23 10:12:21 -05:00
David Benjamin 055d653bc2 Merge pull request #1517 from broadinstitute/rhl_adapter_boundary_err_1406 
Fix adapter bounday for positive strand
 2016-11-18 10:25:46 -05:00
Ron Levine 22d94a7096 Fix adapter bounday for positive strand 2016-11-16 16:41:17 -05:00