c13e3752d6
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-16 16:36:52 -04:00
e0cf6d1985
Merge pull request #1470 from broadinstitute/rhl_rm_nonref_genotypegvcfs
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Remove NON_REF from allSites VCF output
2016-09-16 16:31:13 -04:00
6564066de3
Remove NON_REF from allSites VCF output
2016-09-16 13:55:52 -04:00
091d05370b
Fix 1448 to make alt allele removal by likelihoods robust to ref allele indices ( #1475 )
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* alt alle removal by likelihoods now robust to ref allele indices (no longer assumes 0-indexed ref)
2016-09-13 21:20:44 -04:00
f51d20c517
Merge pull request #1469 from broadinstitute/rhl_upgrade_apache_collections_to_v3.2.2
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Upgrade Apache Commons Collections to version 3.2.2
2016-09-09 12:57:09 -04:00
227038d0f8
Merge pull request #1471 from broadinstitute/rhl_rm_gvcf_blocks_genotype_gvcf
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Do not emit GVCF block definitions in the header
2016-09-09 10:00:15 -04:00
a7b1130224
Do not emit GVCF block definitions in the header
2016-09-09 07:41:03 -04:00
e84359a02e
Merge pull request #1467 from broadinstitute/rhl_fix_rprst_is_usable
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Make ReadPosRankSumTest.isUsableRead() account for deletions
2016-09-08 11:52:54 -04:00
ab454e8812
Upgrade Apache Commons Collections to version 3.2.2
2016-09-07 18:59:21 -04:00
956b18fbb7
Make ReadPosRankSumTest.isUsableRead() account for deletions
2016-09-07 13:52:09 -04:00
3c88e6859f
fix 1430 for genotype filters; refactored filter() method; added unit and integration test; more comprehensive fix must be done first on htsjdk side in JEXLMap ( #1456 )
2016-09-06 17:30:18 -04:00
d582ee6d3c
Merge pull request #1463 from broadinstitute/db_m2
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More Mutect2 refactoring
2016-08-31 15:46:46 -04:00
601c26a592
More small refactorings of Mutect2 code
2016-08-29 12:45:13 -04:00
814ad21006
Merge pull request #1454 from broadinstitute/rrhl_rm_stand_emit_conf
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Remove -stand_emit_conf argument
2016-08-27 08:57:09 -04:00
a883905101
Remove -stand_emit_conf argument
2016-08-26 22:09:11 -04:00
cb0dedeb49
Merge pull request #1462 from broadinstitute/ts_m2_refactor
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Clean up SomaticGenotypingEngine::callMutations and add TODOs
2016-08-26 14:15:33 -04:00
bc3b3ac0ec
Cleaned up SomaticGenotypingEngine::callMutations and added some TODOs.
2016-08-26 14:12:05 -04:00
4aede99697
Merge pull request #1453 from broadinstitute/db_mutect2
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Lots of small improvements to Mutect2 code
2016-08-23 18:35:38 -04:00
53e1d42d28
Merge pull request #1460 from broadinstitute/rhl_rank_sum_test_del_return
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Make getElementForRead() in RankSumTest robust
2016-08-23 16:36:30 -04:00
cd5c04f806
Make getElementForRead() in RankSumTest robust
2016-08-23 14:56:32 -04:00
01142dfb1c
Lots of small improvements to Mutect2 code
2016-08-23 09:50:48 -04:00
ebceb06284
Merge pull request #1445 from broadinstitute/rhl_read_pos_span_del
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Ignore spanning deletions in Rank Sum tests
2016-08-17 20:21:47 -04:00
abc4d5b7b3
Bypass spanning deletions in Rank Sum tests
2016-08-17 14:02:22 -04:00
01fdb90096
Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding
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addresses issue #1280 now interval padding works for exclude intervals
2016-08-17 13:15:15 -04:00
27e56b2bb9
Merge pull request #1441 from broadinstitute/rhl_printreads_bqsr_fail
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Throw an exception if the BQSR input covariants file is not found
2016-08-11 16:16:08 -04:00
f6c18a5182
Throw an exception if the BQSR input covariants file is not found
2016-08-11 12:46:14 -04:00
3510906c7f
addresses issue #1280 now interval padding works for exclude intervals
2016-08-10 13:45:45 -04:00
7959324f08
Merge pull request #1451 from broadinstitute/sl_issue_1345_fix_2
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Changed maximum allowed GQB value to 100.
2016-08-05 15:12:20 -04:00
49507faaa3
Changed maximum allowed GQB value to 100.
2016-08-05 13:06:31 -04:00
0630c7befd
Merge pull request #1423 from broadinstitute/rhl_read_sra
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Added support for directly reading SRA runs
2016-08-02 18:10:33 -04:00
a465c87ff8
Added support for directly reading SRA runs
2016-08-02 15:21:14 -04:00
6bca5a060f
Merge pull request #1446 from broadinstitute/sl_issue_1345_fix
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Fixed MD5 broken by PR #1440 .
2016-07-27 21:53:00 -04:00
832a383acd
Fixed MD5 broken by PR #1440 .
2016-07-27 13:51:20 -04:00
9a6ce7a347
Merge pull request #1440 from broadinstitute/sl_issue_1345
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Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-26 14:55:59 -04:00
e194b52ef3
Merge pull request #1442 from broadinstitute/vrr_genotype_gvcf_performance_fix
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GenotypeGVCFs performance and QUAL miscalculation fix applied to master.
2016-07-26 13:13:52 -04:00
fef63ce6a8
Make sure that multi-alleleic uninformative PLs (0,0,...,0) stay uninformative after biallelization.
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Addresses issue #1439 (thus #1437 ).
Fixes a bug where non informative PLs were not handled appropriatelly when calculating multi-allelic site QUAL values.
This was resulting in long execution times for very large datasets (~200,000 samples in the case of ExAC2).
2016-07-25 17:19:03 -04:00
3daed9e5a1
Added exception for GQB values greater than MAX_GENOTYPE_QUAL and tests.
2016-07-20 16:48:59 -04:00
b4eb479727
Merge pull request #1417 from broadinstitute/rhl_ggvcf_span_del
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Removed spanning deletions if the deletion was removed
2016-07-19 16:55:06 -04:00
7392c4d1b0
Removed spanning deletions if the deletion was removed
2016-07-19 12:23:49 -04:00
b6908f52f0
Merge pull request #1432 from broadinstitute/rhl_invalid_intervals
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Throw an exception for invalid Picard intervals
2016-07-15 13:02:39 -04:00
4f2e312805
Throw an exception for invalid Picard intervals
2016-07-15 11:20:53 -04:00
c406102e03
Merge pull request #1436 from broadinstitute/ldg_fixBetaTestingAnnotationGroup
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Fixed the BetaTesting annotation group
2016-07-13 16:23:19 -04:00
641382eb8b
Fix BetaTestingAnnotation group
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Add test
2016-07-13 16:05:21 -04:00
5255435f0e
Merge pull request #1433 from broadinstitute/rhl_progress_meter_periodicity
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Enable control of reporting periodicity
2016-07-13 10:14:01 -04:00
aace73e884
Enable control of reporting periodicity
2016-07-13 07:24:03 -04:00
5e39b59ef3
Merge pull request #1429 from broadinstitute/ts_readpos_filter
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Port MuTect1 Clustered Read Position filter to MuTect2
2016-07-12 08:30:51 -04:00
d6d0678b50
Build on Laura's code and finish porting MuTect1 clustered read position filter.
2016-07-11 17:33:08 -04:00
77d8da6bb2
Merge pull request #1431 from broadinstitute/sl_issue_1345
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Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel.
2016-07-06 11:46:39 -07:00
9b32cf5291
Fixed merging of GVCF blocks by fixing rounding of GQ values in ReferenceConfidenceModel.
2016-07-06 10:08:08 -04:00
2c94f74a95
Merge pull request #1404 from broadinstitute/ldg_M2_addM1filters
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MuTect 2: port strand artifact filter from MuTect 1
2016-07-05 13:27:35 -04:00
Ron Levine
Steve Huang
David Benjamin
Takuto Sato
Peter Fan
Peter Fan
samuelklee
Samuel Lee
Andrii Nikitiuk
Valentin Ruano Rubio
ldgauthier