cfd3ffa2c0
Replace SAMFileReader with calls to SamReaderFactory
2016-10-14 11:22:54 -04:00
2ee0755c35
Merge pull request #1492 from broadinstitute/vrr_newqual_nan_fix
...
Fixes NaN issue in new Qual calculator
2016-10-11 23:31:19 -04:00
a72be69062
Merge pull request #1488 from broadinstitute/rhl_dup_col_rld
...
Add read group identifier to column names
2016-10-11 18:40:40 -04:00
a301ba1977
Add read group identifier to column names
...
If two SAMReadGroupRecords share the same sample name, the output will contain duplicate column headers.
This PR fix the problem.
2016-10-11 18:37:11 -04:00
16417bbf34
Fixes NaN issue in new Qual calculator
...
Fixes issue #1491
2016-10-11 16:03:06 -04:00
967b4f4ae8
Merge pull request #1487 from broadinstitute/rhl_deprecate_strand_emit_conf
...
Resurrect and deprecate -stand_emit_conf
2016-10-09 12:56:50 -04:00
81a9ece45b
deprecate -stand_emit_conf
2016-10-09 10:24:09 -04:00
7b3af3820e
Merge pull request #1483 from broadinstitute/rhl_fix_unit_tests
...
Remove sra group
2016-09-26 08:20:24 -04:00
2c83081560
Remove sra group
2016-09-23 17:39:10 -04:00
6bfdaa37c3
Merge pull request #1480 from broadinstitute/rhl_farm_wrong_ambig_code_star_allele
...
Assign correct ambiguity code for * allele
2016-09-22 13:03:04 -04:00
4ef396f72e
Assign correct ambiguity code for * allele
2016-09-22 11:02:44 -04:00
3b90b9c7de
Merge pull request #1481 from broadinstitute/db_backport_qual
...
Backport of AlleleFrequencyCalculator aka the new QUAL
2016-09-21 19:54:23 -04:00
318bee2269
Backport new AFCalculator
2016-09-21 15:21:56 -04:00
7b74dc1634
Merge pull request #1478 from broadinstitute/rhl_htsjdk_2.6.1_picard_2.6.0
...
Move htsjdk to ver 2.6.1 and picard to ver 2.6.0
2016-09-19 13:17:34 -04:00
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
...
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 )
...
* 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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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.
...
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
Ron Levine
Valentin Ruano Rubio
Pierre Lindenbaum
David Benjamin
Steve Huang
Takuto Sato
Peter Fan
Peter Fan
samuelklee
Samuel Lee
Andrii Nikitiuk