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14389 Commits (bd6d0501876fc6cf2d1b2a22e4f31cbadcd7aa70)

Author SHA1 Message Date
meganshand b54904dd42 Merge pull request #1349 from broadinstitute/ms_RankSum 
Fixes RankSum Small Sample Size Edge Case #1341
 2016-04-22 16:55:39 -04:00
meganshand 509400495b Changes edge case calculation for RankSumTest #1341 2016-04-22 14:41:05 -04:00
David Benjamin 34a1b7d0b0 Merge pull request #1337 from broadinstitute/db_issue_1121 
Fixed bug in which PrintReads left out @PG header record
 2016-04-22 10:47:31 -04:00
David Benjamin f639564599 Fixed bug in which PrintReads left out @PG header record 2016-04-22 08:46:18 -04:00
David Benjamin a43d2a7ed1 Merge pull request #1338 from broadinstitute/db_issue_1291 
Fixed bug in dbSNP binding in VariantAnnotationEngine.  Closes issue #1291.
 2016-04-21 20:21:08 -04:00
David Benjamin cfbf062f29 fixed bug in dbSNP binding in VariantAnnotationEngine 2016-04-21 14:38:31 -04:00
David Benjamin 44691f036b Merge pull request #1333 from broadinstitute/db_issue_1216 
Replace string literals for annotation groups.  Closes #1216
 2016-04-19 21:55:18 -04:00
David Benjamin c040da427d Replace string literals for annotation groups. Closes #1216. 2016-04-19 15:54:44 -04:00
Ron Levine 70b259a3fb Merge pull request #1347 from broadinstitute/rhl_sv_vf_info_nocall 
SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall
 2016-04-19 10:59:53 -04:00
Ron Levine e2828104b1 SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall 2016-04-17 10:24:05 -04:00
Ron Levine 7e0a9e44fe Merge pull request #1344 from broadinstitute/rhl_contam_downsamp_map 
Change HashMap to LinkedHashMap for predictable iteration order
 2016-04-11 08:29:14 -04:00
Ron Levine 0eba8822e2 Change HashMap to LinkedHashMap for predictable iteration 2016-04-10 20:10:38 -04:00
ldgauthier 2baa7a0b9e Merge pull request #1339 from broadinstitute/ldg_documentGenotypingCode 
Add some comments to AFCalculationResult
 2016-04-08 16:02:21 -04:00
Geraldine Van der Auwera b4197f62f2 Merge pull request #1335 from broadinstitute/gvda_templates 
Added issue and pull request templates
 2016-04-04 18:23:04 -04:00
Geraldine Van der Auwera e6c8c378e8 Added issue and pull request templates 2016-04-04 13:27:45 -04:00
Laura Gauthier d573fc4adf Add some comments to AFCalculationResult 
Add note that VC may be null (in this case because there are too many alts)
Add todo for possible inefficient code
 2016-04-04 09:35:54 -04:00
Ron Levine edbb7e7984 Merge pull request #1331 from broadinstitute/rhl_doc_null_ptr 
Add informative exceptions to getSAMFileSamples()
 2016-03-31 15:38:39 -04:00
Ron Levine e4003bc792 Add informative exceptions to getSAMFileSamples() 2016-03-31 13:41:11 -04:00
Geraldine Van der Auwera 68b068d2b3 Merge pull request #1329 from broadinstitute/cn_murmur_hash 
Use older version of murmur hash implementation included in gatk…
 2016-03-31 13:00:43 -04:00
Ron Levine dcefbe3a2a Merge pull request #1323 from broadinstitute/rhl_output_warnings 
Output a summary of WARN messages
 2016-03-29 14:54:27 -04:00
Ron Levine edc1b20132 Output a summary of WARN messages 2016-03-29 11:39:18 -04:00
Chris Norman 017828e4b7 Use the older murmur hash implementation that is included in the gatk jar. 2016-03-29 10:20:44 -04:00
Chris Norman ea615f8918 Merge pull request #1324 from broadinstitute/cn_droppedreads_license 
Fix license in DroppedReadsTracker.
 2016-03-23 08:52:22 -04:00
Chris Norman c81795cf50 Fix license in DroppedReadsTracker. 2016-03-22 13:39:13 -04:00
Chris Norman b7ecd68f30 Merge pull request #1257 from broadinstitute/cn_dropped_reads 
Implementation of dropped reads tracking for HC/Mutect.
 2016-03-22 09:16:15 -04:00
Chris Norman a8ebf21ac3 Implementation of dropped read tracking. 2016-03-21 18:36:29 -04:00
Ron Levine b873467756 Merge pull request #1321 from broadinstitute/rhl_fix_hr_logger_name 
Change logger class to HomopolymerRun
 2016-03-16 11:44:40 -04:00
ldgauthier cfc32b7419 Merge pull request #1320 from broadinstitute/ldg_AS_QD_fix 
To address weird case with all hom-refs, but alt allele is present, s…
 2016-03-16 10:21:38 -04:00
Ron Levine 5c0e97def4 Change logger class to HomopolymerRun 2016-03-16 10:01:21 -04:00
Laura Gauthier 9ffdfeccd5 Add test case for fix 2016-03-15 11:06:48 -04:00
Laura Gauthier 31fc64f82c To address weird case with all hom-refs, but alt allele is present, skip AS_QD for all-ref sites and remove raw annotations whether or not they can be successfully finalized 2016-03-15 09:34:47 -04:00
Ron Levine 4efde50225 Merge pull request #1318 from broadinstitute/rhl_va_hrun_exception 
Set --reference_window_stop if homopolymer is greater than  window size
 2016-03-14 18:22:40 -04:00
Ron Levine 6d7ec7377c Set --reference_window_stop if homopolymer is greater than window size 2016-03-14 18:09:41 -04:00
Geraldine Van der Auwera 2baf7d8c4e Merge pull request #1314 from broadinstitute/yf_output_more_information_and_fix_copywrite_date 
Output more information and fix copyright date
 2016-03-12 22:48:15 -05:00
Yossi Farjoun b471884d97 Added run-time information to log output 
Also updated copyright date
 2016-03-11 16:43:03 -05:00
Geraldine Van der Auwera 71d816d8f5 Merge pull request #1316 from broadinstitute/gvda_clarify_vqsr_input_doc 
Clarify VQSR inputs documentation
 2016-03-11 16:40:30 -05:00
Geraldine Van der Auwera c81d5b898e Clarify VQSR inputs documentation 2016-03-11 16:38:33 -05:00
Geraldine Van der Auwera eeccc95a7a Merge pull request #1317 from broadinstitute/gvda_fix_licenses 
Fixup for licensing update
 2016-03-11 16:32:47 -05:00
Geraldine Van der Auwera 4990ed706a Fixup for licensing update 2016-03-11 16:23:02 -05:00
Takuto Sato 1072afeb57 Merge pull request #1296 from broadinstitute/ts_addM2TomorOnlyTest 
M2 integration test for tumor-only
 2016-03-11 13:20:36 -05:00
Takuto Sato 6308b0f036 Add MuTect2 Tumor-only test. 2016-03-11 09:10:43 -05:00
ldgauthier d0432713e0 Merge pull request #1311 from broadinstitute/ldg_BetaTestAnnotationsGroup 
Add classes from "annotation party" to BetaTesting group
 2016-03-11 08:13:32 -05:00
Geraldine Van der Auwera 16ef36088e Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307 
Update licenses
 2016-03-10 12:37:53 -05:00
Geraldine Van der Auwera 643516b3b2 Merge pull request #1310 from broadinstitute/rhl_doc_sample_gene_summary_header 
Fix sample_gene_summary reports header order
 2016-03-09 09:12:36 -05:00
ldgauthier 99532f40c1 Merge pull request #1312 from broadinstitute/ldg_fixASheaders 
Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so o…
 2016-03-09 08:46:34 -05:00
Laura Gauthier 28cfb06513 Add AS_culprit and AS_VQSLOD to VCF header in ApplyRecalibration so output passes VCF validation 2016-03-09 08:22:58 -05:00
Laura Gauthier d9f9bd1d56 Add classes from "annotation party" to BetaTesting group 2016-03-09 08:17:44 -05:00
Ron Levine 244a217ee7 Fix sample_gene_summary reports header order 2016-03-08 22:21:51 -05:00
ldgauthier dcc6c0f2aa Merge pull request #1306 from broadinstitute/rhl_doc_overlapping_genes 
Output coverage for all overlapping genes in DepthOfCoverage
 2016-03-08 13:28:30 -05:00
ldgauthier aa7a8e17df Merge pull request #1304 from broadinstitute/ldg_fixROCCurveHomRef 
Remove homRef calls in NA12878 from true positive/false positive counts
 2016-03-07 11:50:40 -05:00