46d41255ba
Merge pull request #1284 from broadinstitute/rhl_htsjdk_picard_2.0.0
...
Move htsjdk and picard to version 2.0.0
2016-04-25 20:29:44 -04:00
f337b45724
Move htsjdk and picard to version 2.0.0
...
Conflicts:
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
2016-04-25 14:51:25 -04:00
4e47db0320
Merge pull request #1350 from broadinstitute/gvda-fix_allelebalance_doc
...
Corrections to AlleleBalance (and AB by sample) docs
2016-04-25 13:13:27 -04:00
662919e5fe
Correction to AlleleBalance doc
...
Addresses https://github.com/broadinstitute/dsde-docs/issues/818
The equations representing the allele balance calculation were confusing and inconsistent with both the description text and the code. This doc change brings consistency and correctness.
Also improves the AB by sample doc accordingly.
2016-04-25 12:10:01 -04:00
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
509400495b
Changes edge case calculation for RankSumTest #1341
2016-04-22 14:41:05 -04:00
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
f639564599
Fixed bug in which PrintReads left out @PG header record
2016-04-22 08:46:18 -04:00
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
cfbf062f29
fixed bug in dbSNP binding in VariantAnnotationEngine
2016-04-21 14:38:31 -04:00
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
c040da427d
Replace string literals for annotation groups. Closes #1216 .
2016-04-19 15:54:44 -04:00
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
e2828104b1
SelectVariants and VariantFiltration not updating AC, AN and AF for --setFilteredGtToNocall
2016-04-17 10:24:05 -04:00
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
0eba8822e2
Change HashMap to LinkedHashMap for predictable iteration
2016-04-10 20:10:38 -04:00
2baa7a0b9e
Merge pull request #1339 from broadinstitute/ldg_documentGenotypingCode
...
Add some comments to AFCalculationResult
2016-04-08 16:02:21 -04:00
b4197f62f2
Merge pull request #1335 from broadinstitute/gvda_templates
...
Added issue and pull request templates
2016-04-04 18:23:04 -04:00
e6c8c378e8
Added issue and pull request templates
2016-04-04 13:27:45 -04:00
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
edbb7e7984
Merge pull request #1331 from broadinstitute/rhl_doc_null_ptr
...
Add informative exceptions to getSAMFileSamples()
2016-03-31 15:38:39 -04:00
e4003bc792
Add informative exceptions to getSAMFileSamples()
2016-03-31 13:41:11 -04:00
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
dcefbe3a2a
Merge pull request #1323 from broadinstitute/rhl_output_warnings
...
Output a summary of WARN messages
2016-03-29 14:54:27 -04:00
edc1b20132
Output a summary of WARN messages
2016-03-29 11:39:18 -04:00
017828e4b7
Use the older murmur hash implementation that is included in the gatk jar.
2016-03-29 10:20:44 -04:00
ea615f8918
Merge pull request #1324 from broadinstitute/cn_droppedreads_license
...
Fix license in DroppedReadsTracker.
2016-03-23 08:52:22 -04:00
c81795cf50
Fix license in DroppedReadsTracker.
2016-03-22 13:39:13 -04:00
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
a8ebf21ac3
Implementation of dropped read tracking.
2016-03-21 18:36:29 -04:00
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
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
5c0e97def4
Change logger class to HomopolymerRun
2016-03-16 10:01:21 -04:00
9ffdfeccd5
Add test case for fix
2016-03-15 11:06:48 -04:00
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
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
6d7ec7377c
Set --reference_window_stop if homopolymer is greater than window size
2016-03-14 18:09:41 -04:00
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
b471884d97
Added run-time information to log output
...
Also updated copyright date
2016-03-11 16:43:03 -05:00
71d816d8f5
Merge pull request #1316 from broadinstitute/gvda_clarify_vqsr_input_doc
...
Clarify VQSR inputs documentation
2016-03-11 16:40:30 -05:00
c81d5b898e
Clarify VQSR inputs documentation
2016-03-11 16:38:33 -05:00
eeccc95a7a
Merge pull request #1317 from broadinstitute/gvda_fix_licenses
...
Fixup for licensing update
2016-03-11 16:32:47 -05:00
4990ed706a
Fixup for licensing update
2016-03-11 16:23:02 -05:00
1072afeb57
Merge pull request #1296 from broadinstitute/ts_addM2TomorOnlyTest
...
M2 integration test for tumor-only
2016-03-11 13:20:36 -05:00
6308b0f036
Add MuTect2 Tumor-only test.
2016-03-11 09:10:43 -05:00
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
16ef36088e
Merge pull request #1308 from broadinstitute/gvda_fix_license_quotes_#1307
...
Update licenses
2016-03-10 12:37:53 -05:00
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
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
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
Ron Levine
David Benjamin
Geraldine Van der Auwera
meganshand
ldgauthier
Chris Norman
Yossi Farjoun
Takuto Sato