158477ea6c
Re-ran the updateAllLicenses.sh script
2015-08-21 11:32:51 -04:00
3f5a5c0a11
Merge pull request #1140 from broadinstitute/bh_ROC_NA12878
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Logit transform to MQ + jitter MQ capped improves VQSR
2015-08-20 18:01:46 -04:00
f61529d254
Logit transform to MQ + jitter MQ capped improves VQSR
2015-08-20 17:53:01 -04:00
900fe3f675
Merge pull request #1132 from broadinstitute/rhl_rev_htsjdk
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Move htsjdk & picard to rev 1.138
2015-08-20 11:58:41 -04:00
c10fcae25d
Merge pull request #1109 from broadinstitute/bh_ROC_NA12878
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Logistic transform of MQ + jitter to capped MQ in VariantDataManager
2015-08-20 11:18:10 -04:00
eae4c875a9
Logistic transform of MQ + jitter to capped MQ in VariantDataManager
2015-08-20 11:10:45 -04:00
beec624a63
Move htsjdk & picard to rev 1.138
2015-08-20 10:42:25 -04:00
cd9db60ce2
Merge pull request #1134 from broadinstitute/gvda_cgp_docfix_1131
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Fixed missing code tag
2015-08-14 14:59:13 -04:00
5a875cb841
Fixed missing code tag
2015-08-14 14:58:28 -04:00
e89c510ac5
Merge pull request #1115 from broadinstitute/ms_wgsmetrics_wrapper
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CollectWgsMetrics wrapper for queue
2015-08-14 10:25:31 -04:00
5c9935ba10
Adding CollectWgsMetrics wrapper for queue
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Fix license
Fixed IncludeBQHistogram
2015-08-14 10:18:12 -04:00
69fd4af15a
Merge pull request #1111 from jsilter/overclippedreadfilter_endsoption
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Add additional option to OverclippedReadFilter
2015-08-12 10:43:52 -04:00
62625b4bc6
Add option to not require soft-clips on both ends
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Previous version of OverclippedReadFilter would only filter a read if both ends of a read had a soft-clipped block.
This adds a boolean option to relax that requirement, and only require 1 soft-clipped block, while also filtering on read length - softclipped length
2015-08-12 10:38:27 -04:00
d77611292f
Merge pull request #1113 from broadinstitute/ks_cram_with_index
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Switched to using CRAM's SamReader.Indexing implementation.
2015-08-11 21:47:10 -03:00
9bee183f6c
Switched to using CRAM's SamReader.Indexing implementation.
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CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
2015-08-11 17:52:49 -03:00
822d6e9b5b
Merge pull request #1123 from broadinstitute/gvda_updatelicenses_1118
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Updated licenses for 2015
2015-08-10 18:46:47 -04:00
19bbe45cbc
Updated licenses for 2015
2015-08-06 15:23:11 -04:00
9554e06952
Merge pull request #1119 from broadinstitute/db_diff_objects
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Moved DiffObjects from test to main (issue #1116 )
2015-08-06 14:43:39 -04:00
ddb01058d3
moved DiffObjects
2015-08-05 21:19:02 -04:00
893c09b6e0
Merge pull request #1107 from broadinstitute/db_issue_1052
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UnifiedGenotypingEngine queries VariantContext for model if not given
2015-08-05 21:16:29 -04:00
5fcc3788bd
UnifiedGenotypingEngine queries VariantContext for model if not given
2015-08-05 15:30:37 -04:00
c34d8174fc
Merge pull request #1114 from broadinstitute/eb_fix_IR_secondary_mates
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Patch for the incorrect "fixing" of mates when supplementary alignments are present
2015-08-05 14:13:24 -04:00
df033f674d
Patch for the incorrect "fixing" of mates when supplementary alignments are present.
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Note that this patch involves ignoring supplementary alignments. Ideally we would want
to fix their mates properly but that would require a major refactoring of this soon-to-be
deprecated tool.
2015-08-05 12:55:39 -04:00
f73871c865
Merge pull request #1098 from broadinstitute/vrr_rcm_is_active_calculateGenotypes
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Faster implementation of the active state profile value calculation w…
2015-07-30 10:57:33 -04:00
604fb7aaf8
Faster implementation of the active state profile value calculation when running HC with a single sample.
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Find out about a dev-bug and added TODOs (reported in #1096 ).
Addresses issue #1095 .
Conflicts:
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
2015-07-30 10:56:05 -04:00
9819624801
Merge pull request #1105 from broadinstitute/gvda_typo_fixes_1087_1042
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Fixed typos and made some argument docs improvements
2015-07-29 23:37:00 -04:00
875c7ffa1a
Fixed typos and made some argument docs improvements
2015-07-29 23:06:19 -04:00
bb4c9fa1d3
Merge pull request #1099 from broadinstitute/vrr_magic_numbers
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Extracted some constant expressions involved HC variation discovery a…
2015-07-29 13:38:23 -04:00
02c7876c72
Extracted some constant expressions involved HC variation discovery and genotyping.
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Addreses issue #1092 .
2015-07-29 11:58:13 -04:00
ac86b22662
Merge pull request #1101 from broadinstitute/ms_remove_KBest_unique
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Removes unique(int maxSize) from KBestHaplotypeFinder
2015-07-28 17:27:48 -04:00
4d4de27ba3
Removes unique(int maxSize) from KBestHaplotypeFinder
2015-07-28 15:54:21 -04:00
9d9827f176
Merge pull request #1031 from broadinstitute/lb_update_for_java8
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Updated gatk so it compiles with java 8
2015-07-28 11:09:19 -04:00
3a3ff558c4
Merge pull request #1085 from broadinstitute/vrr_path_builder
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ReferenceConfidenceModel likelihood calculation in non…
2015-07-28 10:48:03 -04:00
43a37fc746
Merge pull request #1075 from broadinstitute/ldg_bamoutDocs
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Add info about multiple input samples (as relevant for M2)
2015-07-27 16:56:36 -04:00
5939b4c100
Merge pull request #1073 from broadinstitute/ldg_SV-MVtestNameFix
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Fix logging name on SelectVariantsIntegrationTest::testInvertMendelia…
2015-07-27 16:54:59 -04:00
8f6daf70db
Refactoring of ReferenceConfidenceModel likelihood calculation in non variant sites
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Changed a division by -10.0 to a multiplication by -.1 in QualUtils (typically multiplication is faster than division).
Addresses performance issue #1081 .
2015-07-26 08:33:46 -04:00
d4423d8303
Merge pull request #1079 from broadinstitute/vrr_path_builder
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PathBuilder for linear time creation of Graph paths (quadratic currently).
2015-07-24 09:36:06 -04:00
047aea9707
Address performance issue #1077
2015-07-23 13:44:10 -04:00
c98be3dbd6
Merge pull request #1076 from broadinstitute/dr_move_swapext_to_utils
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Move swapExt() methods to QScriptUtils, have versions in QScript class call into the util versions
2015-07-23 12:07:45 -04:00
5fd3d2be76
Move swapExt() methods to QScriptUtils, have versions in QScript class call into the util versions
2015-07-23 10:23:55 -04:00
4fefedfb0b
Fix logging name on SelectVariantsIntegrationTest::testInvertMendelianViolationSelection()
2015-07-23 09:48:15 -04:00
85b340caed
Add info about multiple input samples (as relevant for M2)
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Also generalize references to the tool/caller since this code is now shared by HC and M2
2015-07-23 09:46:10 -04:00
66cf22b28f
Merge pull request #1069 from broadinstitute/vrr_ad_genotype_gvcfs_bugfix
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Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
2015-07-22 18:53:43 -04:00
315e193e51
Fix AD propagation when subsetting alleles in non-diploid GenotypeGVCF.
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Addresses issue #913 .
Also remove some commented out code and toxic debugging code that uses System.out/err.println.
2015-07-22 17:08:13 -04:00
75081bee2b
Merge pull request #1068 from broadinstitute/gvda_remove_beagle_walkers_971
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Removed walkers for handling Beagle data
2015-07-22 15:47:19 -04:00
d89067c791
Merge pull request #1066 from broadinstitute/gvda_fix_TR_license_1065
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Updated license text and fixed a couple of typos in doc block
2015-07-22 12:28:05 -04:00
3bd988825f
Removed walkers for handling Beagle data
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Added deprecation statements to DeprecatedToolChecks.java
Removed integration test for Beagle walker
Added URL for Beagle documentation
2015-07-21 18:36:08 -04:00
ca082bfb76
Updated license text and fixed a couple of typos in doc block
2015-07-21 17:55:48 -04:00
178bf12b27
Merge pull request #1046 from broadinstitute/rhl_catvariants_sort
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Fix for mis-sorted VCF files in CatVariants
2015-07-21 17:37:27 -04:00
9360e1d293
Merge pull request #1059 from broadinstitute/vrr_true_false_list_removal
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More efficient implementation of the indel read qualities recalculati…
2015-07-21 17:13:45 -04:00
Bertrand Haas
Ron Levine
Geraldine Van der Auwera
meganshand
Yossi Farjoun
Jacob Silterra
kshakir
Khalid Shakir
David Benjamin
Eric Banks
Valentin Ruano Rubio
vruano
Louis Bergelson
Lee Lichtenstein
David Roazen
Laura Gauthier
Joseph White