99ff5fb75b
Merge pull request #797 from broadinstitute/vrr_ploidy_limitation_removal
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MERGE AFTER TEST PASS: Fixes explicit limitation of the maximum ploidy of the reference-confide...
2015-01-07 12:38:19 -05:00
aae04b6122
Fixes explicit limitation of the maximum ploidy of the reference-confidence model
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Story:
=====
- https://www.pivotaltracker.com/story/show/83803796
Changes:
=======
- From a fix maximum ploidy indel RCM likelihood cache to a
dynamically resizable one.
- Used the occassion to removed an unused and deprecated method from ReferenceConfidenceModel
Testing:
=======
- Added integration test to check on ploidies larger than the previous limit of 20.
2015-01-07 10:43:22 -05:00
7d58544f17
Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml
2015-01-06 10:32:11 -05:00
ef32c44688
Merge pull request #795 from broadinstitute/ldg_VQSRcmdlineOutput
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VQSR VCF header command line now contains annotations and tranche levels
2015-01-05 14:59:04 -05:00
1d5996dd1d
Merge pull request #796 from broadinstitute/rp_update_bundle_Axiom_poly
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Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resou...
2015-01-05 14:53:45 -05:00
10b23bfb04
Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices
2015-01-05 14:52:31 -05:00
26c46ae05e
Change logger.info to logger.error
2015-01-05 14:14:02 -05:00
b4fda38922
Use logging system instead of stderr
2015-01-05 14:04:10 -05:00
e28ee24fc6
Update private single sample pipeline script
2015-01-05 12:11:21 -05:00
88b6f3aa50
Change []-type arrays to lists so argument parsing works in VCF header commandline output
2015-01-05 10:21:06 -05:00
3240b3538a
Merge pull request #794 from broadinstitute/rhl_read_backed_phasing
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Rhl read backed phasing
2015-01-05 09:47:25 -05:00
6f566a0e66
Merge pull request #793 from broadinstitute/mf_xhmm_add_genotyping
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Add option to genotype additional user-defined interval lists
2015-01-05 09:46:06 -05:00
ac10b9c3cd
Merge pull request #791 from broadinstitute/ldg_fixCGPbug
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Add error handling for genotypes that are called but have no PLs
2015-01-05 09:40:38 -05:00
c6840124fe
clean up, add final
2015-01-04 23:01:24 -05:00
85dc703461
Add TestMergeIntoMNP() and TestReallyMergeIntoMNP()
2015-01-01 09:51:20 -05:00
bb94833750
Add more tests
2014-12-30 22:45:44 -05:00
714d575e3b
correct reference file name
2014-12-25 14:00:39 -05:00
a7fba5c209
restructure and add more tests
2014-12-25 13:57:54 -05:00
64375f6341
Messages that were going to stdout now going to stderr
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Make PairHMM outputs go to stderr instead of stdout
Change output from stdout to stderr in close()
Updated lib with output going to stderr
2014-12-23 11:03:29 -05:00
11cd0080c3
Add option to genotype additional user-defined interval lists
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Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists
Add Qscript 'ONLY_GENOTYPE_xhmmCNVpipeline' to genotype additional user-defined interval lists (and similar option to Qscript 'xhmmCNVpipeline')
2014-12-21 13:02:17 -05:00
069398ad46
Added more tests and documentation
2014-12-19 12:57:43 -05:00
a9694951d2
Add error handling for genotypes that are called but have no PLs
2014-12-18 15:03:20 -05:00
a4a9e73ec8
Merge pull request #789 from broadinstitute/gg_update_vqsr_example
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Updated VQSR tool docs
2014-12-18 13:32:15 -05:00
b0e615251b
Updated VQSR tool docs
2014-12-18 12:59:37 -05:00
4a2ac38308
Merge pull request #790 from broadinstitute/rp_nsubtil_fix-snp-detection
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BQSR bug fix from @nsubtil
2014-12-18 09:19:53 -05:00
071389b507
Merge pull request #785 from broadinstitute/rhl_variant_multiallelic_annotations
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Rhl variant multiallelic annotations
2014-12-18 09:11:42 -05:00
08790e1dab
Fix mmultiallelic info field annotation for VariantAnnotator
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Add multi-allele test for info field annotations
Fix to process all types of INFO annotations
roll back to previous version, removes INFO and FORMAT
Correct @return for VariantAnnotatorEngine.getNonReferenceAlleles()
Enhance comments and clean up multi-allelic logic, handle header info number = R
only parse counts of A & R
Add INFO for AC
update MD5
Performance enhancement, only parse multiallelic with a count A or R
Make argument final in getNonReferenceAlleles()
Code cleanup, add exceptions for bad expression/allele size mismatch and missing header info for an expression
Change exception to warning for expression value/number of alleles check
remove adevertised exceptions
2014-12-17 22:21:00 -05:00
ba949389c5
matchHaplotypeAlleles() no longer calls alleleSegregationIsKnown(), added a TODO to investigate
2014-12-17 14:02:24 -05:00
d84970ff75
BQSR bug fix from @nsubtil
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-- Ignore SNP matches that lie outside the clipped read window
-- This fixes an issue where GATK would skip the entire read if a SNP is entirely
contained within a sequencing adapter.
2014-12-17 10:04:37 -05:00
56f8e4f9cf
Add comments, alleleSegregationIsKnown() check is added to matchHaplotypeAlleles()
2014-12-17 03:25:26 -05:00
3deaa4832c
Merge pull request #788 from broadinstitute/ldg_fixCombineGVCFsBug
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Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first ...
2014-12-16 15:17:33 -05:00
011843c569
Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first contig)
2014-12-16 12:43:32 -05:00
bcc6b73e9b
Merge pull request #786 from broadinstitute/pd_variantstotable_sma
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Fix VariantsToTable output of FORMAT record lists when -SMA is specified
2014-12-16 10:37:22 -05:00
3d32babc29
Merge pull request #787 from broadinstitute/vrr_wrong_reference_base_bugfix
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Fixing CombineGVCFs that writes out the wrong REF allele
2014-12-16 10:35:47 -05:00
736a857e82
Fixing CombineGVCFs that writes out the wrong REF allele
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Story:
=====
- https://www.pivotaltracker.com/story/show/83259038
Changes:
=======
- Done minimal changes to make the fix after an arduous attempt to understand
CombineGVCFs code.
Test:
====
- Added a integration test to explicitly test for the bug.
- Updated a md5 changes as the bug was actually affecting one of the existing
integration tests.
2014-12-13 22:38:24 -05:00
71bdfbe465
Fix VariantsToTable output of FORMAT record lists when -SMA is specified
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* PT 84242218
* Note that FORMAT fields behave the same as INFO fields - if the annotation has a count of A (one entry per Alt Allele), it is split across the multiple output lines. Otherwise, the entire list is output with each field
2014-12-10 21:41:15 -05:00
b561febbfd
Merge pull request #784 from broadinstitute/gg_update_gsalib_version
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Updated gsalib version to 2.1 for resubmitting with updated license to C...
2014-12-10 13:23:47 -05:00
45eddb4ecb
Updated gsalib version to 2.1 for resubmitting with updated license to CRAN
2014-12-09 17:07:48 -05:00
bf2911d62c
Merge pull request #783 from broadinstitute/pd_splitsamfile
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Fix NPE in SplitSamFile
2014-12-08 09:39:03 -05:00
5f2a2642d6
Merge pull request #782 from broadinstitute/vrr_gvcf_gq_inconsistency_fix
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Makes GQ of Hom-Ref Blocks in GVCF output to be consistent with PLs
2014-12-08 09:36:23 -05:00
385186e11b
Makes GQ of Hom-Ref Blocks in GVCF output to be consistent with PLs
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Story:
-----
- https://www.pivotaltracker.com/story/show/83800586
Changes:
-------
- In GVCFWriter GQ is now recalculated out of the fianl PL array for the block.
Testing:
-------
- Updated affected integration test md5s
2014-12-07 16:45:32 -05:00
a5dee8a42e
Fix NPE in SplitSamFile
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* PT 82892316
* Added integration test
* Fixed similar error in debug output of HC
2014-12-07 10:37:30 -05:00
c9175eeee8
Renamed PhasingUtilitiesUnitTest to PhasingUtilsUnitTest
2014-12-02 18:20:12 -05:00
bbe78bd181
Merge pull request #779 from broadinstitute/rhl_output_pairhmm
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Rhl output pairhmm
2014-12-02 14:30:55 -05:00
4e8297360d
Merge pull request #780 from broadinstitute/aw_gatkdoclet_fixes
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Aw gatkdoclet fixes
2014-12-02 10:57:57 -05:00
b8f0f3fdd2
Add argument for loading the vector HMM library once
2014-12-02 10:13:56 -05:00
4fe6ccec98
Add -output-file-extension option to GATKDoclet to produce html instead of php.
2014-12-01 18:06:36 -05:00
62e5d42380
Fix code to filter current directory from paths pass to Reflection library.
2014-12-01 17:45:46 -05:00
2fa8fe2415
Merge pull request #777 from broadinstitute/rhl_specify_pairhmm
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Rhl specify pairhmm
2014-11-26 11:34:51 -05:00
386aeda022
Add HaplotypeCaller argument so integration tests can specify the hardware dependent PairHMM sub-implementation
2014-11-25 21:53:53 -05:00
rpoplin
Valentin Ruano-Rubio
Ron Levine
Laura Gauthier
Menachem Fromer
Geraldine Van der Auwera
Phillip Dexheimer
Ron Levine
Alec Wysoker
droazen