3a64398d07
Cleaned up the isGATKLite check
2012-07-17 12:46:16 -04:00
62c5228048
1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.
2012-07-17 12:23:40 -04:00
40618ac471
A bunch of BQSR changes: 1) by default we do not emit indel quals, but they can be turned on with --enable_indel_quals. 2) We check whether or not we are running in Lite mode (not done yet) and if so and the user is trying to recalibrate indels, we throw a User Error (not supported). 3) Like v1 we now allow the user to set the qual value below which we don't recalibrate (this was the remaining source of differences in the v1 vs. v2 plots).
2012-07-17 10:52:43 -04:00
d5b3a2eabf
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 00:32:53 -04:00
f657b8bda8
Complete overhaul of the BQSRv2 integration tests. Much more comprehensive. Still need to deal with a few tests that need some modifications before I'm done, but I'll take care of that sometime tomorrow.
2012-07-17 00:32:34 -04:00
a003148d50
Move AnalyzeCovariates over too.
2012-07-16 16:11:56 -04:00
0a89adbcdb
Add utility decorators so that classes can tell you which package source they come from if they want to (suggested by Khalid). Using those decorators, we can easily pull out the BQSR updateDataForPileupElement() method into a standard RecalibrationEngine and an AdvancedRecalibrationEngine and use the protected one (AdvancedRE) if available (otherwise, the public one).
2012-07-16 15:34:50 -04:00
52baac1e16
Move BQSRv2 into public and v1 into the archive.
2012-07-16 14:23:38 -04:00
6c6a324583
Loosen a restriction on isOriginalRead()
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* no longer needs to satisfy ReadAndIntervalOverlap.OVERLAP_CONTAINED
2012-07-16 14:07:10 -04:00
07822d6c0f
Fixed input annotations for master/test files on DiffObjectsWalker.
2012-07-16 13:33:11 -04:00
2a830939df
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-14 23:49:59 -04:00
f29cadd7e2
By default, don't quantize quals in BQSRv2
2012-07-14 23:49:48 -04:00
75543a3f22
ReadClipper.clipRead's claim that it doesn't modify the original read was false. Ultimately, GATKSAMRecord.clone (as documented) creates a soft copy of the read - so modifying e.g. the bases of the cloned read means that you modify the bases of the original read too. Because of this, when the BQSRv2 Context covariate was writing Ns over the low quality tails of the reads they got propagated out to the output BAM file (very bad). I've updated the ReadClipper docs and cleaned up the code (no reason to use a clone of the read anymore given that we are already modifying the original). For now, the simplest thing is to have the Context covariate store the original bases, overwrite low quality Ns, compute covariates, and rewrite the original bases; we can update later if needed.
2012-07-13 18:50:27 -04:00
44c532531b
VC priority list needs to be updated after removing unassembled haplotypes.
2012-07-13 16:50:08 -04:00
443f02ffc2
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-13 16:09:24 -04:00
c978e37e5c
updating HC integration tests for all these changes
2012-07-13 16:09:11 -04:00
6dfcc486e8
In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters().
2012-07-13 15:40:56 -04:00
d553905d79
Don't try to genotype both an unassembled symbolic allele and a fully assembled insertion if they both start at the same location. Bug fix for the case of multiple indels that when all combined together make an MNP.
2012-07-13 15:22:22 -04:00
3ab5e2c64b
Don't try to combine together unassembled, symbolic alleles.
2012-07-12 21:20:14 -04:00
d70bb59182
HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.
2012-07-10 14:22:23 -06:00
75e5a50b8a
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-10 12:53:00 -06:00
279dff9f81
Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants
2012-07-10 13:59:00 -04:00
d7bf74fb7e
Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.
2012-07-10 02:04:26 -04:00
7eb45b4038
Fixed BQSR IntegrationTests
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* BinaryTag covariate is Experimental, not Standard (this was breaking integration tests)
* New parameter in the Recalibration report requires new MD5 for one of the integration tests.
2012-07-09 13:55:12 -04:00
6c17c50fa2
Updates to ReduceReads
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* Added optional parameter to not hard clip on the interval border
* Made not clipping the default behavior (hence integration tests changed)
* Updated integration tests.
2012-07-09 13:46:51 -04:00
dd0c47ab7e
Don't cast to a specific walker type since any walker can use the VA engine
2012-07-09 10:25:58 -04:00
5b0ade67c8
Updates to VCF processing for better BCF processing
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-- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order]. Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy
-- Updating GATK code to use the appropriate header function (this is why so many files have changed)
-- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this)
-- Bugfix for adding contig lines to BCF2 header dictionary
-- VCFHeader metaData no longer sorted internally. The system now maintains the data in header order, and only sorts output as requested in API
-- VCFWriter and BCF2Writer now explictly sort their header lines
-- Don't allow filters to be added that are PASS in the contract
2012-07-08 15:44:33 -07:00
63f5262e45
mergeInfoWithMaxAC is no longer hidden in CombineVariants
2012-07-08 15:44:32 -07:00
66aee613e2
Bugfix for set key in mergeInfoWithMaxAC.
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-- Previous version was always setting set=source of info with highest AC. Should actually have been set to the set annotation value itself.
2012-07-08 15:44:32 -07:00
91f0ed8059
Fixed nasty Rscript typo in VariantRecalibrator when compactPDF is available
2012-07-08 15:44:32 -07:00
87b090c362
Update VariantRecalibator error message to use -resource not old -B syntax
2012-07-08 15:44:31 -07:00
08c57db784
Commented out static instantiation of broad-specific capability preventing GATKdocs to build
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-- Joel, you need to fix this
2012-07-08 15:44:31 -07:00
125e6c1a47
added BinaryTagCovariate for ancient dna analysis
2012-07-06 15:03:20 -04:00
e93b025b39
Fixing unit test
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with the new clipping behavior for weird cigars, we no longer can assert the final number of bases in the unit test, so I'm taking this bit off the unit test.
2012-07-06 12:08:09 -04:00
f603d4c48c
Fixing PairHMMIndelErrorModel boundary issue
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When checking the limits of a read to clip, it wasn't considering reads that may already been clipped before.
2012-07-06 11:48:04 -04:00
83e33d14c5
Bug fix in the merging of events into complex substitutions.
2012-07-05 16:00:18 -04:00
c2e1dc63ff
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-05 10:37:40 -04:00
729c5e878d
Bug fix in the merging of events into complex substitutions.
2012-07-05 10:37:04 -04:00
dd571d9aa0
Added a --no_indel_quals argument that when used with -BQSR inhibits the writing of base insertion and base deletion quality tags.
2012-07-04 01:22:20 -04:00
33306d2e20
Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.
2012-07-04 00:21:21 -04:00
7d30558e6f
Only 'pad' the cycle covariate for indels, not substitutions
2012-07-03 23:47:01 -04:00
17efbbf8b1
Fixed ReadClipperUnitTest
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The behavior of the clipping on weird cigar strings such as 1I1S1H and 9S56H has changed, and the test has to change accordingly.
2012-07-03 16:38:51 -04:00
f09141bd2f
Add a Mongo tester which outputs BCFs
2012-07-03 15:15:33 -04:00
22f1afddaa
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-03 14:55:59 -04:00
617eebd204
More misc cleanup
2012-07-03 14:55:37 -04:00
344c3aeb1d
Cleanup from previous commit
2012-07-03 14:42:44 -04:00
9e8e78de15
Adding the model name to the VQSR filter lines so that they don't get clobbered with consecutive VQSR runs for SNPs and then indels.
2012-07-03 14:30:37 -04:00
0b37d44b0d
Optimizations for the RecalDatum to make BQSR (Count Covariates) much faster. Needs some cleanup.
2012-07-03 13:05:11 -04:00
031322ff00
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-03 00:12:59 -04:00
a4670113bd
Refactored/renamed the nested integer array; cleaned up code a bit.
2012-07-03 00:12:33 -04:00
Eric Banks
Joel Thibault
Khalid Shakir
Ryan Poplin
Guillermo del Angel
Mauricio Carneiro
Mark DePristo