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
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
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
f92139dd82
Ooops, UG VA path for rank sum tests aren't happy with empty lists. Disabling clipping rank sum test for now.
2012-07-02 21:12:42 -04:00
7aa3f04402
Updating HC integration tests.
2012-07-02 20:43:52 -04:00
7e7b4cd1b9
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-02 16:37:54 -04:00
b807ff63ef
HaplotypeCaller now creates MNP and complex substitutions by using LD information to decide if events segregate together on haplotypes. Added unit test.
2012-07-02 16:37:39 -04:00
3cea080aa8
Cache SoftStart() and SoftEnd() in the GATKSAMRecord
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these are costly operations when done repeatedly on the same read.
2012-07-02 16:22:00 -04:00
88a02fa2cb
Fixing but for reads with cigars like 9S54H
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When hard-clipping predict when the read is going to be fully hard clipped to the point where only soft/hard-clips are left in the read and preemptively eliminate the read before the SAMRecord mathematics on malformed cigars kills the GATK.
2012-07-02 16:22:00 -04:00
9ee58d323a
Pass the original GATK unsafe parameter to the VcfGatherFunction
2012-07-02 16:03:11 -04:00
1b0a775773
Disabling bcf2 reading from samtools because it's 1 basis; updating select variants integrationtest
2012-07-02 15:55:42 -04:00
cac72bce91
Initial version of int indexed mapping for BQSR. Will be cleaned up in a bit.
2012-07-02 14:33:33 -04:00
602729c09d
Moved parallel tests from SelectVariants to separate SelectVariantsParallelIntegrationTest
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-- Enabled previous tests -- all now working
-- Added modern test against new VCF as well
2012-07-02 11:40:28 -04:00
bcd2e13d8b
Adding duplicate header line keys is a logger.debug not logger.warn message now
2012-07-02 11:39:34 -04:00
01e04992f8
Fixed compatibilities in AbstractVCFCodec that resulted in key=; being parsed as written as key; in VCF output
2012-07-02 11:38:59 -04:00
c94c8a9c09
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-02 08:53:01 -04:00
337e434c01
Test files for LENIENT_VCF_PROCESSING and repairing VCF headers
2012-07-01 15:52:04 -04:00
7aff4446d4
Added unit tests for header repairing capabilities in the GATK engine
2012-07-01 15:38:10 -04:00
480b32e759
BCF2 is now officially zero-based open-interval, and that's how the GATK does it now
2012-07-01 14:59:27 -04:00
b6093ff02c
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-01 10:32:37 -04:00
9b87dcda4f
Fixing remaining integration test errors. Adding missing ex2.bcf
2012-06-30 16:23:11 -04:00
d7d140eb10
Move archived qscripts from private/scala to private/archive/scala
2012-06-30 13:15:57 -04:00
6dc8f7c049
Revert "Moving scala archive files to the actual archive"
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This reverts commit 1ea2cbeda707f3aa72c18221ee97c9b1f3560884.
2012-06-30 13:04:40 -04:00
1ff2384c0c
Revert "Removing extra directory level"
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This reverts commit f83536ecefb7cc2414bbc5e0381c2208ab4eab68.
2012-06-30 13:04:20 -04:00
40c03ab2f5
Removing extra directory level
2012-06-30 12:16:09 -04:00
955bab0802
Moving scala archive files to the actual archive
2012-06-30 11:37:27 -04:00
Eric Banks
Mauricio Carneiro
Mark DePristo
Joel Thibault
Ryan Poplin
David Roazen