9c1ab1b0c0
Move BQSR integration test and its dependent files into public; previously there was a protected->private dependency.
2012-07-18 21:11:33 -04:00
994c5c31c1
Enabling VariantEval integration tests for ValidationReport
2012-07-18 16:07:47 -04:00
74e153ff4a
FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing
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-- Previously used hardcoded MAPQ > 20 && QUAL > 20 but now uses isUsableBase
-- Updating MD5s as appropriate
2012-07-18 16:07:47 -04:00
dede3a30e9
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
2012-07-18 16:07:47 -04:00
559a4826be
Improvements to the validation report of VariantEval
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-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
2012-07-18 16:07:46 -04:00
dc292c0317
FisherStrand now includes all reads and bases, regardless of mapping quality and base quality, just like other annotations
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-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.
2012-07-18 16:07:46 -04:00
2c0f073ab1
Make -qq arg hidden for now since it's still very experimental
2012-07-18 15:43:25 -04:00
b46c85e8b4
More bad BAM file catching
2012-07-18 15:26:31 -04:00
659eee13a6
Handle NPE generated in UG when non-standard reference bases are present in the fasta
2012-07-18 15:16:27 -04:00
9af2cfe283
Catch underlying file system problems that get masked as Tribble index errors. There's also a quick patch to the HMS that isn't really the ultimate fix needed; Mark and I will review at a later point.
2012-07-18 15:11:38 -04:00
4c730542f0
Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.
2012-07-18 13:56:35 -04:00
ae08d35138
Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).
2012-07-18 12:57:34 -04:00
f2fe59a9d4
Wow, there are a ton of errors captured having to do with being unable to merge the temp Tribble output. I'm expanding the error message a bit to help see if we can do anything going forward.
2012-07-18 12:31:59 -04:00
e4db8dde91
Enabled a whole other bunch of integration tests for BQSRv2. While I was there I also changed the default context size for indels to 3 (from 8) since that's what works best in the current implementation (as suggested by Ryan). At this point, all of the new core tools (ReduceReads, BQSRv2, HaplotypeCaller, UG extensions) have been moved over to protected and should be stable. Looks like we are pretty much ready for GATK 2.0!
2012-07-17 23:36:43 -04:00
a8d08ea18d
As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.
2012-07-17 22:18:43 -04:00
29273abab7
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 16:58:12 -04:00
731bbba2e6
Bug fixes for integration test, use correct new UG syntax
2012-07-17 16:57:59 -04:00
33be41ecf5
Cleaning up integration test
2012-07-17 16:06:04 -04:00
8dbc9cb29c
Add the ability to emit the original quals in the OQ tag
2012-07-17 15:52:56 -04:00
40b8c7172c
Pool Caller refactoring in preparation of GATK 2.0: a) PoolCallerUnifiedArgumentCollection disappeared, and arguments moved to UnifiedArgumentCollection. b) PoolCallerWalker is no longer needed and redundant, all functionality subsumed by UG. UG now checks if GATK is lite - if so, don't allow ploidy > 2. c) Moved pool classes from private to protected. d) Changed the way to specify ploidy. Instead of specifying samples per pool and having ploidy = 2*samplesPerPool, have user specify ploidy directly, which is cleaner. Update tests accordingly. We can now call triploid seedless grape genotypes correctly in theory. e) Renamed argument -reference to -reference_sample_calls since the former is ambiguous and it's not clear what it refers to.
2012-07-17 15:27:04 -04:00
68d0e4dd6d
- Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE
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-Updated integrationtests to reflect changes in MVF file output
Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
2012-07-17 15:21:10 -04:00
b0d99fd10d
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 15:12:28 -04:00
305db8c0d1
Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us.
2012-07-17 15:11:03 -04:00
6efbcd99f1
HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.
2012-07-17 14:38:36 -04:00
110886e8b9
Oops, got the logic wrong.
2012-07-17 13:37:11 -04:00
a963b37424
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-17 13:15:37 -04:00
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
1913d1bbd0
Put RunReport S3 upload on timeout thread
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Move the RunReport S3 upload process onto a separate thread with a timeout allowing the parent to continue.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
2012-07-17 12:19:39 -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
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
443f02ffc2
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-07-13 16:09:24 -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
d70bb59182
HaplotypeCaller now calls insertion events that aren't fully assembled as symbolic alleles.
2012-07-10 14:22:23 -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
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
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
Eric Banks
Mark DePristo
Guillermo del Angel
Laurent Francioli
Ryan Poplin
Chris Saunders
Khalid Shakir
Mauricio Carneiro