73119c8e3c
Merge with master
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-- A few bug fixes
2011-11-19 09:56:06 -05:00
f685fff79b
Killing the final versions of old new VariantContext interface
2011-11-18 21:32:43 -05:00
6cf315e17b
Change interface to getNegLog10PError to getLog10PError
2011-11-18 21:07:30 -05:00
c7f2d5c7c7
Final minor fix to contract
2011-11-18 19:40:05 -05:00
b5de182014
isEmpty now checks if mReadBases is null
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Since newly created reads have mReadBases == null. This is an effort to centralize the place to check for empty GATKSAMRecords.
2011-11-18 18:34:05 -05:00
8ab3ee9c65
Merge remote-tracking branch 'unstable/master' into rr
2011-11-18 16:50:25 -05:00
333e5de812
returning read instead of GATKSAMRecord
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Do not create new GATKSAMRecord when read has been fully clipped, because it is essentially the same as returning the currently fully clipped read.
2011-11-18 16:49:59 -05:00
8bb4d4dca3
First pass of the asynchronous block loader.
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Block loads are only triggered on queue empty at this point. Disabled by
default (enable with nt:io=?).
2011-11-18 15:02:59 -05:00
a2e79fbe8a
Fixes to contracts
2011-11-18 14:18:53 -05:00
660d6009a2
Documentation and contracts for GenotypesContext and VariantContextBuilder
2011-11-18 13:59:30 -05:00
f54afc19b4
VariantContextBuilder
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-- New approach to making VariantContexts modeled on StringBuilder
-- No more modify routines -- use VariantContextBuilder
-- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono
-- getChromosomeCount -> getCalledChrCount
-- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain
-- VCFCodec now uses optimized cached information to create GenotypesContext.
2011-11-18 12:39:10 -05:00
6459784351
Merged bug fix from Stable into Unstable
2011-11-18 12:34:57 -05:00
c62082ba1b
Making this class public again as per request from Cancer folks
2011-11-18 12:34:27 -05:00
8710673a97
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-18 12:29:33 -05:00
768b27322b
I figured out why we were getting tons of hom var genotype calls with Mauricio's low quality (synthetic) reduced reads: the RR implementation in the UG was not capping the base quality by the mapping quality, so all the low quality reads were used to generate GLs. Fixed.
2011-11-18 12:29:15 -05:00
7490dbb6eb
First version of VariantContextBuilder
2011-11-18 11:06:15 -05:00
f48d4cfa79
Bug fix: fully clipping GATKSAMRecords and flushing ops
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Reads that are emptied after clipping become new GATKSAMRecords.
When applying ClippingOps, the ops are cleared after the clipping
2011-11-18 00:24:39 -05:00
fa454c88bb
UnitTests for VariantContext for chrCount, getSampleNames, Order function
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-- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2.
-- Naming changes for getSamplesNameInOrder()
2011-11-17 20:37:22 -05:00
02f22cc9f8
No more VC integration tests. All tests are now unit tests
2011-11-17 15:33:09 -05:00
23359d1c6c
Bugfix for pruneVariantContext, which was dropping the ref base for padding
2011-11-17 15:32:52 -05:00
473b860312
Major determinism fix for UG and RankSumTest
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-- Now these routines all iterate in sample name order (genotypes.iterateInSampleNameOrder) so that the results of UG and the annotator do not depend on the particular order of samples we see for the exact model and the RankSumTest
2011-11-17 15:31:45 -05:00
c50274e02e
During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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Moved flanking interval utilies to IntervalUtils with UnitTests.
2011-11-17 13:56:42 -05:00
bad19779b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-17 13:29:43 -05:00
16a021992b
Updated header description for the INFO and FORMAT DP fields to be more accurate.
2011-11-17 13:17:53 -05:00
e7d41d8d33
Minor cleanup
2011-11-17 12:00:28 -05:00
7e66677769
Expanded UnitTests for VariantContext
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Tests for
-- getGenotype and getGenotypes
-- subContextBySample
-- modify routines
2011-11-16 20:45:15 -05:00
72f00e2883
Merging Roger's Unit tests for Reduce Reads from RR repository
2011-11-16 17:26:49 -05:00
aa0610ea92
GenotypeCollection renamed to GenotypesContext
2011-11-16 16:24:05 -05:00
974daaca4d
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-16 16:08:46 -05:00
caf6080402
Better algorithm for merging genotypes in CombineVariants
2011-11-16 15:17:33 -05:00
101ffc4dfd
Expanded, contrastive VariantContextBenchmark
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-- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4
-- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-16 13:35:16 -05:00
e56d52006a
Continuing bugfixes to get new VC working
2011-11-16 10:39:17 -05:00
eb8e031f75
Merged bug fix from Stable into Unstable
2011-11-16 09:57:37 -05:00
6a5d5e7ac9
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-11-16 09:57:13 -05:00
7ac5cf8430
Getting rid of unsupported CountReadPairs walker in stable. Removal of
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remainder of pairs processing framework to follow in unstable.
2011-11-16 09:53:59 -05:00
c2ebe58712
Merge remote-tracking branch 'Laurent/master'
2011-11-16 09:34:47 -05:00
7d77fc51f5
Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type
2011-11-16 03:32:43 -05:00
0d163e3f52
SnpEff 2.0.4 support
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-Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format
-Assigning functional classes and effect impacts now handled directly
by SnpEff rather than the GATK
-Removed support for SnpEff 2.0.2, as we no longer trust the output of that
version since it doesn't exclude effects associated with certain nonsensical
transcripts. These effects are excluded as of 2.0.4.
-Updated unit and integration tests
This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject
to change between now and the next GATK release.
2011-11-15 18:36:22 -05:00
df415da4ab
More bug fixes on the way to passing all tests
2011-11-15 17:38:12 -05:00
0be23aae4e
Bugfixes on way to a working refactored VariantContext
2011-11-15 17:20:14 -05:00
231c47c039
Bugfixes on way to a working refactored VariantContext
2011-11-15 16:42:50 -05:00
fb685f88ec
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-15 16:23:53 -05:00
2b2514dad2
Moved many unused phasing walkers and utilities to archive
2011-11-15 16:14:50 -05:00
460a51f473
ID field now stored in the VariantContext itself, not the attributes
2011-11-15 14:56:33 -05:00
7fada320a9
The right fix for this test is just to delete it.
2011-11-15 14:53:27 -05:00
b45d10e6f1
The DP in the FORMAT field (per sample) must also use the representative count or else it's always 1 for reduced reads.
2011-11-15 10:23:59 -05:00
233e581828
Merging in Master
2011-11-15 09:28:24 -05:00
b66556f4a0
Update error message so that it's clear ReadPair Walkers are exceptions
2011-11-15 09:22:57 -05:00
6e1a86bc3e
Bug fixes to VariantContext and GenotypeCollection
2011-11-15 09:21:30 -05:00
284430d61d
Added more basic UnitTests for ReadClipper
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hardClipByReadCoordinatesWorks
hardClipLowQualTailsWorks
2011-11-15 00:13:52 -05:00
Mark DePristo
Mauricio Carneiro
Matt Hanna
Eric Banks
Roger Zurawicki
Khalid Shakir
Laurent Francioli
David Roazen