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
68b2a0968c
Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3
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This will have to be done again when the 2.0.4 release becomes official,
but it's necessary to do now in order to re-enable the pipeline tests.
2011-11-17 14:46:12 -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
f250b47228
Someone broke this for SNPs when adding support for indels
2011-11-16 10:49:27 -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
231b8e9f74
Do not output deletion only synthetic reads
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If a synthetic read is composed exclusively of deletions, do not output it.
2011-11-15 13:24:43 -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
8e91e19229
Merge branch 'master' of ssh://nickel/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-15 00:13:37 -05:00
cde829899d
compress Reduce Read counts bytes by offset
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compressed the representation of the reduce reads counts by offset results in 17% average compression in final BAM file size.
Example compression -->
from : 10, 10, 11, 11, 12, 12, 12, 11, 10
to: 10, 0, 1, 1,2, 2, 2, 1, 0
2011-11-14 18:30:24 -05:00
a1ce3d8141
Not reporting counts to reduced deletions (temporary patch)
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Deletions will not have counts represented in the reduced form. This may change in the future with a ReadBackedPileup refactor.
2011-11-14 18:30:24 -05:00
4ff8225d78
GenotypeMap -> GenotypeCollection part 3
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-- Test code actually builds
2011-11-14 17:51:41 -05:00
f0234ab67f
GenotypeMap -> GenotypeCollection part 2
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-- Code actually builds
2011-11-14 17:42:55 -05:00
ab0ee9b847
Perform only necessary validation in VariantContext modify methods
2011-11-14 16:49:59 -05:00
2e9d5363e7
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 15:32:06 -05:00
1fbdcb4f43
GenotypeMap -> GenotypeCollection
2011-11-14 15:32:03 -05:00
5c38a9cfd6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 15:00:03 -05:00
f1db31f072
Attempt to reduce memory footprint of ValidationSiteSelector (if this doesn't work then a radical rewrite of the walker to make it two-pass will be necessary): don't log any attributes of original VCF, if we need chr counts later we can reannotate from original inputs. As things stand, we can't select SNP's genomewide due to memory usage.
2011-11-14 14:56:09 -05:00
4dc9dbe890
One quick fix to previous commit
2011-11-14 14:42:12 -05:00
b3313e1445
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-14 14:31:38 -05:00
7b2a7cfbe7
Transfer headers from the resource VCF when possible when using expressions. While there, VA was modified so that it didn't assume that the ID field was present in the VC's info map in preparation for Mark's upcoming changes.
2011-11-14 14:31:27 -05:00
Roger Zurawicki
Mark DePristo
David Roazen
Khalid Shakir
Eric Banks
Mauricio Carneiro
Matt Hanna
Laurent Francioli
Guillermo del Angel