dbb69a1e10
Need to use ints for quals in HaplotypeScore instead of bytes because of overflow (they are summed when haplotypes are combined)
2013-01-16 22:33:16 -05:00
4cf34ee9da
Bug fix to FisherStrand: do not let it output INFINITY. This all needs to be unit tested, but that's coming on the horizon.
2013-01-16 15:35:04 -05:00
2a42b47e4a
Massive expansion of ActiveRegionTraversal unit tests, resulting in several bugfixes to ART
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-- UnitTests now include combinational tiling of reads within and spanning shard boundaries
-- ART now properly handles shard transitions, and does so efficiently without requiring hash sets or other collections of reads
-- Updating HC and CountReadsInActiveRegions integration tests
2013-01-16 15:30:00 -05:00
e47a389b26
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-16 14:59:11 -05:00
d18dbcbac1
Added tests for changing IUPAC bases to Ns, for failing on bad ref bases, and for the HaplotypeCaller not failing when running over a region with an IUPAC base.
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Out of curiosity, why does Picard's IndexedFastaSequenceFile allow one to query for start position 0? When doing so, that base is a line feed (-1 offset to the first base in the contig) which is an illegal base (and which caused me no end of trouble)...
2013-01-16 14:55:33 -05:00
4ffb43079f
Re-committing the following changes from Dec 18:
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Refactored interval specific arguments out of GATKArgumentCollection into InvtervalArgumentCollection such that it can be used in other CommandLinePrograms.
Updated SelectHeaders to print out full interval arguments.
Added RemoteFile.createUrl(Date expiration) to enable creation of presigned URLs for download over http: or file:.
2013-01-16 12:43:15 -05:00
445735a4a5
There was no reason to be sharing the Haplotype infrastructure between the HaplotypeCaller and the HaplotypeScore annotation since they were really looking for different things.
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Separated them out, adding efficiencies for the HaplotypeScore version.
2013-01-16 11:10:13 -05:00
392b5cbcdf
The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases.
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This way walkers won't see anything except the standard bases plus Ns in the reference.
Added option to turn off this feature (to maintain backwards compatibility).
As part of this commit I cleaned up the BaseUtils code by adding a Base enum and removing all of the static indexes for
each of the bases. This uncovered a bug in the way the DepthOfCoverage walker counts deletions (it was counting Ns instead!) that isn't covered by tests. Fortunately that walker is being deprecated soon...
2013-01-16 10:22:43 -05:00
4fb3e48099
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-16 00:13:38 -05:00
0d282a7750
Bam writing from HaplotypeCaller seems to be working on all my test cases. Note that it's a hidden debugging option for now.
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Please let me know if you notice any bad behavior with it.
2013-01-16 00:12:02 -05:00
d3baa4b8ca
Have Haplotype extend the Allele class.
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This way, we don't need to create a new Allele for every read/Haplotype pair to be placed in the PerReadAlleleLikelihoodMap (very inefficient). Also, now we can easily get the Haplotype associated with the best allele for a given read.
2013-01-15 11:36:20 -05:00
3c37ea014b
Retire original TraverseActiveRegion, leaving only the new optimized version
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-- Required some updates to MD5s, which was unexpected, and will be sorted out later with more detailed unit tests
2013-01-15 10:24:45 -05:00
94800771e3
1. Initial implementation of bam writing for the HaplotypeCaller with -bam argument; currently only assembled haplotypes are emitted.
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2. Framework is set up in the VariantAnnotator for the HaplotypeCaller to be able to call in to annotate dbSNP plus comp RODs. Until the HC uses meta data though, this won't work.
2013-01-15 10:19:18 -05:00
682c59ff04
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-14 13:27:34 -05:00
61bc334df1
Ensure output table formatting does not contain NaNs. For (0 eval ref calls)/(0 comp ref calls), set the proportion to 0.00.
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Added integration tests (checked against manual tabulation)
2013-01-14 09:21:30 -05:00
a7fe334a3f
calculating the md5s for the new tests.
2013-01-11 15:43:52 -05:00
65afec2a53
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-11 15:22:52 -05:00
85b529cced
Updating MD5s in HC and UG that changed due to new LIBS
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-- Resolved what was clearly a bug in UG (GGA mode was returning a neighboring, equivalent indel site that wasn't in input list. Not ideal)
-- Trivial read count differences in HC
2013-01-11 15:17:19 -05:00
8b83f4d6c7
Near final cleanup of PileupElement
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-- All functions documented and unit tested
-- New constructor interface
-- Cleanup some uses of old / removed functionality
2013-01-11 15:17:17 -05:00
fb9eb3d4ee
PileupElement and LIBS cleanup
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-- function to create pileup elements in AlignmentStateMachine and LIBS
-- Cleanup pileup element constructors, directing users to LIBS.createPileupFromRead() that really does the right thing
2013-01-11 15:17:17 -05:00
cc1d259cac
Implement get Length and Bases of OfImmediatelyFollowingIndel in PileupElement
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-- Added unit tests for this behavior. Updated users of this code
2013-01-11 15:17:17 -05:00
2c38310868
Create LIBS using new AlignmentStateMachine infrastructure
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-- Optimizations to AlignmentStateMachine
-- Properly count deletions. Added unit test for counting routines
-- AlignmentStateMachine.java is no longer recursive
-- Traversals now use new LIBS, not the old one
2013-01-11 15:17:17 -05:00
b53286cc3c
HaplotypeCaller mode to skip assembly and genotyping for performance testing
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-- Added HCPerformance evaluation Qscript
-- Added some docs about one of the HC integration tests
-- HaplotypeCaller / ART performance evaluation script
2013-01-11 15:17:16 -05:00
e952296c10
Adding HC GGA integration test to cover duplicated input alleles.
2013-01-11 15:01:27 -05:00
7f7f40f851
Adding additional HC GGA integration tests to cover more complicated input alleles.
2013-01-11 14:36:21 -05:00
85baf71b39
Merged bug fix from Stable into Unstable
2013-01-11 11:05:27 -05:00
d78539774f
Another RR bug: off by one error led to ArrayIndexOutOfBoundsException when working with multiple samples and the variant region ended 1 base after the end of the last read for a given sample.
2013-01-11 11:05:09 -05:00
79b93f659c
Merged bug fix from Stable into Unstable
2013-01-11 09:20:13 -05:00
67fafbb625
Forgot an include
2013-01-11 09:19:46 -05:00
6bf0cc32f9
When reducing multiple samples it is possible to try to close a region that for a given sample has no reads. Currently we'd NPE. Fixed.
2013-01-11 09:16:19 -05:00
e7906713d9
Moving some random walkers back to public as requested by Mark. Mauricio will the licenses get updated automatically?
2013-01-11 02:03:43 -05:00
3a51823c2a
Clean up imports
2013-01-10 23:35:01 -05:00
e4b7b1955c
Forgot to add the note about length normalization to the QD docs
2013-01-10 23:34:06 -05:00
ff5ac986d8
Fix docs for QD
2013-01-10 23:31:46 -05:00
2a4ccfe6fd
Updated all JAVA file licenses accordingly
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GSATDG-5
2013-01-10 17:06:41 -05:00
dd177b1714
Removing fully commented out varianteval evaluators
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- Files were completely commmented out, and were screwing up my license script. Dont like them. Removed them.
GSATDG-5
2013-01-10 17:06:12 -05:00
80dec72c53
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-10 14:35:59 -05:00
31a5f88c4f
Expanded unit tests to cover the Concordance Metrics class fairly uniformly.
2013-01-10 14:33:47 -05:00
1a18947abf
Adding new command line argument requested on the forum to control the maximum number of haplotypes that are sent forward for genotyping. In the presence of a large degree of heterozygosity the current algorithm breaks down and so this argument would need to be increased.
2013-01-09 15:54:02 -05:00
487fb2afb4
Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.
2013-01-09 15:30:46 -05:00
6787f86803
Eliminate the import of DiploidGenotype, which switched public/private underneath me but for some reason didn't stop me from compiling...
2013-01-09 13:23:24 -05:00
c1de92b511
Add in some todo items
2013-01-09 13:16:06 -05:00
8d126161e2
Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable
2013-01-09 13:15:04 -05:00
3a0dd4b175
Oops, I broke the build. NOW we shouldn't have any more public->protected dependancies.
2013-01-09 11:12:28 -05:00
a921b06e02
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
2013-01-09 11:06:17 -05:00
4fa439d89e
Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now
2013-01-09 11:06:10 -05:00
396bce1f28
Reverting this change until we can figure out the right thing to do here.
2013-01-09 10:51:30 -05:00
676e79542a
Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.
2013-01-09 10:39:48 -05:00
c87ad8c0ef
Bug fixes related to HC's GGA mode. Tracking just the artificial allele isn't sufficient when there are multiple GGA records that change the reference basis. Also, duplicated records screw up the tracking of merged alleles.
2013-01-09 10:00:46 -05:00
ad7c2a08d4
Normalize by the event type counts, not the total genotype counts: more useful normalization.
2013-01-09 09:12:41 -05:00
Eric Banks
Mark DePristo
Khalid Shakir
Chris Hartl
Ryan Poplin
Mauricio Carneiro