c6ad26e04f
1) When quals/GQs are really integers (x.00), strip off the floating points.
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2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 18:01:45 +00:00
f742980864
1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.
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2. Moved Jared's VCFTool code into archive so that everything would compile.
3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader.
4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 06:16:45 +00:00
6b5c88d4d6
The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 04:56:58 +00:00
61e2b2e39b
Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3710 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-02 13:32:33 +00:00
4995950d04
IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 04:40:31 +00:00
6eeb1693ca
JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 00:33:02 +00:00
3ea506fe52
No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3489 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:03:55 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
e365d308d4
add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 16:00:55 +00:00
0e9a6826b0
Update to VCF code to get it up to spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 06:12:42 +00:00
9a6b384adb
Support for no qual fields in VCF; better support for Mendelian violation calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 00:29:17 +00:00
8072e9aed5
should never commit without running intergration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 23:42:37 +00:00
934d4b93a2
VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 19:02:25 +00:00
94f892ad42
VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 01:22:05 +00:00
3b1ab86d11
Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-06 16:26:06 +00:00
1494dc875f
fixing up tests. Moves are complete
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2789 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 14:24:00 +00:00
c6d86da4b8
almost managed to move things around perfectly in move go
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 14:18:26 +00:00
ebanks
depristo
hanna
aaron