88495a39d4
better formating
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2737 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 15:38:21 +00:00
956b570c8e
V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 18:37:17 +00:00
f6bca7873c
V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-28 04:10:16 +00:00
3399ad9691
Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 17:19:37 +00:00
ed9b7edee3
Changed " to ' to stop the
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[javadoc] /humgen/gsa-scr1/chartl/sting/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java:99: warning: unmappable character for encoding ASCII
[javadoc] * if one of the alleles is deleted (?-?).
warnings on compile.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2703 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 15:23:55 +00:00
c231547204
Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 13:53:29 +00:00
depristo
chartl