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gatk-3.8/java/test/org/broadinstitute/sting/gatk/refdata
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ebanks 4558375575 Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 
VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper.  UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).

This is a fairly all-encompassing check in.  It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout.  All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.

Stage 2 of the process will happen later this week.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-16 02:41:20 +00:00
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ReferenceOrderedDataTest.java added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option 2009-08-11 22:10:20 +00:00
RodGLFTest.java A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 2009-10-02 19:35:35 +00:00
RodVCFTest.java Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 2009-11-16 02:41:20 +00:00
TabularRODTest.java Changing the carpet under your feet!! New incremental update to th eROD system has arrived. 2009-09-21 16:55:22 +00:00
rodDbSNPTest.java intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles. 2009-10-23 06:31:15 +00:00