- Fixed and cleaned code to produce trailing and padding bases in alleles around indels.
- Deal better with missing fields.
Pending:
- Chopping missing fields at end of genotypes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3679 348d0f76-0448-11de-a6fe-93d51630548a
Also, moved the flag indicating VCF4.0 to the VCFWriter constructor.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a
See VCF4WriterTestWalker for usage example: it just amounts to adding
vcfWriter.add(vc,ref.getBases()) in walker.
add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete.
addRecord is still supported so all backward compatibility is maintained.
Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically:
a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1").
b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles.
Both issues should be corrected with better header parsing.
2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a
depristo
delangel
aaron