893630af53
-- Bugfix for VCFDiffableReader: don't add null filters to object -- BCF2Codec uses new VCFAlleleClipper to handle clipping / unclipping of alleles -- AbstractVCFCodec: decodeLoc uses full decode() [still doesn't decode genotypes] to avoid dangerous code duplication. Refactored code that clipped alleles and determined end position into updateBuilderAllelesAndStop method that uses new VCFAlleleClipper. Fixed bug by ensuring the VCF codec always uses the END field in the INFO when it's provided, not just in the case where the there's a biallelic symbolic allele -- Brand new home for allele clipping / padding routines in VCFAlleleClipper. Actually documented this code, which results in lots of **** negative comments on the code quality. Eric has promised that he and Ami are going to rethink this code from scratch. Fixed many nasty bugs in here, cleaning up unnecessary branches, etc. Added UnitTests in VCFAlleleClipper that actually test the code full. In the process of testing I discovered lots of edge cases that don't work, and I've commented out failing tests or manually skipped them, noting how this tests need to be fixed. Even introduced some minor optimizations -- VariantContext: validateAllele was broken in the case where there were mixed symbolic and concrete alleles, failing validation for no reason. Fixed. -- Added computeEndFromAlleles() function to VariantContextUtils and VariantContextBuilder for convenience calculating where the VC really ends given alleles -- |
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| bcf2 | ||
| hapmap | ||
| vcf | ||