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Bugfix for BCF2 reader / writer for > 0x0FFF samples :-) 

-- Should be 0x00FFFFFF in the mask
This commit is contained in:
Mark DePristo 2012-06-04 19:02:59 -04:00
parent 1d4eb46606
commit 6f7a01e00d
2 changed files with 5 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -208,9 +208,9 @@ public class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceDepende
final int nAlleleInfo = decoder.decodeInt(BCF2Type.INT32); final int nAlleleInfo = decoder.decodeInt(BCF2Type.INT32);
final int nFormatSamples = decoder.decodeInt(BCF2Type.INT32); final int nFormatSamples = decoder.decodeInt(BCF2Type.INT32);
final int nAlleles = nAlleleInfo >> 16; final int nAlleles = nAlleleInfo >> 16;
final int nInfo = nAlleleInfo & 0x00FF; final int nInfo = nAlleleInfo & 0x0000FFFF;
final int nFormatFields = nFormatSamples >> 24; final int nFormatFields = nFormatSamples >> 24;
final int nSamples = nFormatSamples & 0x0FFF; final int nSamples = nFormatSamples & 0x00FFFFF;
decodeID(builder); decodeID(builder);
final ArrayList<Allele> alleles = decodeAlleles(builder, pos, nAlleles); final ArrayList<Allele> alleles = decodeAlleles(builder, pos, nAlleles);

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -169,8 +169,8 @@ class BCF2Writer extends IndexingVariantContextWriter {
final int nGenotypeFormatFields = getNGenotypeFormatFields(vc); final int nGenotypeFormatFields = getNGenotypeFormatFields(vc);
final int nSamples = vc.getNSamples(); final int nSamples = vc.getNSamples();
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x00FF), BCF2Type.INT32); encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x0000FFFF), BCF2Type.INT32);
encoder.encodeRawInt((nGenotypeFormatFields << 24) | (nSamples & 0x0FFF), BCF2Type.INT32); encoder.encodeRawInt((nGenotypeFormatFields << 24) | (nSamples & 0x00FFFFF), BCF2Type.INT32);
buildID(vc); buildID(vc);
buildAlleles(vc); buildAlleles(vc);