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Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging 

-- New tribble library now uses 64 bit sizes.  The 26K VCF has so much data that low-level tribble block indices where overflowing their int size values.  This includes a to-be-committed tribble jar that fixes this problem
-- See https://jira.broadinstitute.org/browse/GSA-652
-- Minor cleanup of error messages that were useful on the way to solving this monster problem
This commit is contained in:
Mark DePristo 2012-11-02 09:09:32 -04:00
parent 6185e8c432
commit f8a0a947e3
4 changed files with 2 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -587,7 +587,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR); int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
if ( nParts != genotypeParts.length ) if ( nParts != genotypeParts.length )
generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo); generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records at " + chr + ":" + pos, lineNo);
ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts); ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
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@ -76,7 +76,6 @@ public class BCF2FieldWriterManager {
if ( map.containsKey(field) ) if ( map.containsKey(field) )
throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders"); throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders");
map.put(field, writer); map.put(field, writer);
if ( logger.isDebugEnabled() ) logger.debug(writer);
} }
// ----------------------------------------------------------------- // -----------------------------------------------------------------

BIN
settings/repository/org.broad/tribble-110.jar → settings/repository/org.broad/tribble-119.jar
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2
settings/repository/org.broad/tribble-110.xml → settings/repository/org.broad/tribble-119.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="110" status="integration" /> <info organisation="org.broad" module="tribble" revision="119" status="integration" />
</ivy-module> </ivy-module>