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Fixed compatibilities in AbstractVCFCodec that resulted in key=; being parsed as written as key; in VCF output

This commit is contained in:
Mark DePristo 2012-07-02 11:38:59 -04:00
parent 337e434c01
commit 01e04992f8
1 changed files with 5 additions and 2 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -363,10 +363,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
int eqI = infoFieldArray[i].indexOf("="); int eqI = infoFieldArray[i].indexOf("=");
if ( eqI != -1 ) { if ( eqI != -1 ) {
key = infoFieldArray[i].substring(0, eqI); key = infoFieldArray[i].substring(0, eqI);
String str = infoFieldArray[i].substring(eqI+1); String valueString = infoFieldArray[i].substring(eqI+1);
// split on the INFO field separator // split on the INFO field separator
int infoValueSplitSize = ParsingUtils.split(str, infoValueArray, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR, false); int infoValueSplitSize = ParsingUtils.split(valueString, infoValueArray, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR, false);
if ( infoValueSplitSize == 1 ) { if ( infoValueSplitSize == 1 ) {
value = infoValueArray[0]; value = infoValueArray[0];
final VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key); final VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key);
@ -396,6 +396,9 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
} }
} }
// this line ensures that key/value pairs that look like key=; are parsed correctly as MISSING
if ( "".equals(value) ) value = VCFConstants.MISSING_VALUE_v4;
attributes.put(key, value); attributes.put(key, value);
} }
} }