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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2011-10-31 14:56:59 -04:00
parent cdde32acbd f62af0291b
commit 31ee5432c5
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -163,7 +163,10 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
*/
public Feature decodeLoc(String line) {
String[] locParts = new String[6];
ParsingUtils.split(line, locParts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
int nParts = ParsingUtils.split(line, locParts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
if ( nParts != 6 )
throw new UserException.MalformedVCF("there aren't enough columns for line " + line, lineNo);
// get our alleles (because the end position depends on them)
String ref = getCachedString(locParts[3].toUpperCase());