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Generate User Error for bad POS value

This commit is contained in:
Eric Banks 2012-04-12 09:49:35 -04:00
parent cc71baf691
commit b659b16b31
1 changed files with 6 additions and 1 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -204,7 +204,12 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
final List<Allele> alleles = parseAlleles(ref, alts, lineNo); final List<Allele> alleles = parseAlleles(ref, alts, lineNo);
// find out our location // find out our location
final int start = Integer.valueOf(locParts[1]); int start = 0;
try {
start = Integer.valueOf(locParts[1]);
} catch (Exception e) {
generateException("the value in the POS field must be an integer but it was " + locParts[1], lineNo);
}
int stop = start; int stop = start;
// ref alleles don't need to be single bases for monomorphic sites // ref alleles don't need to be single bases for monomorphic sites