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Prevent NumberFormatExceptions when parsing the VCF POS field

This commit is contained in:
Eric Banks 2012-08-06 11:19:54 -04:00
parent e1bba91836
commit 8f95a03bb6
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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@ -237,7 +237,12 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
// parse out the required fields // parse out the required fields
final String chr = getCachedString(parts[0]); final String chr = getCachedString(parts[0]);
builder.chr(chr); builder.chr(chr);
int pos = Integer.valueOf(parts[1]); int pos = -1;
try {
pos = Integer.valueOf(parts[1]);
} catch (NumberFormatException e) {
generateException(parts[1] + " is not a valid start position in the VCF format");
}
builder.start(pos); builder.start(pos);
if ( parts[2].length() == 0 ) if ( parts[2].length() == 0 )