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Catch exception for bad type and throw as a TribbleException

This commit is contained in:
Eric Banks 2012-01-25 12:15:51 -05:00
parent 96b62daff3
commit 2799a1b686
1 changed files with 6 additions and 1 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
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@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils.codecs.vcf; package org.broadinstitute.sting.utils.codecs.vcf;
import org.broad.tribble.TribbleException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.Arrays; import java.util.Arrays;
@ -149,7 +150,11 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
count = Integer.valueOf(numberStr); count = Integer.valueOf(numberStr);
} }
type = VCFHeaderLineType.valueOf(mapping.get("Type")); try {
type = VCFHeaderLineType.valueOf(mapping.get("Type"));
} catch (Exception e) {
throw new TribbleException(mapping.get("Type") + " is not a valid type in the VCF specification (note that types are case-sensitive)");
}
if (type == VCFHeaderLineType.Flag && !allowFlagValues()) if (type == VCFHeaderLineType.Flag && !allowFlagValues())
throw new IllegalArgumentException("Flag is an unsupported type for this kind of field"); throw new IllegalArgumentException("Flag is an unsupported type for this kind of field");