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Throw UserException for bad dict / chain files

This commit is contained in:
Mark DePristo 2012-04-10 07:22:43 -04:00
parent 979a84a252
commit 8507cd7440
1 changed files with 2 additions and 3 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import net.sf.picard.PicardException;
import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval;
import net.sf.samtools.SAMFileHeader;
@ -73,7 +72,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
public void initialize() {
try {
liftOver = new LiftOver(CHAIN);
} catch (PicardException e) {
} catch (RuntimeException e) {
throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
}
@ -82,7 +81,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
try {
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
} catch (PicardException e) {
} catch (RuntimeException e) {
throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");
}