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Bad chain files are user errors 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5059 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-23 06:04:36 +00:00
parent 2bbcc9275a
commit 2ba35dc7ba
1 changed files with 6 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -70,7 +70,12 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
private long successfulIntervals = 0, failedIntervals = 0; private long successfulIntervals = 0, failedIntervals = 0;
public void initialize() { public void initialize() {
try {
liftOver = new LiftOver(CHAIN); liftOver = new LiftOver(CHAIN);
} catch (PicardException e) {
throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage());
}
liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH); liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
try { try {