From 8507cd7440f3aa58b9f47bbc8a2d434eeb5de9d3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 10 Apr 2012 07:22:43 -0400 Subject: [PATCH] Throw UserException for bad dict / chain files --- .../sting/gatk/walkers/variantutils/LiftoverVariants.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 50fafa202..43aa273c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -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 { 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 { 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"); }