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Incompatible chain files are user exceptions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5008 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-16 05:26:47 +00:00
parent cc4e193670
commit 366c3a0b8f
1 changed files with 8 additions and 2 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -28,6 +28,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -39,6 +40,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils
import java.io.File;
import java.util.*;
import net.sf.picard.PicardException;
import net.sf.picard.liftover.LiftOver;
import net.sf.picard.util.Interval;
import net.sf.samtools.SAMFileHeader;
@ -71,8 +73,12 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
liftOver = new LiftOver(CHAIN);
liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH);
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
try {
final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader();
liftOver.validateToSequences(toHeader.getSequenceDictionary());
} catch (PicardException 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");
}
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList("variant"));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("variant"));