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Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4537 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-21 02:44:10 +00:00
parent 88a0d77433
commit 8f38ebf98e
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
public class ClusteredSnps {
private int window = 10;
@ -22,10 +23,10 @@ public class ClusteredSnps {
if ( variants[i] == null || variants[i+snpThreshold-1] == null )
continue;
// note: not all calls are variant, so we need to be careful.
// if we don't start with a variant, skip to the next one
// note: the documentation tells users we'll blow up if ref calls are present.
// if we ever get a windowed rod context that isn't a hack, we can actually allow this...
if ( !variants[i].getVariantContext().isVariant() )
continue;
throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details");
// find the nth variant
GenomeLoc left = VariantContextUtils.getLocation(variants[i].getVariantContext());