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Add an indel rod which represents the initial point of the indel only 

(useful for alternate reference making)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-02 19:32:29 +00:00
parent 58debd7e56
commit 3dfc77dc89
2 changed files with 16 additions and 0 deletions
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15
java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java 100755
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@ -0,0 +1,15 @@
package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
public class PointIndelROD extends SimpleIndelROD {
public PointIndelROD(String name) {
super(name);
}
public GenomeLoc getLocation() {
return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
}
}

1
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -75,6 +75,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("CleanedOutSNP", CleanedOutSNPROD.class);
addModule("SangerSNP", SangerSNPROD.class);
addModule("SimpleIndel", SimpleIndelROD.class);
addModule("PointIndel", PointIndelROD.class);
addModule("HapMapGenotype", HapMapGenotypeROD.class);
addModule("Intervals", IntervalRod.class);
addModule("Variants", rodVariants.class);