diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java new file mode 100755 index 000000000..c214b0c35 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java @@ -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"))); + } +} \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java index e198bf0c2..7bb4ea379 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java @@ -75,6 +75,7 @@ public class ReferenceOrderedData 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);