package org.broadinstitute.sting.gatk.refdata;

import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;


public class CleanedOutSNPROD extends TabularROD {

    private static final String REAL_SNP_STRING = "SAME_SNP";
    private static final String FALSE_SNP_STRING = "NOT_SNP";

    public CleanedOutSNPROD(String name) {
        super(name);
    }

    public GenomeLoc getLocation() {
        return GenomeLocParser.parseGenomeLoc(this.get("0"));
    }

    public boolean isRealSNP() { return this.get("1").equals(REAL_SNP_STRING); }
 }
package org.broadinstitute.sting.gatk.refdata;

import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;


public class CleanedOutSNPROD extends TabularROD {

    private static final String REAL_SNP_STRING = "SAME_SNP";
    private static final String FALSE_SNP_STRING = "NOT_SNP";

    public CleanedOutSNPROD(String name) {
        super(name);
    }

    public GenomeLoc getLocation() {
        return GenomeLocParser.parseGenomeLoc(this.get("0"));
    }

    public boolean isRealSNP() {
        String s = this.get("1");
        return s != null && s.equals(REAL_SNP_STRING);
    }
 }
Allow this ROD to consist of just the positions
Allow this ROD to consist of just the positions


git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@1497 348d0f76-0448-11de-a6fe-93d51630548a
