zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added a sequenom rod to empower Carrie to convert 1KG validation SNPs to sequenom format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1706 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-23 20:22:09 +00:00
parent 63f3d45ca4
commit 423a3ee894
2 changed files with 55 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
View File

@ -67,6 +67,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("Table", TabularROD.class);
addModule("PooledEM", PooledEMSNPROD.class);
addModule("CleanedOutSNP", CleanedOutSNPROD.class);
addModule("Sequenom", SequenomROD.class);
addModule("SangerSNP", SangerSNPROD.class);
addModule("SimpleIndel", SimpleIndelROD.class);
addModule("PointIndel", PointIndelROD.class);

54
java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java 100755
View File

@ -0,0 +1,54 @@
package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.util.*;
public class SequenomROD extends TabularROD implements AllelicVariant {
public SequenomROD(String name) {
super(name);
}
public GenomeLoc getLocation() {
long pos = Long.parseLong(this.get("1"));
return GenomeLocParser.createGenomeLoc(this.get("0"), pos);
}
public List<String> getFWDAlleles() {
return Arrays.asList(this.get("2"));
}
public String getFWDRefBases() { return ""; }
public String getAltBasesFWD() { return getFWDAlleles().get(0); }
public String getRefBasesFWD() { return ""; }
public char getRefSnpFWD() { return 'N'; }
public char getAltSnpFWD() { return getAltBasesFWD().charAt(0); }
public char getRef() { return 'N'; }
public List<String> getGenotype() { return getFWDAlleles(); }
public boolean isGenotype() { return false; }
public boolean isPointGenotype() { return true; }
public boolean isIndelGenotype() { return false; }
public boolean isSNP() { return true; }
public boolean isReference() { return false; }
public boolean isInsertion() { return false; }
public boolean isDeletion() { return false; }
public boolean isIndel() { return false; }
public double getVariantConfidence() { return 0.0; }
public double getVariationConfidence() { return 0.0; }
public double getConsensusConfidence() { return 0.0; }
public boolean isBiallelic() { return true; }
public boolean isHom() { return false; }
public boolean isHet() { return false; }
public double getHeterozygosity() { return 0.0; }
public double getMAF() { return 0.0; }
public int getPloidy() { return 2; }
public int length() { return 1; }
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t" + getFWDAlleles().get(0));
return sb.toString();
}
}