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add FLT toString method (to be used in PrintRODs) and add it to ROD list 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-20 02:47:50 +00:00
parent 8da754eb4e
commit 1d2b545608
2 changed files with 12 additions and 0 deletions
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1
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -65,6 +65,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
addModule("SAMPileup", rodSAMPileup.class);
addModule("GELI", rodGELI.class);
addModule("FLT", rodFLT.class);
addModule("RefSeq", rodRefSeq.class);
addModule("Table", TabularROD.class);
addModule("PooledEM", PooledEMSNPROD.class);

11
java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
View File

@ -29,6 +29,17 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
else
return bases[1];
}
public String toString() {
StringBuffer sb = new StringBuffer();
sb.append(loc.getContig() + "\t" + loc.getStart() + "\t");
sb.append(getRefSnpFWD() + "\t-1\t-1\t" + getAltBasesFWD());
for (int i=0; i < 12; i++)
sb.append("\t0");
sb.append("\n");
return sb.toString();
}
public boolean isReference() { return false; }
public boolean isSNP() { return true; }
public boolean isInsertion() { return false; }