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depricate this ROD yet again 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1245 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-15 13:33:03 +00:00
parent 5d1345539d
commit d369136bda
1 changed files with 6 additions and 3 deletions
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9
java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java
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@ -17,7 +17,7 @@ import net.sf.samtools.util.CloseableIterator;
* This class wraps Picard Geli CHiP data and presents it as a ROD. * This class wraps Picard Geli CHiP data and presents it as a ROD.
*/ */
public class rodGELI extends BasicReferenceOrderedDatum implements Genotype { public class rodGELI extends BasicReferenceOrderedDatum {
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
// //
// Constructors // Constructors
@ -93,6 +93,9 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
return new rodGELI.rodGELIIterator(name,file); return new rodGELI.rodGELIIterator(name,file);
} }
/****
* We no longer want to use this class as truth data (sigh)
*
public List<String> getFWDAlleles() { public List<String> getFWDAlleles() {
return new ArrayList<String>(); return new ArrayList<String>();
} }
@ -123,8 +126,8 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype {
public double getConsensusConfidence() { public double getConsensusConfidence() {
return gh.getBestToSecondBestLod(); return gh.getBestToSecondBestLod();
} }
*
*/
public static void main(String argv[]) { public static void main(String argv[]) {
String testFile = "NA12878.geli"; String testFile = "NA12878.geli";