diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java index 1c4c0e80b..64bf552df 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java @@ -17,7 +17,7 @@ import net.sf.samtools.util.CloseableIterator; * 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 @@ -93,6 +93,9 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype { return new rodGELI.rodGELIIterator(name,file); } + /**** + * We no longer want to use this class as truth data (sigh) + * public List getFWDAlleles() { return new ArrayList(); } @@ -123,8 +126,8 @@ public class rodGELI extends BasicReferenceOrderedDatum implements Genotype { public double getConsensusConfidence() { return gh.getBestToSecondBestLod(); } - - + * + */ public static void main(String argv[]) { String testFile = "NA12878.geli";