diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java index bfb6b1711..f15b429b3 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java @@ -65,6 +65,7 @@ public class ReferenceOrderedData 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); diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java index 11761f58f..c0f963346 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java @@ -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; }