From 800f7e6360b49c4b47ef9118d87c97f10c550ba5 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 15 Jul 2009 19:25:06 +0000 Subject: [PATCH] make AllelicVariant extend ReferenceOrderedDatum (not Comparable) since ROD itself is Comparable. Then we can generalize RMD tags. Blame Matt if this doesn't work - he said it wouldn't break anything. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1256 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/refdata/AllelicVariant.java | 2 +- java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java index 4671848d0..0e1ccd313 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java @@ -12,7 +12,7 @@ import java.util.List; * Time: 11:02:03 AM * To change this template use File | Settings | File Templates. */ -public interface AllelicVariant extends Comparable { +public interface AllelicVariant extends ReferenceOrderedDatum { // ---------------------------------------------------------------------- // // manipulating the SNP information diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java index 42180ac8f..11761f58f 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java @@ -37,7 +37,10 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes { public double getMAF() { return 0.0; } public double getHeterozygosity() { return 0.0; } public boolean isGenotype() { return false; } - public double getVariationConfidence() { return Double.parseDouble(this.get("6")); } + public double getVariationConfidence() { + double value = Double.parseDouble(this.get("6")); + return (value > 0.0 ? value : 1.0); + } public double getConsensusConfidence() { return -1; } public List getGenotype() throws IllegalStateException { throw new IllegalStateException(); } public int getPloidy() throws IllegalStateException { return 2; }