From 5ce11c3dada1ef5060b7b16c1017e10d947185cf Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 6 Jan 2010 15:01:20 +0000 Subject: [PATCH] toString method git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2512 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/utils/genotype/vcf/VCFGenotypeRecord.java | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java index 781e870e0..42b4c0ad2 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java @@ -31,7 +31,7 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked { public static final String UNFILTERED = "."; public static final double MAX_QUAL_VALUE = 99.0; - + // what kind of phasing this genotype has public enum PHASE { UNPHASED, PHASED, PHASED_SWITCH_PROB, UNKNOWN @@ -150,7 +150,7 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked { if ( encoding.getType() == VCFGenotypeEncoding.TYPE.UNCALLED ) continue; if ( encoding.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE || - encoding.getBases().charAt(0) != ref ) + encoding.getBases().charAt(0) != ref ) return true; } return false; @@ -212,11 +212,15 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked { } first = false; } - } + } return str; } + @Override public String toString() { + return String.format("[VCFGenotype %s %s %s %s]", getLocation(), mSampleName, this.mGenotypeAlleles, mFields); + } + public boolean isEmptyGenotype() { for ( VCFGenotypeEncoding encoding : mGenotypeAlleles ) { if ( encoding.getType() != VCFGenotypeEncoding.TYPE.UNCALLED )