From 81bd7646d69f14c5f21857d6d98e19b29abd96c6 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 10 May 2012 11:29:57 -0400 Subject: [PATCH] Fix for MISSING floats -- Restructured code to separate the MISSING value in java (currently everywhere a null) from the byte representation on disk (an int). -- Now handles correctly MISSING qual fields --- .../sting/utils/variantcontext/VariantContext.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 6a861bcd3..3e6f9dbb0 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1225,8 +1225,10 @@ public class VariantContext implements Feature { // to enable tribble integratio } public String toString() { - return String.format("[VC %s @ %s of type=%s alleles=%s attr=%s GT=%s", - getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), this.getType(), + return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s GT=%s", + getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), + hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".", + this.getType(), ParsingUtils.sortList(this.getAlleles()), ParsingUtils.sortedString(this.getAttributes()), this.getGenotypes());