From 682b76553696d4ed98024b21e704ab8388376752 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 22 Sep 2009 18:20:43 +0000 Subject: [PATCH] bug: need to upper case chars so that == works throughout git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1684 348d0f76-0448-11de-a6fe-93d51630548a --- .../src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java index d84bac130..cff4d03d0 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodGeliText.java @@ -65,7 +65,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation throw new IOException("Invalid rodVariant row found -- too few elements. Expected 18+, got " + parts.length); if (!parts[0].startsWith("#")) { loc = GenomeLocParser.createGenomeLoc(parts[0], Long.valueOf(parts[1])); - refBase = parts[2].charAt(0); + refBase = Character.toUpperCase(parts[2].charAt(0)); depth = Integer.valueOf(parts[3]); maxMappingQuality = Integer.valueOf(parts[4]); @@ -148,6 +148,7 @@ public class RodGeliText extends BasicReferenceOrderedDatum implements Variation } public char getAltSnpFWD() throws IllegalStateException { + // both ref and bestGenotype have been uppercased, so it's safe to use == char c = (bestGenotype.charAt(0) == refBase) ? bestGenotype.charAt(1) : bestGenotype.charAt(0); //System.out.printf("%s : %c and %c%n", bestGenotype, refBase, c); return c;