From 8f95a03bb61ae886a7ead3d7e836766d964c4d06 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 11:19:54 -0400 Subject: [PATCH] Prevent NumberFormatExceptions when parsing the VCF POS field --- .../sting/utils/codecs/vcf/AbstractVCFCodec.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 996cef8a4..043e5e185 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -237,7 +237,12 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec // parse out the required fields final String chr = getCachedString(parts[0]); builder.chr(chr); - int pos = Integer.valueOf(parts[1]); + int pos = -1; + try { + pos = Integer.valueOf(parts[1]); + } catch (NumberFormatException e) { + generateException(parts[1] + " is not a valid start position in the VCF format"); + } builder.start(pos); if ( parts[2].length() == 0 )