From b659b16b31a747a3134a75d0ec50ec47d09c7d6e Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 12 Apr 2012 09:49:35 -0400 Subject: [PATCH] Generate User Error for bad POS value --- .../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 3c2ed18e4..65e42c1d3 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 @@ -204,7 +204,12 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec { final List alleles = parseAlleles(ref, alts, lineNo); // find out our location - final int start = Integer.valueOf(locParts[1]); + int start = 0; + try { + start = Integer.valueOf(locParts[1]); + } catch (Exception e) { + generateException("the value in the POS field must be an integer but it was " + locParts[1], lineNo); + } int stop = start; // ref alleles don't need to be single bases for monomorphic sites