From b316abd20ff30e3bcbc79854a2e3b2ac7a5a1282 Mon Sep 17 00:00:00 2001 From: aaron Date: Fri, 21 Aug 2009 21:05:28 +0000 Subject: [PATCH] catch a malformed column header name more gracefully git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1453 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/utils/genotype/vcf/VCFReader.java | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java index 0f1228504..0349982ea 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java @@ -146,7 +146,13 @@ public class VCFReader implements Iterator, Iterable { if (str.startsWith("#") && !str.startsWith("##")) { String[] strings = str.substring(1).split("\\s+"); for (String s : strings) { - if (headerFields.contains(VCFHeader.HEADER_FIELDS.valueOf(s))) + VCFHeader.HEADER_FIELDS field; + try { + field = VCFHeader.HEADER_FIELDS.valueOf(s); + } catch (IllegalArgumentException e) { + throw new RuntimeException("VCFReader: Unknown column name \"" + s + "\", it does not match a known column header name."); + } + if (headerFields.contains(field)) throw new RuntimeException("VCFReader: Header field duplication is not allowed"); try { headerFields.add(VCFHeader.HEADER_FIELDS.valueOf(s));