e5bca336b3a879884c7cd865cc2c1758e5ffbb3e
angie
Fri Oct 13 14:32:01 2017 -0700
Check for NULL to support VCF files with missing header definitions.
diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c
index 80ce88f..b536064 100644
--- src/hg/hgc/vcfClick.c
+++ src/hg/hgc/vcfClick.c
@@ -255,31 +255,31 @@
dyStringClear(tmp1);
dyStringAppend(tmp1, rec->format);
struct vcfFile *vcff = rec->file;
enum vcfInfoType formatTypes[256];
char *formatKeys[256];
int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys));
puts("Genotype info key:
");
int i;
for (i = 0; i < formatCount; i++)
{
if (sameString(formatKeys[i], vcfGtGenotype))
continue;
const struct vcfInfoDef *def = vcfInfoDefForGtKey(vcff, formatKeys[i]);
char *desc = def ? def->description : "not described in VCF header";
printf(" %s: %s
\n", formatKeys[i], desc);
- formatTypes[i] = def->type;
+ formatTypes[i] = def ? def->type : vcfInfoString;
}
hTableStart();
puts("