5390b51b1beb4c37c736b3b910dce64f065892e2
angie
  Thu Sep 5 11:03:31 2013 -0700
VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator.  Also, that lets us get rid of the
ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.

diff --git src/inc/vcf.h src/inc/vcf.h
index a5c7f32..ca3d942 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -259,22 +259,21 @@
 /* Find the genotype and associated info for the individual, or return NULL.
  * This calls vcfParseGenotypes if it has not already been called. */
 
 struct vcfInfoDef *vcfInfoDefForGtKey(struct vcfFile *vcff, const char *key);
 /* Look up the type of genotype FORMAT component key, in the definitions from the header,
  * and failing that, from the keys reserved in the spec. */
 
 char *vcfFilePooledStr(struct vcfFile *vcff, char *str);
 /* Allocate memory for a string from vcff's shared string pool. */
 
 #define VCF_NUM_COLS 10
 
 struct asObject *vcfAsObj();
 // Return asObject describing fields of VCF
 
-char *vcfGetSlashSepAllelesFromWords(char **words, struct dyString *dy,
-				     boolean *retSkippedFirstBase);
+char *vcfGetSlashSepAllelesFromWords(char **words, struct dyString *dy);
 /* Overwrite dy with a /-separated allele string from VCF words,
  * skipping the extra initial base that VCF requires for indel alleles if necessary.
  * Return dy->string for convenience. */
 
 #endif // vcf_h