2b5eb866f050d964d8964ec5a84f7b63889cc6b1
angie
  Mon Jun 3 14:39:36 2013 -0700
New CGI, hgVai (Variant Annotation Integrator): simple checklist-styleUI by which user can select variants that they have uploaded; gene
predictions to identify which part of a gene, if any, is hit by each
variant; several additional sources of annotations/predictions e.g.
dbNSFP scores and conserved elements/scores; and several filters to
constrain output to the variants most likely to have a functional effect.
Along with the new CGI, there are various lib bugfixes and improvements,
a new hg/lib/tests/ testcase, and some test file changes to accomodate
data updates to both knownGene and the pg* tables in knownGene.
refs #6152

diff --git src/inc/vcf.h src/inc/vcf.h
index f6bcb10..a5c7f32 100644
--- src/inc/vcf.h
+++ src/inc/vcf.h
@@ -259,20 +259,22 @@
 /* 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);
-/* Overwrite dy with a /-separated allele string from VCF words;
- * return dy->string for convenience. */
+char *vcfGetSlashSepAllelesFromWords(char **words, struct dyString *dy,
+				     boolean *retSkippedFirstBase);
+/* 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