dacecbaf00b2193872633dde175c53d263922ff9
angie
  Wed May 11 16:18:38 2011 -0700
Feature #2823 (VCF track handler): request from alpha-test user CarlosBorroto: call Belinda's coding variant functional prediction function
as on the pgSnp details page.

diff --git src/hg/inc/pgSnp.h src/hg/inc/pgSnp.h
index 2213829..65ea949 100644
--- src/hg/inc/pgSnp.h
+++ src/hg/inc/pgSnp.h
@@ -1,29 +1,28 @@
 /* pgSnp.h was originally generated by the autoSql program, which also 
  * generated pgSnp.c and pgSnp.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef PGSNP_H
 #define PGSNP_H
 
 #include "jksql.h"
 #include "trackDb.h"
-#define PGSNP_NUM_COLS 8
-
-#ifndef BED_H
 #include "bed.h"
-#endif
+#include "vcf.h"
+
+#define PGSNP_NUM_COLS 8
 
 struct pgSnp
 /* personal genome SNP */
     {
     struct pgSnp *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom */
     unsigned chromEnd;	/* End position in chrom */
     char *name;	/* alleles */
     int alleleCount;	/* number of alleles */
     char *alleleFreq;	/* comma separated list of frequency of each allele */
     char *alleleScores;	/* comma separated list of quality scores */
     unsigned short bin; /* A field to speed indexing */
     };
 
@@ -112,17 +111,21 @@
 void printSeqCodDisplay (char *db, struct pgSnp *item);
 /* print the display of sequence changes for a coding variant */
 
 void printPgDbLink(char *db, struct trackDb *tdb, struct pgSnp *item);
 /* print the links to phenotype and other databases for pgSnps */
 
 extern char *pgSnpAutoSqlString;
 
 struct pgSnp *pgSnpLoadNoBin (char **row);
 /* load struct from row without bin */
 
 struct pgSnp *pgSnpLineFileLoad(char **row, struct lineFile *lf);
 /* Load pgSnp from a lineFile line, with error checking. */
 /* Requires comma separated zeroes for frequency and scores. */
 
+struct pgSnp *pgSnpFromVcfRecord(struct vcfRecord *rec);
+/* Convert VCF rec to pgSnp; don't free rec->file (vcfFile) until
+ * you're done with pgSnp because pgSnp points to rec->chrom. */
+
 #endif /* PGSNP_H */