b1c2fdec9a31078a56333427830a760757d22a51
angie
  Fri Jun 17 14:44:44 2016 -0700
Command line wrapper script for hgVai: hg/utils/vai.pl .  hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line.  Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not).
Has been tested somewhat on GBiB.  Needs documentation.
refs #12216

diff --git src/hg/inc/pgSnp.h src/hg/inc/pgSnp.h
index 59ceddc..8569fac 100644
--- src/hg/inc/pgSnp.h
+++ src/hg/inc/pgSnp.h
@@ -98,28 +98,31 @@
     int regEnd;
     };
 
 struct pgCodon *fetchCodons (char *db, struct bed *gene, unsigned chrStart, unsigned chrEnd);
 /* get codon sequence to compute aa changes */
 
 void printSeqCodDisplay (char *db, struct pgSnp *item, char *genePredTable);
 /* 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 */
 
 struct asObject *pgSnpAsObj();
 // Return asObject describing fields of pgSnp
 
+struct asObject *pgSnpFileAsObj();
+// Return asObject describing fields of pgSnp file (no bin)
+
 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 */