060ada2535fca719656219c1214a3e1c16490693
tdreszer
  Wed Nov 9 16:06:41 2011 -0800
Moved as code in hgTables down to lib and access it from hgc and hgTrackUi.  This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
diff --git src/hg/inc/pgSnp.h src/hg/inc/pgSnp.h
index 65ea949..8851e36 100644
--- src/hg/inc/pgSnp.h
+++ src/hg/inc/pgSnp.h
@@ -1,26 +1,27 @@
 /* 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"
 #include "bed.h"
 #include "vcf.h"
+#include "asParse.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 */
@@ -102,30 +103,31 @@
     int cdEnd;
     int firstCodon;
     int regStart; /* in coding sequence positions */
     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);
 /* 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 asObject *pgSnpAsObj();
+// Return asObject describing fields of pgSnp
 
 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 */