acd43c8cb2e79ad5c456c9589b1b5b0b49e4c723
angie
  Tue Dec 13 09:50:04 2011 -0800
MLQ #6291 (pgSNP format): the pgSnp lib function printSeqCodDisplaywas firing off a query to knownGene without first testing whether
knownGene exists, causing error for knownGene-less databases.
Now the lib function takes genePredTable as argument and tests
existence before querying.

diff --git src/hg/inc/pgSnp.h src/hg/inc/pgSnp.h
index 8851e36..3e29118 100644
--- src/hg/inc/pgSnp.h
+++ src/hg/inc/pgSnp.h
@@ -1,133 +1,133 @@
 /* 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 */
     };
 
 void pgSnpStaticLoad(char **row, struct pgSnp *ret);
 /* Load a row from pgSnp table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct pgSnp *pgSnpLoad(char **row);
 /* Load a pgSnp from row fetched with select * from pgSnp
  * from database.  Dispose of this with pgSnpFree(). */
 
 struct pgSnp *pgSnpLoadAll(char *fileName);
 /* Load all pgSnp from whitespace-separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 struct pgSnp *pgSnpLoadAllByChar(char *fileName, char chopper);
 /* Load all pgSnp from chopper separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 #define pgSnpLoadAllByTab(a) pgSnpLoadAllByChar(a, '\t');
 /* Load all pgSnp from tab separated file.
  * Dispose of this with pgSnpFreeList(). */
 
 struct pgSnp *pgSnpLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all pgSnp from table that satisfy the query given.
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something =
  * anotherTable.something'.
  * Dispose of this with pgSnpFreeList(). */
 
 void pgSnpSaveToDb(struct sqlConnection *conn, struct pgSnp *el, char *tableName, int updateSize);
 /* Save pgSnp as a row to the table specified by tableName.
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include"
  * If worried about this use pgSnpSaveToDbEscaped() */
 
 void pgSnpSaveToDbEscaped(struct sqlConnection *conn, struct pgSnp *el, char *tableName, int updateSize);
 /* Save pgSnp as a row to the table specified by tableName.
  * As blob fields may be arbitrary size updateSize specifies the approx size.
  * of a string that would contain the entire query. Automatically
  * escapes all simple strings (not arrays of string) but may be slower than pgSnpSaveToDb().
  * For example automatically copies and converts:
  * "autosql's features include" --> "autosql\'s features include"
  * before inserting into database. */
 
 struct pgSnp *pgSnpCommaIn(char **pS, struct pgSnp *ret);
 /* Create a pgSnp out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new pgSnp */
 
 void pgSnpFree(struct pgSnp **pEl);
 /* Free a single dynamically allocated pgSnp such as created
  * with pgSnpLoad(). */
 
 void pgSnpFreeList(struct pgSnp **pList);
 /* Free a list of dynamically allocated pgSnp's */
 
 void pgSnpOutput(struct pgSnp *el, FILE *f, char sep, char lastSep);
 /* Print out pgSnp.  Separate fields with sep. Follow last field with lastSep. */
 
 #define pgSnpTabOut(el,f) pgSnpOutput(el,f,'\t','\n');
 /* Print out pgSnp as a line in a tab-separated file. */
 
 #define pgSnpCommaOut(el,f) pgSnpOutput(el,f,',',',');
 /* Print out pgSnp as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct pgCodon
 /* codons covering region */
     {
     char *seq;
     int cdStart;
     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);
+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 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 */