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
@@ -1,125 +1,128 @@
 /* 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. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #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. Strings are automatically escaped to allow insertion into the 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, 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 */