src/hg/snp/snpLoad/illuminaLookup1M.c 1.2

Index: src/hg/snp/snpLoad/illuminaLookup1M.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/snp/snpLoad/illuminaLookup1M.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/snp/snpLoad/illuminaLookup1M.c	1 Aug 2008 23:14:23 -0000	1.1
+++ src/hg/snp/snpLoad/illuminaLookup1M.c	5 Dec 2009 00:22:49 -0000	1.2
@@ -1,150 +1,149 @@
-/* illuminaLookup1M - generate data for Illumina 1M SNP arrays track. */
+/* illuminaLookup1M - generate data for Illumina 1M and other SNP arrays track. */
 /* use UCSC snpXXX if dbSNP ID is found */
 /* use Illumina data if not found */
 /* This program is adopted from Heather's illuminaLookup2.c, with substantial simplyfication */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 
 static char const rcsid[] = "$Id$";
 
+char *snpDb = NULL;
 struct snpSubset 
     {
     char *chrom;
     int start;
     int end;
     char *strand;
     char *observed;
     char *class;
     char *locType;
     };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "illuminaLookup1M - just use rsId/chrom/pos from illumina\n"
     "usage:\n"
     "    illuminaLookup db illuminaPrelimTable snpTable\n");
 }
 
 struct hash *storeSnps(char *tableName)
 /* store subset data for SNPs in a hash */
 /* exclude SNPs that align multiple places */
 {
 struct hash *ret = NULL;
 char query[512];
-struct sqlConnection *conn = hAllocConn();
+struct sqlConnection *conn = hAllocConn(snpDb);
 struct sqlResult *sr;
 char **row;
 struct snpSubset *subsetElement = NULL;
 
 verbose(1, "creating SNP hash...\n");
 ret = newHash(16);
 safef(query, sizeof(query), 
       "select name, chrom, chromStart, chromEnd, strand, observed, class, locType from %s", 
       tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(subsetElement);
     subsetElement->chrom = cloneString(row[1]);
     subsetElement->start = sqlUnsigned(row[2]);
     subsetElement->end = sqlUnsigned(row[3]);
     subsetElement->strand = cloneString(row[4]);
     subsetElement->observed = cloneString(row[5]);
     subsetElement->class = cloneString(row[6]);
     subsetElement->locType = cloneString(row[7]);
     hashAdd(ret, cloneString(row[0]), subsetElement);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 void processSnps(struct hash *snpHash, char *illuminaTable)
 /* read illuminaTable */
 /* lookup details in snpHash */
 /* report and skip if SNP missing, class != single, locType != exact */
 {
 char query[512];
-struct sqlConnection *conn = hAllocConn();
+struct sqlConnection *conn = hAllocConn(snpDb);
 struct sqlResult *sr;
 char **row;
 struct hashEl *hel = NULL;
 struct snpSubset *subsetElement = NULL;
 struct snpSubset *snp = NULL;
 
 char *SNPname, *dbSNPrefStrand, *ILMNrefStrand, *SNPalleles, *GenomeBuild, *Chromosome, *Coordinate;
 			    
 FILE *output = mustOpen("illuminaLookup.out", "w");
 FILE *errors = mustOpen("illuminaLookup.err", "w");
 
 verbose(1, "process SNPs...\n");
 safef(query, sizeof(query), "select * from %s", illuminaTable);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     SNPname 		= row[0];
     dbSNPrefStrand 	= row[1];
     ILMNrefStrand	= row[2];
     SNPalleles		= row[3];
     GenomeBuild		= row[4];
     Chromosome		= row[5];
     Coordinate		= row[6];
     
     hel = hashLookup(snpHash, SNPname);
     if (hel == NULL) 
         {
 	fprintf(errors, "chr%s\t%d\t%d\t%s\t0\t%s\t%s\n", Chromosome, 
 		atoi(Coordinate)-1, atoi(Coordinate), SNPname, ILMNrefStrand, SNPalleles);
 	continue;
 	}
 
     /* include all alignments */
     for (hel = hashLookup(snpHash, SNPname); hel != NULL; hel = hashLookupNext(hel))
  	{
     	subsetElement = (struct snpSubset *)hel->val;
     	snp = (struct snpSubset *)hel->val;
     
     	fprintf(output, "%s\t%d\t%d\t%s\t0\t%s\t%s\n", 
     	    	snp->chrom, snp->start, snp->end, SNPname, snp->strand, snp->observed);
    	}
     }
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 carefulClose(&errors);
 carefulClose(&output);
 }
 
 int main(int argc, char *argv[])
 /* load SNPs into hash */
 {
-char *snpDb = NULL;
 char *illuminaTableName = NULL;
 char *snpTableName = NULL;
 
 struct hash *snpHash = NULL;
 
 if (argc != 4)
     usage();
 
 snpDb = argv[1];
+
 illuminaTableName = argv[2];
 snpTableName = argv[3];
 
 /* process args */
-hSetDb(snpDb);
-if (!hTableExists(illuminaTableName))
+if (!hTableExists(snpDb, illuminaTableName))
     errAbort("no %s table in %s\n", illuminaTableName, snpDb);
-if (!hTableExists(snpTableName))
+if (!hTableExists(snpDb, snpTableName))
     errAbort("no %s table in %s\n", snpTableName, snpDb);
-
 snpHash = storeSnps(snpTableName);
 processSnps(snpHash, illuminaTableName);
 
 return 0;
 }