c600c640f2ecba7827091fda0bf741a6b4927d68
larrym
  Mon Jun 13 16:14:46 2011 -0700
sort by chrom to get normal chroms before _random, _hap etc. (see redmine #4257)
diff --git src/hg/hgSuggest/hgSuggest.c src/hg/hgSuggest/hgSuggest.c
index 7ee88e7..cc685dd 100644
--- src/hg/hgSuggest/hgSuggest.c
+++ src/hg/hgSuggest/hgSuggest.c
@@ -32,47 +32,49 @@
 
 if(prefix == NULL || database == NULL)
     fail("Missing prefix or database parameter");
 
 conn = hAllocConn(database);
 table = connGeneSuggestTable(conn);
 if(table == NULL)
     fail("gene autosuggest is not supported for this assembly");
 
 hasKnownCanonical = sameString(table, "knownCanonical");
 
 puts("Content-Type:text/plain");
 puts("\n");
 
 dyStringPrintf(str, "[\n");
+
+// We have to choose one isoform, so we choose the largest one; we order by chrom to make sure we choose normal chromosomes 
+// over _random and _hap chromosomes (see redmine #4257).
 if(exact)
     {
     if(hasKnownCanonical)
-        safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol = '%s' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
+        safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, k2.txEnd - k2.txStart desc", prefix);
     else
-        safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from %s r where r.name2 = '%s' order by r.name2, r.txEnd - r.txStart desc", table, prefix);
+        safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from %s r where r.name2 = '%s' order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, prefix);
     }
 else
     {
     // We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
     // Also note that we take advantage of the fact that searches are case-insensitive in mysql.
     // Some tables have duplicates (e.g. 2 TTn's in mm9 knownCanonical); currently the larger one wins.
     if(hasKnownCanonical)
-        safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k2.txEnd - k2.txStart desc", prefix);
+        safef(query, sizeof(query), "select x.geneSymbol, k.chrom, k2.txStart, k2.txEnd from knownCanonical k, knownGene k2, kgXref x where k.transcript = x.kgID and k.transcript = k2.name and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, k2.txEnd - k2.txStart desc", prefix);
     else
-        // arbitrarily prefer the longest isoform
-        safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from %s r where r.name2 LIKE '%s%%' order by r.name2, r.txEnd - r.txStart desc", table, prefix);
+        safef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd from %s r where r.name2 LIKE '%s%%' order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, prefix);
     }
 sr = sqlGetResult(conn, query);
 previous[0] = 0;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if(!previous[0] || !sameString(previous, row[0]))
         {
         count++;
         dyStringPrintf(str, "%s{\"value\": \"%s\", \"id\": \"%s:%d-%s\"}", count == 1 ? "" : ",\n",
                        row[0], row[1], atoi(row[2])+1, row[3]);
         safecpy(previous, sizeof(previous), row[0]);
         }
     }
 dyStringPrintf(str, "\n]\n");
 puts(dyStringContents(str));