06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/hg/near/hgNear/getSeq.c src/hg/near/hgNear/getSeq.c
index 130556f..d962e3c 100644
--- src/hg/near/hgNear/getSeq.c
+++ src/hg/near/hgNear/getSeq.c
@@ -33,31 +33,31 @@
     hPrintf(" %s", name);
 if (description != NULL)
     hPrintf(" - %s", description);
 freeMem(name);
 freeMem(description);
 }
 
 static void getSeqFromBlob(struct sqlConnection *conn, struct column *colList,
 	struct genePos *geneList, char *tableId)
 /* Get sequence from blob field in table and print it as fasta. */
 {
 struct sqlResult *sr;
 char **row;
 char query[256];
 struct genePos *gp;
-struct sqlConnection *conn2 = hAllocConn(database);
+struct sqlConnection *conn2 = hAllocConn(sqlGetDatabase(conn));
 char *tableName = genomeSetting(tableId);
 struct column *descCol = findNamedColumn("description");
 struct column *nameCol = findNamedColumn("name");
 
 hPrintf("<TT><PRE>");
 for (gp = geneList; gp != NULL; gp = gp->next)
     {
     char *id = gp->name;
     sqlSafef(query, sizeof(query), 
     	"select seq from %s where name = '%s'", tableName, id);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL)
 	{
 	char *seq = row[0];
 	hPrintf(">%s", id);
@@ -215,31 +215,31 @@
 struct hTableInfo *hti = hFindTableInfo(database, NULL, genomeSetting("geneTable"));
 makeTitle("Get Genomic Sequence Near Gene", NULL);
 hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=GET>\n");
 cartSaveSession(cart);
 hgSeqOptionsHtiCart(hti, cart);
 hPrintf("<BR>\n");
 cgiMakeButton(getGenomicSeqVarName, "get sequence");
 hPrintf("</FORM>");
 }
 
 void doGetGenomicSeq(struct sqlConnection *conn, struct column *colList,
 	struct genePos *geneList)
 /* Retrieve genomic sequence sequence according to options. */
 {
 char *table = genomeSetting("geneTable");
-struct hTableInfo *hti = hFindTableInfo(database, NULL, table);
+struct hTableInfo *hti = hFindTableInfo(sqlGetDatabase(conn), NULL, table);
 struct genePos *gp;
 char query[256];
 struct sqlResult *sr;
 char **row;
 boolean hasBin = hOffsetPastBin(database, NULL, table);
 makeTitle("Genomic Sequence", NULL);
 
 hPrintf("<TT><PRE>");
 for (gp = geneList; gp != NULL; gp = gp->next)
     {
     char *id = gp->name;
     sqlSafef(query, sizeof(query), "select * from %s where name='%s'", 
     	table, id);
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)