src/hg/hgGenome/import.c 1.14

Index: src/hg/hgGenome/import.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgGenome/import.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 4 -r1.13 -r1.14
--- src/hg/hgGenome/import.c	17 Sep 2008 18:36:35 -0000	1.13
+++ src/hg/hgGenome/import.c	6 Apr 2009 05:31:18 -0000	1.14
@@ -16,8 +16,9 @@
 #include "hPrint.h"
 #include "customTrack.h"
 #include "trashDir.h"
 #include "hgGenome.h"
+#include "genoLay.h"
 
 #include "jsHelper.h"
 #include "grp.h"
 #include "hdb.h"
@@ -47,22 +48,13 @@
 else
     return "hgGenome";
 }
 
-struct slName *getChroms()
+struct genoLayChrom *getChroms()
 /* Get a chrom list. */
 {
 struct sqlConnection *conn = hAllocConn(database);
-struct sqlResult *sr;
-char **row;
-struct slName *chromList = NULL;
-sr = sqlGetResult(conn, "select chrom from chromInfo");
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    slNameAddHead(&chromList, cloneString(row[0]));
-    }
-slReverse(&chromList);
-sqlFreeResult(&sr);
+struct genoLayChrom *chromList = genoLayDbChromsExt(conn, FALSE, FALSE);
 hFreeConn(&conn);
 return chromList;
 }
 
@@ -1145,17 +1137,17 @@
 struct dyString *dy = dyStringNew(0);
 struct rbTree *tree = NULL;
 char *chrom = "";
 int chromSize = 0;
-struct slName *chr, *chromList = getChroms();
+struct genoLayChrom *chr, *chromList = getChroms();
 for (chr = chromList; chr != NULL; chr = chr->next)
     {
     char *table = curTable;
     struct hTableInfo *hti = getHti(database, table);
     int fields = hTableInfoBedFieldCount(hti);
     struct bed *bedList = NULL, *bed;
     struct lm *lm = lmInit(64*1024);
-    chrom = chr->name;
+    chrom = chr->fullName;
     bedList = getBeds(chrom, lm, &fields);
 
     if (!bedList)
 	continue;
@@ -1207,17 +1199,17 @@
 int windowSize = 10000;
 int numWindows = 0;
 double *depth = NULL;
 int overlap = 0;
-struct slName *chr, *chromList = getChroms();
+struct genoLayChrom *chr, *chromList = getChroms();
 for (chr = chromList; chr != NULL; chr = chr->next)
     {
     char *table = curTable;
     struct hTableInfo *hti = getHti(database, table);
     int fields = hTableInfoBedFieldCount(hti);
     struct bed *bedList = NULL, *bed;
     struct lm *lm = lmInit(64*1024);
-    chrom = chr->name;
+    chrom = chr->fullName;
     bedList = getBeds(chrom, lm, &fields);
 
     if (!bedList)
 	continue;
@@ -1272,17 +1264,17 @@
 int windowSize = 10000;
 int numWindows = 0;
 double *depth = NULL;
 int overlap = 0;
-struct slName *chr, *chromList = getChroms();
+struct genoLayChrom *chr, *chromList = getChroms();
 for (chr = chromList; chr != NULL; chr = chr->next)
     {
     char *table = curTable;
     struct hTableInfo *hti = getHti(database, table);
     int fields = hTableInfoBedFieldCount(hti);
     struct bed *bedList = NULL, *bed;
     struct lm *lm = lmInit(64*1024);
-    chrom = chr->name;
+    chrom = chr->fullName;
     bedList = getBeds(chrom, lm, &fields);
 
     if (!bedList)
 	continue;
@@ -1342,13 +1334,13 @@
 double *depth = NULL;
 bool *hit = NULL;
 int overlap = 0;
 unsigned long long grandTotalValues=0;
-struct slName *chr, *chromList = getChroms();
+struct genoLayChrom *chr, *chromList = getChroms();
 for (chr = chromList; chr != NULL; chr = chr->next)
     {
     int totalValues=0;
-    chrom = chr->name;
+    chrom = chr->fullName;
     struct wiggleDataStream *wds = wigChromRawStats(chrom);
     struct wiggleStats *stats=NULL, *statsList = wds->stats;
 
     if (!wds->stats)