Index: src/utils/qa/net.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/net.csh,v
retrieving revision 1.19
retrieving revision 1.20
diff -b -B -U 4 -r1.19 -r1.20
--- src/utils/qa/net.csh	21 May 2009 01:28:08 -0000	1.19
+++ src/utils/qa/net.csh	9 Jul 2009 21:19:54 -0000	1.20
@@ -12,8 +12,9 @@
 
 onintr cleanup
 
 set db=""
+set chromNum=""
 set trackname=""
 set currDir=$cwd
 
 if ($2 == "") then
@@ -115,9 +116,11 @@
     # echo "$chrom is ok"   # debug
   endif
 end
 
-
+if ( `egrep . chromlist$$` < 100 ) then
+  set chromNum="small"
+endif
 
 # -------------------------------------------------
 # check ends for off-end coords:
 
@@ -125,8 +128,32 @@
 echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
 
 checkOffend.csh $db net$Org
 
+# -------------------------------------------------
+# check sort
+
+echo
+echo "*~*~*~*~*~*~*~*~*~*~*~*~*~*"
+echo "check sort:"
+
+positionalTblCheck -verbose=0 $db net$Org
+if ( ! $status ) then
+  echo "sort is ok"
+endif
+echo
+
+# -------------------------------------------------
+# check countPerChrom
+
+echo "check countPerChrom"
+if ( $chromNum == "small" ) then
+  countPerChrom.csh $db net$Org
+else
+  echo "too many chroms to do a count per chrom"
+endif
+echo
+
 
 # -------------------------------------------------
 # check that all levels fall between 1-12 inclusive:
 

