src/utils/qa/GS1.csh 1.5

Index: src/utils/qa/GS1.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/GS1.csh,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/utils/qa/GS1.csh	24 Mar 2009 19:10:43 -0000	1.4
+++ src/utils/qa/GS1.csh	11 Apr 2009 00:37:00 -0000	1.5
@@ -1,5 +1,6 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ############################
 #  03-11-04
 #  last updated
@@ -73,9 +74,9 @@
   echo
   echo $table
   echo "================="
   rm -f junk 
-  set old=`hgsql -h hgwbeta -N  -e "SELECT COUNT(*) FROM $table" $betaDb`
+  set old=`hgsql -h $sqlbeta -N  -e "SELECT COUNT(*) FROM $table" $betaDb`
   set new=`hgsql -N  -e "SELECT COUNT(*) FROM $table" $db`
   if ($old != "") then
     set newRows=`expr $new - $old`
     set percent=`echo $newRows $old | awk '{printf "%.2f\n", ($1/$2)*100}'`
@@ -95,9 +96,9 @@
 echo 
 echo "compare description of all tables with previous (shows diffs):"
 foreach table (`cat $tablelist`)
   echo $table
-  hgsql -h hgwbeta -N  -e "DESCRIBE $table" $betaDb >  $betaDb.beta.$table.desc
+  hgsql -h $sqlbeta -N  -e "DESCRIBE $table" $betaDb >  $betaDb.beta.$table.desc
   hgsql -N  -e "DESCRIBE $table" $db > $db.dev.$table.desc
   diff $betaDb.beta.$table.desc $db.dev.$table.desc
   echo
 end
@@ -159,14 +160,14 @@
 
 echo
 echo
 echo "check that there are more in new release:"
-hgsql -h hgwbeta -N -e "SELECT name FROM knownGene" $betaDb \
+hgsql -h $sqlbeta -N -e "SELECT name FROM knownGene" $betaDb \
   > beta.$betaDb.KG.name
 sort beta.$betaDb.KG.name | uniq > beta.$betaDb.KG.name.uniq
-hgsql -h hgwbeta -N -e "SELECT transcript FROM knownCanonical" $betaDb \
+hgsql -h $sqlbeta -N -e "SELECT transcript FROM knownCanonical" $betaDb \
   > beta.$betaDb.knCanonical.transcript
-hgsql -h hgwbeta -N -e "SELECT transcript FROM knownIsoforms" $betaDb \
+hgsql -h $sqlbeta -N -e "SELECT transcript FROM knownIsoforms" $betaDb \
   > beta.$betaDb.knIsoforms.transcript
 sort beta.$betaDb.knCanonical.transcript | uniq \
   > beta.$betaDb.knCanonical.transcript.uniq
 sort beta.$betaDb.knIsoforms.transcript  | uniq \
@@ -280,13 +281,13 @@
   echo "one record:"
   hgsql -t -e "SELECT * FROM $table LIMIT 1" $db
   if ($table == "knownToSuper") then
   # ?? they are the same -- where were you going with this?
-    set old=`hgsql -h hgwbeta -N -e "SELECT gene FROM $table" $betaDb \
+    set old=`hgsql -h $sqlbeta -N -e "SELECT gene FROM $table" $betaDb \
         | sort | uniq | wc -l`
     set this=`hgsql -N -e "SELECT gene FROM $table" $db | sort | uniq | wc -l`
   else
-    set old=`hgsql -h hgwbeta -N -e "SELECT name FROM $table" $betaDb \
+    set old=`hgsql -h $sqlbeta -N -e "SELECT name FROM $table" $betaDb \
         | sort | uniq | wc -l`
     set this=`hgsql -N -e "SELECT name FROM $table" $db | sort | uniq | wc -l`
   endif
   set kgNames=`hgsql -N -e  'SELECT name FROM knownGene' $db \