Index: src/utils/qa/checkScaffoldGaps.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkScaffoldGaps.csh,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/utils/qa/checkScaffoldGaps.csh	13 Dec 2004 18:36:20 -0000	1.2
+++ src/utils/qa/checkScaffoldGaps.csh	11 Apr 2009 00:37:02 -0000	1.3
@@ -1,55 +1,56 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ###############################################
 # 
 #  12-01-04
 #  Robert Kuhn
 # 
 #  Checks that gaps and gold add up to size for scaffold-based assemblies.
 # 
 ###############################################
 
 set db=""
 set table=""
 set column=""
 
 
 if ($#argv != 1) then
   # no command line args
   echo
   echo "  checks that gaps and gold add up to size for scaffold-based assemblies."
   echo
   echo "    usage:  database"
   echo
   exit
 else
   set db=$argv[1]
 endif
 
 # --------------------------------------------
 
 set count=0
 set errFlag="0"
 hgsql -N -e "SELECT chrom FROM chromInfo" $db | sort  > $db.chromInfo.dev
 foreach chrom (`cat $db.chromInfo.dev`)
   set count=`echo $count | gawk '{print $1 + 1}'`
   set size=`hgsql -N -e 'SELECT size FROM chromInfo WHERE chrom = "'$chrom'"' $db`
   set gaps=`hgsql -N -e 'SELECT SUM(chromEnd) - SUM(chromStart) FROM gap WHERE chrom = "'$chrom'"' $db`
   set gold=`hgsql -N -e 'SELECT SUM(chromEnd) - SUM(chromStart) FROM gold \
        WHERE chrom = "'$chrom'"' $db`
   set totalsize=`echo "$gaps $gold" | gawk '{print $1 + $2}'`
   if ($totalsize != $size) then
     echo "gap + gold not equal to size for $chrom"
     echo "gap + gold not equal to size for $chrom" >> $db.gapGoldWrong
     set errFlag="1"
   else
     echo $count $chrom
   endif
 end
 
 if ($errFlag == "0") then
   echo "gap + gold = chromInfo.size for all chroms."
 else
   echo cat $db.gapGoldWrong
 endif
 # rm -f $db.chromInfo.dev

