src/utils/qa/full_joinerCheck.csh 1.3

Index: src/utils/qa/full_joinerCheck.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/full_joinerCheck.csh,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/utils/qa/full_joinerCheck.csh	19 Aug 2004 17:51:16 -0000	1.2
+++ src/utils/qa/full_joinerCheck.csh	11 Apr 2009 00:37:03 -0000	1.3
@@ -1,41 +1,42 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 # Script to run joinerCheck for full database with -key options
 # 08-17-04 M. Chalup
 # ---------
 
 # Check number of arguments
 if ($#argv != 1) then
         echo "Usage: full_joinerCheck.csh <current_db_release>"
         exit 1
 endif
 
 set current_dir = $cwd
 set db=$argv[1]
 
 # Update all.joiner and make symbolic link into local directory
 
 echo "cd into ~/kent/src/hg/makeDb/schema"
 cd ~/kent/src/hg/makeDb/schema
 echo ""
 echo "Update files from cvs root"
 cvs update -dP
 echo ""
 echo "Return to previous directory"
 cd $current_dir
 echo ""
 echo "Establish a symbolic link to all.joiner"
 ln -s ~/kent/src/hg/makeDb/schema/all.joiner all.joiner
 echo ""
 echo "Running joinerCheck - this may take quite a while"
 nice joinerCheck -database=$db -keys all.joiner >& $db.complete_release_joinerCheck.txt
 
 # Filter the output
 
 echo ""
 echo "Remove all lines for unique entries and those where hits = hits"
 echo ""
  
 grep -v unique $db.complete_release_joinerCheck.txt | \
 gawk '{ if (( $3 ~ /^hits/) && ( $4 != $6)) { print $0 }; \
 if ($3 !~ /hits/ ) { print $0 };}'