src/utils/qa/getChainLines.csh 1.2

Index: src/utils/qa/getChainLines.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/getChainLines.csh,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/qa/getChainLines.csh	23 Sep 2009 17:55:29 -0000	1.1
+++ src/utils/qa/getChainLines.csh	23 Sep 2009 18:01:57 -0000	1.2
@@ -1,72 +1,72 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 
 ###############################################
 # 
 #  09-23-2009
 #  Gets the two variables needed for chain blocks in trackDb.ra files.
 #  Written by Ann Zweig
 # 
 ###############################################
 
 
 set db1=""
 set db2=""
 set out1=""
 set out2=""
 set chainMinScore=""
 set chainLinearGap=""
 set fullLine=""
 
 if ( $#argv != 2 ) then
   echo
   echo '  Searches the documentation to find the correct parameters for the '
   echo '  $chainMinScore and $chainLinearGap variables. ' 
   echo
   echo '    usage:  fromDb toDb (these can be in either order)'
   echo
   exit
 else
   set db1=$argv[1]
   set db2=$argv[2]
 endif
 
 if ( "$HOST" != "hgwdev" ) then
   echo "\n ERROR: you must run this script on dev!\n"
   exit 1
 endif
 
 set Db1=`echo $db1 | perl -wpe '$_ = ucfirst($_)'`
 set Db2=`echo $db2 | perl -wpe '$_ = ucfirst($_)'`
 
 set out1=`grep -s "Chain minimum score" /data/apache/htdocs/goldenPath/$db1/vs$Db2/README.txt`
 set out2=`grep -s "Chain minimum score" /data/apache/htdocs/goldenPath/$db2/vs$Db1/README.txt`
 
 if ( "$out1" != "") then
   set fullLine="$out1"
 else 
   if ( "$out2" != "") then
     set fullLine="$out2"
   else
     echo ' \nERROR: cannot find either $chain variable for this pair\n'
     exit 1
   endif
 endif
 
 # strip any white space from start and end of line
 set fullLine=`echo $fullLine | sed -e "s/^\s+//"`
 set fullLine=`echo $fullLine | sed -e "s/\z//"`
 
 if ( "$fullLine" != "" ) then
   # extract the chainMinScore value
   set minScore=`echo $fullLine | sed -e "s/Chain minimum score: //" \
   | awk '{print $1}' | sed -e "s/,//"`
-  echo '$chainMinScore '$minScore
+  echo "chainMinScore $minScore"
   
   # extract the chainLinearGap method
   set linearGap=`echo $fullLine | awk '{print $9}' | sed "s/://" \
   | sed "s/(//" | sed "s/)//"`
-  echo '$chainLinearGap '$linearGap
+  echo "chainLinearGap $linearGap"
 
 exit