c462c04a3e2cbc628841222f9edcdda4b787f930
chmalee
  Mon Aug 27 15:00:03 2018 -0700
getMatrixLines was searching for 'blastz' specifically, which fails since now our READMEs mention lastz instead, refs #20979

diff --git src/utils/qa/getMatrixLines.csh src/utils/qa/getMatrixLines.csh
index b30b525..cc86201 100755
--- src/utils/qa/getMatrixLines.csh
+++ src/utils/qa/getMatrixLines.csh
@@ -1,82 +1,82 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 
 ###############################################
 # 
 #  10-23-2007
 #  Gets the two lines needed for chain blocks in trackDb.ra files.
 #  Written by Ann Zweig
 # 
 ###############################################
 
 
 set db1=""
 set db2=""
 set out1=""
 set out2=""
 set matrix=""
 
 if ( $#argv != 2 ) then
   echo
   echo '  Searches the README.txt files to find the correct parameters for the '
   echo '  $matrix variable.  This is the q-parameter from the blastz run. '
   echo
   echo '    usage:  fromDb toDb (these can be in either order)'
   echo
   exit
 else
   set db1=$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 -sA7 "The blastz scoring" /data/apache/htdocs-hgdownload/goldenPath/$db1/vs$Db2/README.txt \
+set out1=`grep -sA7 "The [b]*lastz scoring" /data/apache/htdocs-hgdownload/goldenPath/$db1/vs$Db2/README.txt \
   | tail -6`
-set out2=`grep -sA7 "The blastz scoring" /data/apache/htdocs-hgdownload/goldenPath/$db2/vs$Db1/README.txt \
+set out2=`grep -sA7 "The [b]*lastz scoring" /data/apache/htdocs-hgdownload/goldenPath/$db2/vs$Db1/README.txt \
   | tail -6`
 
 if ( "$out1" != "") then
   set matrix="$out1"
 else 
   if ( "$out2" != "") then
     set matrix="$out2"
   else
     echo ' \nERROR: cannot find a $matrix variable for this pair\n'
     exit 1
   endif
 endif
 
 # strip any white space from start and end of line
 set matrix=`echo $matrix | sed -e "s/^\s+//"`
 set matrix=`echo $matrix | sed -e "s/\z//"`
 
 if ( "$matrix" != "" ) then
   # line1 is for the 'matrixHeader' line
   
   # remove everything after the "A C G T"
   set line1=`echo $matrix | sed -e "s/.A.*//"`
   
   # Add the word 'matrixHeader' to the start of the line, and commas after that
   set line1=`echo $line1 | sed -e "s/ /, /g" | sed -e "s/^/matrixHeader /"`
   echo "\n$line1"
 
   # line2 is for the 'matrix 16' line
   # remove the "A C G T A"
   set line2=`echo $matrix | sed -e "s/A C G T A //"`
 
   # remove all of the interspersed letters
   set line2=`echo $line2 | sed -e "s/[CGT]//g"`
 
   # add the words 'matrix 16' to the start of the line, and commas after that
   set line2=`echo $line2 | sed -e "s/ /,/g" | sed -e "s/^/matrix 16 /"`
   echo "$line2\n"
 endif
 exit