src/utils/qa/checkOffend.csh 1.12

Index: src/utils/qa/checkOffend.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkOffend.csh,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/utils/qa/checkOffend.csh	17 Apr 2009 18:48:20 -0000	1.11
+++ src/utils/qa/checkOffend.csh	5 Mar 2010 18:29:48 -0000	1.12
@@ -1,68 +1,69 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 ###############################################
 #  05-10-04
 # 
 #  Checks for table values off the end of chrom
 # 
 ###############################################
 
 set db=""
 set chr=""
 set track=""
 set end=""
 
 if ($#argv != 2) then
   echo
   echo "  checks for entries beyond the end of the chromsome."
   echo '    finds the proper column names if "chrom", "tName" or "genoName".'
   echo
   echo "    usage:  database table"
   echo
   exit
 else
   set db=$1
   set track=$2
 endif
 
 set chr=""
 set end=""
 
 set chr=`getChromFieldName.csh $db $track`
 if ($status) then
+  echo "\nERROR: not a chromosome-based table.\n"
   exit 1
 endif
 
 set end=`hgsql -N -e "DESC $track" $db | gawk '{print $1}' | egrep -w "chromEnd"`
 if ($status) then
   set end=`hgsql -N -e "DESC $track" $db | gawk '{print $1}' | egrep -w "tEnd"`
   if ($status) then
     set end=`hgsql -N -e "DESC $track" $db | gawk '{print $1}' | egrep -w "txEnd"`
     if ($status) then
       set end=`hgsql -N -e "DESC $track" $db | gawk '{print $1}' | egrep -w "genoEnd"`
       if ($status) then
         echo '\n  '$db.$track' has no "chromEnd", "tEnd", "txEnd" or "genoEnd" fields.\n'
          exit 1 
       endif
     endif 
   endif 
 endif 
 
 
 echo
 echo "Looking for off the end of each chrom"
 
 # Will also use the chromInfo table
 hgsql -e "SELECT chromInfo.chrom, chromInfo.size, MAX($track.$end) \
      FROM chromInfo, $track \
      WHERE chromInfo.chrom = $track.$chr \
      GROUP BY chromInfo.chrom" $db > $db.$track.tx.offEnd
 
 head -1 $db.$track.tx.offEnd
 awk '{if($2<$3) {print $1, $2, $3} }' $db.$track.tx.offEnd
 echo "expect blank. any chrom with annotations off the end would be printed."
 echo
 
 rm $db.$track.tx.offEnd