4b666b1c585cd29776c86cac527f26037b671383
steve
  Thu Aug 8 10:51:58 2013 -0700
Made changes suggested in code review to limit loading of .hg.conf.beta to a subshell (redmine #11481)
diff --git src/utils/qa/qaEnsGenes.csh src/utils/qa/qaEnsGenes.csh
index 342cbe5..af8e644 100755
--- src/utils/qa/qaEnsGenes.csh
+++ src/utils/qa/qaEnsGenes.csh
@@ -166,37 +166,36 @@
  else
   echo "$db is a scaffold assembly: skipping countPerChrom"
  endif
  echo
 
  echo "\n\n----------------------"
  echo "featureBits for new (dev) and old (beta) tables"
  echo "\nfeatureBits $db ensGene (on hgwdev):"
  featureBits $db ensGene
  echo "featureBits $db -countGaps ensGene (on hgwdev):"
  featureBits $db -countGaps ensGene
  echo "featureBits $db -countGaps ensGene gap (on hgwdev):"
  featureBits $db -countGaps ensGene gap
 
  if ( $db == $ensTrack ) then
-  setenv HGDB_CONF $HOME/.hg.conf.beta
   echo "\nfeatureBits $db ensGene (on hgwbeta):"
-  featureBits $db ensGene
+  (setenv HGDB_CONF $HOME/.hg.conf.beta; featureBits $db ensGene)
   echo "featureBits $db -countGaps ensGene (on hgwbeta):"
-  featureBits $db -countGaps ensGene
+  (setenv HGDB_CONF $HOME/.hg.conf.beta; featureBits $db -countGaps ensGene)
   echo "featureBits $db -countGaps ensGene gap (on hgwbeta):"
-  featureBits $db -countGaps ensGene gap
+  (setenv HGDB_CONF $HOME/.hg.conf.beta; featureBits $db -countGaps ensGene gap)
  endif
  echo
 
  echo "\n\n----------------------"
  echo "check that the ensGene track is sorted by chrom:"
  echo "positionalTblCheck -verbose=2 $db ensGene\n"
  positionalTblCheck -verbose=2 $db ensGene
  echo
 
  echo "\n\n----------------------"
  echo "run Joiner Check. look for errors in the following two lines only:"
  echo "ensPep.name and ensGtp.transcript"
  echo "\nrunning joinerCheck for $db on ensemblTranscriptId:"
  joinerCheck -keys -database=$db -identifier=ensemblTranscriptId ~/kent/src/hg/makeDb/schema/all.joiner
 
