4a2e4209dd33c8e627c179264b266ca25a76a4fa
mspeir
  Wed Sep 28 13:06:04 2016 -0700
Adding alts to list of things we ignore in histogram mode, refs #17987

diff --git src/utils/qa/countPerChrom.csh src/utils/qa/countPerChrom.csh
index 2491d84..2eb665d 100755
--- src/utils/qa/countPerChrom.csh
+++ src/utils/qa/countPerChrom.csh
@@ -152,31 +152,31 @@
   if ( $split != "" ) then
     set table="${c}_$table"
   endif
   set new=`nice hgsql -N -e 'SELECT COUNT(*) FROM '$table' \
      WHERE '$chrom' = "'$c'"' $db`
   if ( $machineOut != "" ) then
     set old=`nice $host2 -Ne 'SELECT COUNT(*) FROM '$table' \
       WHERE '$chrom' = "'$c'"' $oldDb`
   endif 
   # output
   echo "$c\t$new\t$old" >> Xout$$
   set table=$argv[2]
 end
 
 if ( $histo == "true" ) then
-  cat Xout$$ | grep chr | egrep -v "random|hap|Un|$db" | sed "s/chr//" \
+  cat Xout$$ | grep chr | egrep -v "random|hap|Un|alt|$db" | sed "s/chr//" \
     | sort -n -k1,1  > XgraphFile0$$
   set max1=`cat XgraphFile0$$ | awk '{print $2}' | sort -n | tail -1`
   set max=$max1
   if ( $machineOut != "" ) then
     # get max values for 2nd dataset for scaling purposes
     set max2=`cat XgraphFile0$$ | awk '{print $3}' | sort -n | tail -1`
     if ( $max1 > $max2 ) then
       # shrink second histogram proportionately
       set histosize2=`echo $max1 $max2 $histosize | awk '{printf("%2d", $2/$1*$3)}'`
       set max=$max1
     else
       # shrink first histogram proportionately
       set histosize1=`echo $max1 $max2 $histosize | awk '{printf("%2d", $1/$2*$3)}'`
       set max=$max2
     endif