457dada7aa5bfd55505168c7c28eea47a2011e74
kuhn
  Thu Feb 28 12:55:15 2013 -0800
pulled a statement outside a loop so it only writes to the file once at the end
diff --git src/utils/qa/makeCytoBandIdeo.csh src/utils/qa/makeCytoBandIdeo.csh
index eb921d3..d0c4fea 100755
--- src/utils/qa/makeCytoBandIdeo.csh
+++ src/utils/qa/makeCytoBandIdeo.csh
@@ -65,32 +65,32 @@
     if ( $qStart != $qEnd ) then # no qArm if acrocentric (yes, it happens: see ornAna1 chrX2)
       echo $cenchrom $qStart $qEnd q gneg | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5}' \
         >> $db.splitChroms
     endif
   
     # split the centromere into halves for making triangles in ideogram
     set cen1start=$pEnd
     set   cen2end=$qStart
     @ censize = $cen2end - $cen1start
     @ cen1end = $cen1start + $censize / 2
     @ cen2start = $cen1end
     echo $cenchrom $cen1start $cen1end cen acen | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5}' \
       >> $db.splitChroms
     echo $cenchrom $cen2start $cen2end cen acen | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5}' \
       >> $db.splitChroms
-    cat $db.splitChroms > $db.cytoBand
   end
+  cat $db.splitChroms > $db.cytoBand
   # remove cen chroms from full list of chroms and format for cytoBandIdeo table
   cat $db.chroms | grep -w -v -f $db.cenNames | sort > $db.chromsNoCens
   cat $db.chromsNoCens | awk '{print $1"\t"0"\t"$2"\t""\t""gneg"}' >> $db.cytoBand
 else
   cat $db.chroms | awk '{print $1"\t"0"\t"$2"\t""\t""gneg"}' > $db.cytoBand
 endif
 bedSort $db.cytoBand $db.cytoBand
 
 hgLoadSqlTab $db cytoBandIdeo $sql $db.cytoBand
 if ( $status ) then
   set char=`hgsql -N -e "SELECT MAX(LENGTH(chrom)) FROM chromInfo" $db`
   echo
   echo "Load failed.  Possibly due to long chrom names."
   echo "Edit kent/src/hg/lib/cytoBandIdeo.sql to increase chrom KEY size:"
   grep  PRIMARY ~/kent/src/hg/lib/cytoBandIdeo.sql
