src/utils/qa/checkCoverage.csh 1.6

Index: src/utils/qa/checkCoverage.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkCoverage.csh,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/utils/qa/checkCoverage.csh	30 Oct 2007 17:22:32 -0000	1.5
+++ src/utils/qa/checkCoverage.csh	11 Apr 2009 00:37:01 -0000	1.6
@@ -1,118 +1,119 @@
 #!/bin/tcsh
+source `which qaConfig.csh`
 
 ####################
 #  09-20-07 Bob Kuhn
 #
 #  find all the places where data missing from a track.
 #
 ####################
 
 set db=""
 set table=""
 set limit=""
 set chr=""
 set start=""
 set send=""
 
 if ($#argv < 2 || $#argv > 3 ) then
   echo
   echo "  find all the places where data missing from a track."
   echo
   echo "      usage:  database table [chrom]"
   echo
   echo '      where "chrom" limits to single chrom'
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
 endif
 
 if ($#argv == 3 ) then
   set limit='-chrom='$argv[3]
 endif
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 # find the correct names for starts and ends
 set chr=`getChromFieldName.csh $db $table`
 if ( $status ) then
   echo "\n error.  Quitting.\n"
   exit 1
 endif
 if ( $chr == "chrom" ) then
   set start=`hgsql -Ne "DESC $table" $db | awk '{print $1}' \
     | egrep "txStart|chromStart" | head -1 | awk '{print $1}'`
   set end=`hgsql -Ne "DESC $table" $db | awk '{print $1}' \
     | egrep "txEnd|chromEnd" | head -1 | awk '{print $1}'`
 else 
   if ( $chr == "tName" ) then
     set start="tStart"
     set end="tEnd"
   else 
     if ( $chr == "genoName" ) then
       set start="genoStart"
       set end="genoEnd"
     endif
   endif
 endif
 
 # echo $db
 # echo $table
 # echo $chr $start $end
 
 # make bed file of large blocks, ignoring intron/exons
 hgsql -Ne "SELECT $chr, $start, $end FROM $table" $db > blockBedFile.bed
 
 # make negative of table (block file) as bed file
 # and make negative of gap track
 # then intersect them
 featureBits $db blockBedFile.bed -not $limit -bed=$table.not.bed \
   >& /dev/null
 featureBits $db gap    -not $limit -bed=gap.not.bed \
   >& /dev/null
 featureBits $db $table.not.bed gap.not.bed $limit \
   -bed=$table.holes.bed >& /dev/null
 # save coords and size and sort for biggest
 cat $table.holes.bed | awk '{print $1, $2, $3, $3-$2}' | sort -k4,4nr \
   > $table.holes.sort
 
 # report
 echo
 echo "non-gap holes in track are in this file: "
 echo "    $table.holes.bed"
 echo
 echo "largest missing non-gap regions are here:"
 
 echo
 echo "chrom chromStart chromEnd size" \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
 echo "----- ---------- -------- ----" \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
 head -20 $table.holes.sort \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
 echo
 
 echo
 # make links for three biggest
 set url1="http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=$db&position="
 set url2="&$table=pack&gap=dense"
 set bigThree=`head -3 $table.holes.sort \
   | awk '{print $1 ":" $2-300 "-" $3+300}'` 
 echo "links to the three biggest voids in ${table}:"
 echo " (with 300 bp padding on each end)"
 foreach item ( $bigThree )
   echo "$url1$item$url2"
 end
 echo
 
 # clean up
 rm -f blockBedFile.bed
 rm -f gap.not.bed
 rm -f $table.not.bed
 
 exit