src/utils/qa/checkCoverage.csh 1.9

Index: src/utils/qa/checkCoverage.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/checkCoverage.csh,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/utils/qa/checkCoverage.csh	11 May 2009 05:29:21 -0000	1.8
+++ src/utils/qa/checkCoverage.csh	13 May 2009 01:38:46 -0000	1.9
@@ -1,163 +1,160 @@
 #!/bin/tcsh
 
 ####################
 #  09-20-07 Bob Kuhn
 #
 #  find all the places where data missing from a track.
 #
 ####################
 
 set db=""
 set table=""
 set limit=""
 set whereLimit=""
 set split=""
 set chr=""
 set chromList=""
 set start=""
 set end=""
 
 if ( $#argv < 2 || $#argv > 3 ) then
   echo
-  echo "  find all the places where data missing from a track."
+  echo "  find all non-gap places where data missing from a track."
   echo
   echo "      usage:  database table [chrom]"
   echo
   echo '      where "chrom" limits to single chrom'
   echo
   exit
 else
   set db=$argv[1]
   set table=$argv[2]
 endif
 
 if ( $#argv == 3 ) then
+  # limit to a chrom
   set limit='-chrom='$argv[3]
   set whereLimit='WHERE chrom = "'$argv[3]'"'
+  set chromList=${argv[3]}_
+else
+  set chromList=`hgsql -Ne "SELECT chrom FROM chromInfo" $db | sed -r "s/(.*)/\1_/"`
 endif
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n error: you must run this script on dev!\n"
  exit 1
 endif
 
 set split=`getSplit.csh $db $table`
 if ( $status ) then
   exit 1
 endif
 if ( $split != "unsplit" ) then
   set split=${split}_
 else 
   set split=""
 endif
 
 # echo "split /${split}/"
 # echo "splittable $split$table"
 
 # find the correct names for starts and ends
 set chr=`getChromFieldName.csh $db $split$table`
 if ( $status ) then
   echo "\n error.  not a positional table?  quitting.\n"
   exit 1
 endif
 
 # echo "chr $chr"
 # echo "split /${split}/"
 # echo "split_table ${split}$table"
 
 
 if ( $chr == "chrom" ) then
   set start=`hgsql -Ne "DESC $split$table" $db | awk '{print $1}' \
-    | egrep "txStart|chromStart" | head -1 | awk '{print $1}'`
+    | egrep "txStart|chromStart"`
   set end=`hgsql -Ne "DESC $split$table" $db | awk '{print $1}' \
-    | egrep "txEnd|chromEnd" | head -1 | awk '{print $1}'`
+    | egrep "txEnd|chromEnd"`
 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
 
 # make simple BED3 file from track with introns filled in
 rm -f blockBedFile.bed
 if ( $split != "" ) then
-  set chromList=`hgsql -Ne "SELECT chrom FROM chromInfo" $db | sed -r "s/(.*)/\1_/"`
-  if ( $limit != "" ) then
-    set chromList=$argv[3]
-  endif
   foreach chrom ( $chromList )
     hgsql -Ne "SELECT $chr, $start, $end FROM $chrom$table" $db >> blockBedFile.bed
   end
 else
   hgsql -Ne "SELECT $chr, $start, $end FROM $table $whereLimit" $db > blockBedFile.bed
 endif
 
 # echo $db
 # echo $table
 # echo $chr $start $end
 
 # make negative of track and of gap track
 featureBits $db blockBedFile.bed -not $limit -bed=$table.not.bed \
   >& /dev/null
 featureBits $db gap    -not $limit -bed=gap.not.bed \
   >& /dev/null
 
 # then intersect them
 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
 
 if ( -z $table.holes.bed ) then
   echo
   echo "there are no non-gap regions not covered by $table."
   echo "or there may be no gap table."
   echo
-  rm -f blockBedFile.bed
-  rm -f gap.not.bed
-  rm -f $table.not.bed
-  exit 0
-endif
-
-# 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:"
+else 
+  # 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" \
+  echo
+  echo "chrom chromStart chromEnd size" \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
-echo "----- ---------- -------- ----" \
+  echo "----- ---------- -------- ----" \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
-head -10 $table.holes.sort \
+  head -10 $table.holes.sort \
   | awk '{ printf("%13s %14s %14s %12s \n", $1, $2, $3, $4) }'
-echo
+  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 $table.holes.sort \
+  echo
+  # make links for three biggest
+  set url1="http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=$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 "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
+  end
+  echo
+endif
 
 # clean up
 rm -f blockBedFile.bed
 rm -f gap.not.bed
 rm -f $table.not.bed
+rm -f $table.holes.bed 
+rm -f $table.holes.sort
 
-exit
-
+exit 0