src/utils/qa/runBits.csh 1.17

Index: src/utils/qa/runBits.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/runBits.csh,v
retrieving revision 1.16
retrieving revision 1.17
diff -b -B -U 1000000 -r1.16 -r1.17
--- src/utils/qa/runBits.csh	21 May 2009 01:28:08 -0000	1.16
+++ src/utils/qa/runBits.csh	22 May 2009 18:45:20 -0000	1.17
@@ -1,148 +1,156 @@
 #!/bin/tcsh
 source `which qaConfig.csh`
 
 
 ###############################################
 # 
 #  05-11-07 
 #  Small module that runs featureBits and checks for overlap with gaps [incl unbridged]
 #  Written by Bob Kuhn 
 # 
 ###############################################
 
 onintr cleanup
 
 set checkUnbridged="false"
 set db=""
 set chrom=""
 set split=""
 set track=""
 set gapUrlFile=( "" "" )
 set comment=( "" "" )
 set url1=""
 set url3=""
 
 if ( $#argv < 2 |  $#argv > 3 |  ) then
   # no command line args
   echo
   echo "  runs featureBits and checks for overlap with gaps."
   echo
   echo "    usage:  database trackname [checkUnbridged]"
   echo "              where overlap with unbridged gaps can be turned on"
   echo
   exit
 else
   set db=$argv[1]
   set track=`echo $argv[2] | sed -e "s/chr.*_//"`
 endif
 
 if ( "$HOST" != "hgwdev" ) then
  echo "\n  error: you must run this script on dev!\n"
  exit 1
 endif
 
 if ( $#argv == 3 ) then
   if ( $argv[3] == "checkUnbridged" ) then
     set checkUnbridged="true"
   else
     echo
     echo 'third argument must be "checkUnbridged"'
     echo
     echo $0
     $0
     exit 1
   endif
 endif
 
 set split=`getSplit.csh $db gap hgwdev` 
 
+#check to see if track can pack.
+if ( 1 == `hgsql -Ne 'SELECT canPack FROM trackDb \
+     WHERE tableName = "'$track'"' $db` ) then
+  set pack=pack
+else
+  set pack=full
+endif
+
 #set up urls
 set url1="http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=$db"
-set url3="&$track=pack&gap=pack"
+set url3="&$track=$pack&gap=pack"
 
 # ------------------------------------------------
 # featureBits
 
 echo
 echo "featureBits -countGaps $db $track"
 featureBits -countGaps $db $track
 
 if ($status) then
   echo "failed. quitting"
   echo
   exit
 endif
 
 echo "featureBits -countGaps $db $track gap"
 featureBits -countGaps $db $track gap -bed=$db.gapFile
 echo
 
 if ( -z $db.gapFile ) then
   # no overlap to gap.  clean up and quit
   echo
   rm -f $db.gapFile
   exit
 else
   set gapUrlFile[1]=$db.gapFile
   set comment[1]="There are gaps overlapping $track (gaps may be bridged or not):"
 endif
 
 
 if ( $checkUnbridged == "true" ) then
   echo "checking for annotations spanning unbridged gaps."
   # note: this means that the annotation need not intersect, 
   #   introns spanning the gap are flagged
   rm -f $db.unbridgedGap.bed
   # create file of unbridged gaps
   if ( $split == "unsplit" ) then
     # gap is not split
     hgsql $db -N -e "SELECT chrom, chromStart, chromEnd FROM gap \
      WHERE bridge = 'no'" > $db.unbridgedGap.bed
   else
     # gap is split.  go thru all chroms
     getChromlist.csh $db > $db.chromlist$$
     foreach chrom (`cat $db.chromlist$$`)
       hgsql $db -N -e "SELECT chrom, chromStart, chromEnd FROM ${chrom}_gap \
        WHERE bridge = 'no'" >> $db.unbridgedGap.bed
     end
   endif
   # check for intersection of track and gap
   # make a file with introns filled in
   makeFilledBlockBed.csh $db $track $track.bed
   rm -f $db.$track.unbridged.gaps
   featureBits $db $track.bed $db.unbridgedGap.bed -bed=$db.$track.unbridged.gaps
   echo
   set gapUrlFile[2]=$db.$track.unbridged.gaps
   set comment[2]="total number of unbridged gaps:"
 endif
 
 # print three records, either from gap overlap or unbridged gap overlap.
 foreach n ( 1 2 )
   if ( ! -e "$gapUrlFile[$n]" ) then
     continue
   else
     # print 3 records as links with 300 bp padding 
     echo $comment[$n]
     wc -l  $gapUrlFile[$n]
     echo
     # set number to print: 3 or less
     set num=`wc -l  $gapUrlFile[$n] | awk '{print $1}'`
     set j=`echo "3 $num" | sed "s/ /\n/g" | sort -n | head -1`
     while ( $j )
       set pos=`sed -n -e "${j}p"  $gapUrlFile[$n] \
         | awk '{print $1":"$2-300"-"$3+300}'`
       echo "$url1&position=$pos$url3"
       set j=`echo $j | awk '{print $1-1}'`
     end
     echo
   endif
 end
 
 cleanup:
 rm -f $db.unbridgedGap.bed
 rm -f $track.bed
 rm -f $db.chromlist$$
 rm -f $db.gapFile
 rm -f $gapUrlFile[1]
 rm -f $gapUrlFile[2]