src/utils/qa/runBits.csh 1.16

1.16 2009/05/21 01:28:08 rhead
Changed getChromlist.csh so that it does not create a file, just prints results. Changed all of the scripts that call it to redirect output to a unique file name, and then remove only that file at the end. Added onintr command that allow for cleanup of files created if scripts are ended prematurely.

Index: src/utils/qa/runBits.csh
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/qa/runBits.csh,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/utils/qa/runBits.csh	30 Apr 2009 20:43:02 -0000	1.15
+++ src/utils/qa/runBits.csh	21 May 2009 01:28:08 -0000	1.16
@@ -9,8 +9,9 @@
 #  Written by Bob Kuhn 
 # 
 ###############################################
 
+onintr cleanup
 
 set checkUnbridged="false"
 set db=""
 set chrom=""
@@ -79,9 +80,8 @@
 if ( -z $db.gapFile ) then
   # no overlap to gap.  clean up and quit
   echo
   rm -f $db.gapFile
-  rm -f $db.chromlist
   exit
 else
   set gapUrlFile[1]=$db.gapFile
   set comment[1]="There are gaps overlapping $track (gaps may be bridged or not):"
@@ -99,12 +99,10 @@
     hgsql $db -N -e "SELECT chrom, chromStart, chromEnd FROM gap \
      WHERE bridge = 'no'" > $db.unbridgedGap.bed
   else
     # gap is split.  go thru all chroms
-    if (! -e $db.chromlist ) then
-      getChromlist.csh $db > /dev/null
-    endif
-    foreach chrom (`cat $db.chromlist`)
+    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
@@ -139,11 +137,12 @@
     echo
   endif
 end
 
+cleanup:
 rm -f $db.unbridgedGap.bed
 rm -f $track.bed
-rm -f $db.chromlist
+rm -f $db.chromlist$$
 rm -f $db.gapFile
 rm -f $gapUrlFile[1]
 rm -f $gapUrlFile[2]