jpayne@69: #!__CSH_PATH -f
jpayne@69: #
jpayne@69: # Find exact tandem repeats in specified file involving an
jpayne@69: # exact duplicate of at least the specified length
jpayne@69: 
jpayne@69: set filename = $1
jpayne@69: set matchlen = $2
jpayne@69: 
jpayne@69: set bindir = __BIN_DIR
jpayne@69: set scriptdir = __SCRIPT_DIR
jpayne@69: 
jpayne@69: if  ($filename == '' || $matchlen == '')  then
jpayne@69:     echo "USAGE:  $0 <file> <min-match-len>"
jpayne@69:     exit -1
jpayne@69: endif
jpayne@69: 
jpayne@69: echo "Finding matches"
jpayne@69: $bindir/repeat-match -t -n $matchlen $filename | tail +3 > $$.tmp.matches
jpayne@69: if  ($status != 0)  exit -1
jpayne@69: 
jpayne@69: echo "Tandem repeats"
jpayne@69: sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk
jpayne@69: rm -f $$.tmp.matches