jpayne@69: #! -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 = $2
jpayne@69: 
jpayne@69: set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
jpayne@69: set scriptdir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts
jpayne@69: 
jpayne@69: if  ($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