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