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|
#!/bin/sh -e
#
# Copyright (c) 2005-2006 Gordon Gremme <gordon@gremme.org>
# Copyright (c) 2005-2006 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
range=
force=
verbose=
gzip=
bzip2=
range_value=5;
usage() {
echo "Usage: $0 [-r range] [-f] [-v] [-g | -b] intermediate_files" >&2
exit 1
}
while getopts fvgbr: name
do
case $name in
r) range=1
range_value="$OPTARG";;
f) force=1;;
v) verbose=1;;
g) gzip=1;;
b) bzip2=1;;
?) usage;;
esac
done
range_opt=
force_opt=
verbose_opt=
gzip_opt=
bzip2_opt=
if [ -n "$force" ]
then
force_opt="-force"
fi
if [ -n "$range" ]
then
range_opt="-range $range_value"
fi
if [ -n "$verbose" ]
then
verbose_opt="-v"
fi
if [ -n "$gzip" ]
then
gzip_opt="-gzip"
fi
if [ -n "$bzip2" ]
then
bzip2_opt="-bzip2"
fi
shift $(($OPTIND - 1))
if [ $# -eq 0 ]
then
usage
fi
if [ -n "$verbose" ]
then
echo '$ split according to alignment score'
fi
gthsplit -alignmentscore $range_opt $force_opt $verbose_opt $gzip_opt $bzip2_opt $*
if [ -n "$verbose" ]
then
echo '$ split according to coverage'
fi
for filenamebase in $*
do
upperrange=100
lowerrange=`expr 100 - $range_value`
while [ $lowerrange -ge 0 ]
do
filename="$filenamebase.scr$lowerrange-$upperrange"
if [ -r "$filename" ]
then
gthsplit -coverage $range_opt $force_opt $verbose_opt $gzip_opt $bzip2_opt $filename
rm -f $filename
if [ -n "$verbose" ]
then
echo "\$ split file removed: $filename"
fi
fi
upperrange=$lowerrange
lowerrange=`expr $lowerrange - $range_value` || true
done
shift
done
|
