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#!/bin/bash
# run_histo.sh
# (c) 2012 - Ryan M. Layer
# Hall Laboratory
# Quinlan Laboratory
# Department of Computer Science
# Department of Biochemistry and Molecular Genetics
# Department of Public Health Sciences and Center for Public Health Genomics,
# University of Virginia
# rl6sf@virginia.edu
#
# Licenced under the GNU General Public License 2.0 license.
if [ -z $4 ]
then
echo "usage:$0 <bam file> <out file> <Z> <read lengh>"
exit
fi
INF=$1
OUTF=$2
CZ=$3
RL=$4
SCRIPT_DIR=`dirname $0`
OUT=`samtools view $INF\
| $SCRIPT_DIR/pairend_distro.pl \
-rl 150 \
-X $CZ \
-N 100000 \
-o $OUTF`
MEAN=`echo $OUT | cut -d" " -f1 | cut -d":" -f2`
STDEV=`echo $OUT | cut -d" " -f2 | cut -d":" -f2`
echo $MEAN
echo $STDEV
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