changeWidthOfBedWRTPeak.sh

#!/bin/bash

:<<'COMMENT'



Copyright 2010 Wu Albert Cheng <albertwcheng@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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THE SOFTWARE.

COMMENT

if [ $# -lt 5 ]; then
	echo $0 filename centerCol plus minus ofilename
	exit
fi

filename=$1
centerCol=$2
plus=$3
minus=$4
ofilename=$5

awk -v FS="\t" -v OFS="\t" -v centerCol=$centerCol -v plus=$plus -v minus=$minus '{center=$centerCol; newStart=center-minus; newEnd=center+plus+1; $2=newStart; $3=newEnd; print;}' $filename > $ofilename