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#!/bin/bash

#if [ "$1" == "-h" ]; then
if [[ -z $1 || -z $2 || $1 == "-h" ]]; then
    echo "This program will remove mismatches from sam file."
    echo "Usage: `basename $0` test.sam 3"
    exit 0
fi

cmd="echo perl -ne 'print if((/XM:i:[0-$2][^0-9]/) || (/^@/));' $1"
eval `$cmd`