view 01_RemoveSNPs/RemoveSNPs @ 5:67dc94f950fd draft default tip

Uploaded
author dktanwar
date Mon, 16 Oct 2017 13:52:09 -0400
parents 21aaaa2d3004
children
line wrap: on
line source

#!/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`