adding bam to text script, adjusting stats

#!/bin/bash

# Converts bam file to merged_nodups.txt file

# Calls samtools to filter duplicates then 

# chimeric_blacklist to associate read pair group

# Then assigns fragment and sorts

# Sorting should be optional

# Usage: bamtotxt.sh <bam_file> <site_file> <output_file> [sort]

set -e

if [ $# -lt 3 ] || [ $# -gt 4 ]

then

    echo "Usage: $0 <bam_file> <site_file> <output_file> [sort]"

    exit 1

else

    bamfile=$1

    sitefile=$2 

    outputfile=$3

fi

if [ $# -eq 4 ]

then

    sort=1

fi

samtools view -F 1024 "$bamfile" | awk -v fname=$bamfile -f "$( dirname "${BASH_SOURCE[0]}" )"/chimeric_blacklist.awk

"$( dirname "${BASH_SOURCE[0]}" )"/fragment.pl "${bamfile}_norm.txt" "${bamfile}.frag.txt" "$sitefile"

if [ -n $sort ]

then

    sort -k2,2d -k6,6d -k4,4n -k8,8n -k1,1n -k5,5n -k3,3n "${bamfile}.frag.txt" > "$outputfile"

else

    mv "${bamfile}.frag.txt" "$outputfile"

fi

rm "${bamfile}_norm.txt" "${bamfile}.frag.txt"