bamstats

#!/bin/env bash
set -e
helpstr="READLEN - get read length from the first read of a FASTQ file
Usage: readlen [OPTIONS] FILE

Options:
 -z: File is compressed using gzip; decompress before reading
 -h: Print this help message and exit."

unset file gzipped
while [[ $OPTIND -le $# ]]; do
    while getopts "zh" opt; do
        case "$opt" in
            z)
                gzipped=true
                ;;
            h)
                echo "$helpstr"
                exit
                ;;
            *)
                echo "Invalid argument:" $opt >&2
                echo "$helpstr"
                exit 1
        esac
    done
    if [[ -z "$file" ]]; then
        file=${@:$OPTIND:1}
        OPTIND=$(expr $OPTIND + 1)
    fi
done
shift $((OPTIND-1))

# Argument errors and warnings:
if [[ -z "$file" ]]; then
    >&2 echo "Error: Input file required."
    echo "$helpstr"
    exit 1
fi

############
## SCRIPT ##
############

bn=$(basename -f "$file")
prefix=${bn%%\.*} ## remove file extensions

samtools view -b "$file" > ${prefix}.bam
samtools sort ${prefix}.bam > ${prefix}.sorted.bam
samtools index ${prefix}.sorted.bam > ${prefix}.sorted.bai
samtools idxstats ${prefix}.sorted.bam > ${prefix}.idxstats.txt

exit