Bash script to convert all SAM files found in a directory to BAM. Directory is passed as positional command line argument.

sam2bam

#!/usr/bin/env bash

for i in $(ls $1); do
    filename_prefix="${i%.*}"
    filename_extension="${i##*.}"
    if [ "$filename_extension" == "sam" ]; then
        samtools view -bs $i > $filename_prefix.bam
        samtools sort $filename_prefix.bam -o $2
        samtools index $2 $2.index
        rm $filename_prefix.bam
    fi;
done;