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# sra-toolkit can be installed into different path on different platforms
bin_prefetch=$(which prefetch)
bin_sam-dump=$(which sam-dump)

output_dir="../data"

accessions="SRR3879778 SRR3879779 SRR3879780 SRR4244377 SRR4244378 SRR4244385"

base_url="https://s3.us-east-2.amazonaws.com/nudlerlab/rpoS/"


    

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# This will output replicate .bam files as one combined file

for accession in $accessions
do
    $bin_prefetch $accession
    $bin_sam-dump -u $sra_dir/$accession \
        | samtools view -bhS - > $output_dir/$accession
done


    

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# This ill download original untouched .bam files we received 
# from the sequencing facility

files=$(cat ../data/datafiles.txt | cut -f11 -d' ' | grep bam)

for f in $files
do
    wget $base_url/$f -P $output_dir
done