shell.prefix('set -x;')

include: 'common.snakemake'

with open(data_dir + '/bam_files.txt', 'r') as f:

    bam_files = dict(line.strip().split('\t') for line in f)

rule all:

    input:

        fasta=expand('{output_dir}/unmapped/{sample_id}/clean.fa.gz',

            output_dir=output_dir, sample_id=sample_ids)

rule bam_to_fasta:

    input:

        bam=lambda wildcards: bam_files[wildcards.sample_id]

    output:

        fasta='{output_dir}/unmapped/{sample_id}/clean.fa.gz'

    params:

        flags=2816

    shell:

        '''samtools fastq -F {params.flags} {input.bam} \

        | fastq_to_fasta -r -z -o {output}

        '''