rule unpack_reference_for_octopus:
    input:
        fasta = config['reference']
    output:
        fasta = temp( "results/variants/tmp/reference.fa" ),
        fai = temp( "results/variants/tmp/reference.fa.fai" )
    shell: """
        gunzip -c {input.fasta} > {output.fasta}
        ~gav/Projects/Software/usr/bin/samtools faidx {output.fasta}
    """


rule call_variants_using_octopus:
    input:
        fasta = rules.unpack_reference_for_octopus.output.fasta,
        fai = rules.unpack_reference_for_octopus.output.fai,
        alignments = expand(
            "results/aligned/{name}.bam",
            name = [ sample['name'] for sample in config['samples']]
        )
    output:
        vcf = "results/variants/variants.vcf.gz",
        log = "logs/octopus.log"
    params:
        regions = [ "Pf3D7_02_v3:616190-656190", "Pf3D7_02_v3:779288-859288", "Pf3D7_11_v3:1023035-1081305" ]
    shell: """
        octopus -R {input.fasta} -I {input.alignments} -P 1 -o {output.vcf} --debug {output.log} --regions {params.regions}
    """

rule index_variants_vcf:
    input:
        vcf = rules.call_variants_using_octopus.output.vcf
    output:
        vcf = "results/aligned/variants.vcf.gz.tbi"
    shell: """
        tabix -p vcf {input.vcf}
    """