import sys

# simple script to print QC results

infile = sys.argv[1]

flagin = 0
flagout = 0
with open(infile) as f:
    r1 = []
    r2 = []
    for line in f:
        bits = line.split(' ')
        for bit in bits:
            if bit.find("in1=") == 0 and len(r1) == 0:
                r1.append(bit)
                print(bit)
            elif bit.find("in2=") == 0 and len(r2) == 0:
                r2.append(bit)
                print(bit)
            elif bit.find("Input:") == 0:
                print(line)
                flagin = 1
                data = []
            elif bit.find('Result:') == 0 and flagin == 1:
                flagin = 0
                r1 = []
                r2 = []
                print("".join(data) + "\n------\n")
                data = []
            elif flagin == 1:
                data.append(bit)
            else:
                pass

shell:
    """
    rm -f genome/genome.*
    rm -f logs/*
    rm -f bams/*
    rm -f clean_reads/*gz
    rm -f vcf/*
    """

    shell:
        "mkdir -p "+' '.join(DIRS)

rule get_genome:
    output:
        "genome/genome.fa"

shell:
    """
    wget {params.genome} -O {output}.gz -o {log}
    gunzip {output}.gz
    """

shell:
    "samtools sort -o {output} {input}"

shell:
    """
    samtools flagstat {input} > {output.aln}
    echo alignment report for sample {output.aln}
    grep 'mapped' {output.aln}
    python scripts/report_qc.py logs/read_qc.log | tee logs/qc_report.txt
    """

shell:
    "bgzip {input}"

shell:
    "vcf-merge vcf/*gz > {output}"