[General_settings]
    tmpdir = '/home/jope/melon_all/tmp'
    project_name = 'melon_all'
    project_path = '/home/jope/melon_all'
    threads = True

[Other_settings]
    default_sanger_quality = 23
    java_memory = 16000
    picard_path = None
    gatk_path = None

[Cleaning]
    adaptors_file_454 = None
    adaptors_file_sanger = None
    adaptors_file_illumina = None
    short_adaptors_sanger = []
    short_adaptors_454 = []
    short_adaptors_illumina = []
    vector_database = 'UniVec'
    strip_n_percent = 2.0
    [[min_seq_length]]
        solid = 30
        sanger = 100
        454 = 100
        illumina = 30
    [[edge_removal]]
        454_left = None
        454_right = None
        sanger_left = None
        sanger_right = None
        illumina_left = None
        illumina_right = None
    [[lucy]]
        vector_settings = None
        window = [50, 0.080000000000000002, 10, 0.29999999999999999]
        bracket = [10, 0.02]
        error = [0.014999999999999999, 0.014999999999999999]

[Mira]
    job_options = ['denovo', 'est']
    general_settings = ['-AS:sd=1']
    454_settings = ['-LR:mxti=no', '-CO:rodirs=5', '-AL:mrs=80', '-OUT:sssip=0:stsip=0']
    sanger_settings = ['-AS:epoq=no', '-AS:bdq=30', '-CO:rodirs=5', '-AL:mrs=80', '-OUT:sssip=0:stsip=0']

[Mappers]
    mapper_for_solid = 'bwa'
    mapper_for_454 = 'gmap'
    mapper_for_illumina = 'bwa'
    mapper_for_sanger = 'gmap'

[Sam_processing]
    add_default_qualities = True

[Sam_stats]
    sampling_size = None

[Annotation]
    [[go_annotation]]
        blast_database = 'nr'
        java_memory = 2048
        create_dat_file = False
        blast2go_path = None
        b2g_properties_file = None
    [[ortholog_annotation]]
        ortholog_databases = []
    [[description_annotation]]
        description_databases = []
    [[Cdna_intron_annotation]]
        genomic_db = None
        genomic_seq_file = None
    [[orf_annotation]]
        estscan_matrix = 'path to estscan matrix'

[blast]
    # Add as much blast databases as you need. Here a example
    [[nr]]
        path = '/path/to/nr/database'
        species = 'all'
        subj_def_as_acc = None

[Snvs]
    min_quality = 70
    min_mapq = 15
    min_num_alleles = 2
    min_num_reads_for_allele = 3
    max_maf = None
    vcf_grouping = 'libraries'
    [[edge_removal]]
        454_left = None
        454_right = None
        sanger_left = None
        sanger_right = None
        illumina_left = None
        illumina_right = None
        solid_left = 4
        solid_right = 4

[snv_filters]
    [[filter1]]
        name = 'uniq_contiguous'
        use = False
        genomic_db = 'path to blast db'
        genomic_seqs_fpath = 'path to seqs file'
    [[filter2]]
        name = 'close_to_intron'
        use = False
        distance = 30
    [[filter3]]
        name = 'high_variable_region'
        use = False
        max_variability = 0.059999999999999998
        window = None
    [[filter4]]
        unique_name = 'close_to_snv_with_maf'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.95
    [[filter5]]
        name = 'close_to_limit'
        use = False
        distance = 60
    [[filter6]]
        name = 'maf'
        use = True
        frequency = 0.9
        group_kind = 'read_groups'
        groups = []
    [[filter7]]
        name = 'by_kind'
        use = True
        kind = 'SNP'
    [[filter8]]
        name = 'cap_enzyme'
        use = False
        all_enzymes = False
    [[filter9]]
        unique_name = 'is_variable_in_rg'
        name = 'is_variable'
        use = False
        group_kind = 'read_groups'
        groups = []
    [[filter10]]
        unique_name = 'is_variable_in_lb'
        name = 'is_variable'
        use = False
        group_kind = 'libraries'
        groups = []
    [[filter11]]
        unique_name = 'is_variable_in_sm'
        name = 'is_variable'
        use = False
        group_kind = 'samples'
        groups = []
    [[filter12]]
        name = 'ref_not_in_list'
        use = False
        list_path = 'path_to_file_with_list'
    [[filter13]]
        name = 'min_groups'
        use = False
        min_groups = 4
        group_kind = 'samples'
    [[filter14]]
        unique_name = 'is_variable_in_conomon'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon']
    [[filter15]]
        unique_name = 'is_variable_in_agrestis_acidulus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus']
    [[filter16]]
        unique_name = 'is_variable_in_agrestis_africanos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos']
    [[filter17]]
        unique_name = 'is_variable_in_cantalupo'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo']
    [[filter18]]
        unique_name = 'is_variable_in_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus']
    [[filter19]]
        unique_name = 'is_variable_in_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['melos']
    [[filter20]]
        unique_name = 'is_variable_in_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim']
    [[filter21]]
        unique_name = 'is_variable_in_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['t111']
    [[filter22]]
        unique_name = 'is_variable_in_conomon__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter23]]
        unique_name = 'is_variable_in_agrestis_acidulus__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus']
        maf = 0.7
        min_num_reads = 6
    [[filter24]]
        unique_name = 'is_variable_in_agrestis_africanos__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos']
        maf = 0.7
        min_num_reads = 6
    [[filter25]]
        unique_name = 'is_variable_in_cantalupo__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo']
        maf = 0.7
        min_num_reads = 6
    [[filter26]]
        unique_name = 'is_variable_in_inodorus__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus']
        maf = 0.7
        min_num_reads = 6
    [[filter27]]
        unique_name = 'is_variable_in_melos__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['melos']
        maf = 0.7
        min_num_reads = 6
    [[filter28]]
        unique_name = 'is_variable_in_momordica_dudaim__m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim']
        maf = 0.7
        min_num_reads = 6
    [[filter29]]
        unique_name = 'is_variable_in_t111_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['t111']
        maf = 0.7
        min_num_reads = 6
    [[filter30]]
        unique_name = 'is_not_variable_in_conomon'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon']
    [[filter31]]
        unique_name = 'is_not_variable_in_agrestis_acidulus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus']
    [[filter32]]
        unique_name = 'is_not_variable_in_agrestis_africanos'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos']
    [[filter33]]
        unique_name = 'is_not_variable_in_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo']
    [[filter34]]
        unique_name = 'is_not_variable_in_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus']
    [[filter35]]
        unique_name = 'is_not_variable_in_melos'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['melos']
    [[filter36]]
        unique_name = 'is_not_variable_in_momordica_dudaim'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim']
    [[filter37]]
        unique_name = 'is_not_variable_in_t111'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['t111']
    [[filter38]]
        unique_name = 'is_variable_between_conomon_and_agrestis_acidulus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'agrestis_acidulus']
        in_union = True
    [[filter39]]
        unique_name = 'is_variable_between_conomon_and_agrestis_africanos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'agrestis_africanos']
        in_union = True
    [[filter40]]
        unique_name = 'is_variable_between_conomon_and_cantalupo'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'cantalupo']
        in_union = True
    [[filter41]]
        unique_name = 'is_variable_between_conomon_and_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'inodorus']
        in_union = True
    [[filter42]]
        unique_name = 'is_variable_between_conomon_and_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'melos']
        in_union = True
    [[filter43]]
        unique_name = 'is_variable_between_conomon_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'momordica_dudaim']
        in_union = True
    [[filter44]]
        unique_name = 'is_variable_between_conomon_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 't111']
        in_union = True
    [[filter45]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_agrestis_africanos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'agrestis_africanos']
        in_union = True
    [[filter46]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_cantalupo'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo']
        in_union = True
    [[filter47]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'inodorus']
        in_union = True
    [[filter48]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'melos']
        in_union = True
    [[filter49]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'momordica_dudaim']
        in_union = True
    [[filter50]]
        unique_name = 'is_variable_between_agrestis_acidulus_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 't111']
        in_union = True
    [[filter51]]
        unique_name = 'is_variable_between_agrestis_africanos_and_cantalupo'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'cantalupo']
        in_union = True
    [[filter52]]
        unique_name = 'is_variable_between_agrestis_africanos_and_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'inodorus']
        in_union = True
    [[filter53]]
        unique_name = 'is_variable_between_agrestis_africanos_and_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'melos']
        in_union = True
    [[filter54]]
        unique_name = 'is_variable_between_agrestis_africanos_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'momordica_dudaim']
        in_union = True
    [[filter55]]
        unique_name = 'is_variable_between_agrestis_africanos_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 't111']
        in_union = True
    [[filter56]]
        unique_name = 'is_variable_between_cantalupo_and_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo', 'inodorus']
        in_union = True
    [[filter57]]
        unique_name = 'is_variable_between_cantalupo_and_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo', 'melos']
        in_union = True
    [[filter58]]
        unique_name = 'is_variable_between_cantalupo_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo', 'momordica_dudaim']
        in_union = True
    [[filter59]]
        unique_name = 'is_variable_between_cantalupo_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo', 't111']
        in_union = True
    [[filter60]]
        unique_name = 'is_variable_between_inodorus_and_melos'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus', 'melos']
        in_union = True
    [[filter61]]
        unique_name = 'is_variable_between_inodorus_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus', 'momordica_dudaim']
        in_union = True
    [[filter62]]
        unique_name = 'is_variable_between_inodorus_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['inodorus', 't111']
        in_union = True
    [[filter63]]
        unique_name = 'is_variable_between_melos_and_momordica_dudaim'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['melos', 'momordica_dudaim']
        in_union = True
    [[filter64]]
        unique_name = 'is_variable_between_melos_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['melos', 't111']
        in_union = True
    [[filter65]]
        unique_name = 'is_variable_between_momordica_dudaim_and_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 't111']
        in_union = True
    [[filter66]]
        unique_name = 'maf0.1'
        name = 'maf'
        use = True
        frequency = 0.1
        group_kind = 'read_groups'
        groups = []
    [[filter67]]
        name = 'in_segment_bed'
        use = True
        bed_fpath = '/home/jope/melon_all/config_data/exons.chado.bed'
        edge_avoidance = 60
    [[filter68]]
        unique_name = 'close_to_snv_without_maf'
        name = 'close_to_snv'
        use = True
        distance = 60
    [[filter69]]
        unique_name = 'close_to_snv_maf_0.96'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.96
    [[filter70]]
        unique_name = 'close_to_snv_maf_0.97'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.97
    [[filter71]]
        unique_name = 'close_to_snv_maf_0.98'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.98
    [[filter72]]
        unique_name = 'close_to_snv_maf_0.99'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.99
    [[filter73]]
        unique_name = 'is_not_variable_between_conomon_t111'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 't111']
        in_union = True
    [[filter74]]
        unique_name = 'is_not_variable_between_conomon_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'inodorus']
        in_union = True
    [[filter75]]
        unique_name = 'is_not_variable_between_conomon_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'cantalupo']
        in_union = True
    [[filter76]]
        unique_name = 'is_not_variable_between_agrestis_africanos_t111'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 't111']
        in_union = True
    [[filter77]]
        unique_name = 'is_not_variable_between_agrestis_africanos_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'inodorus']
        in_union = True
    [[filter78]]
        unique_name = 'is_not_variable_between_agrestis_africanos_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'cantalupo']
        in_union = True
    [[filter79]]
        unique_name = 'is_variable_between_africanos_conomon_t111'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 't111']
        in_union = True
    [[filter80]]
        unique_name = 'is_variable_between_africanos_conomon_inodorus'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 'inodorus']
        in_union = True
    [[filter81]]
        unique_name = 'is_variable_between_africanos_conomon_cantalupo'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 'cantalupo']
        in_union = True
    [[filter82]]
        unique_name = 'close_to_snv_maf_0.7'
        name = 'close_to_snv'
        use = True
        distance = 60
        maf = 0.7
    [[filter83]]
        unique_name = 'is_not_variable_in_africanos_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos']
        maf = 0.7
        min_num_reads = 6
    [[filter84]]
        unique_name = 'is_not_variable_in_conomon_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter85]]
        unique_name = 'is_not_variable_between_conomon_t111_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 't111']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter86]]
        unique_name = 'is_not_variable_between_conomon_inodorus_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'inodorus']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter87]]
        unique_name = 'is_not_variable_between_conomon_cantalupo_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['conomon', 'cantalupo']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter88]]
        unique_name = 'is_not_variable_between_agrestis_africanos_t111_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 't111']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter89]]
        unique_name = 'is_not_variable_between_agrestis_africanos_inodorus_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'inodorus']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter90]]
        unique_name = 'is_not_variable_between_agrestis_africanos_cantalupo_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'cantalupo']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter91]]
        unique_name = 'is_variable_between_africanos_conomon_t111_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 't111']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter92]]
        unique_name = 'is_variable_between_africanos_conomon_inodorus_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 'inodorus']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter93]]
        unique_name = 'is_variable_between_africanos_conomon_cantalupo_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon', 'cantalupo']
        in_union = True
        maf = 0.7
        min_num_reads = 6
    [[filter94]]
        unique_name = 'is_not_variable_between_africanos_and_conomon'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon']
    [[filter95]]
        unique_name = 'is_not_variable_between_africanos_and_conomon_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter96]]
        unique_name = 'is_not_variable_between_t111_and_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['t111', 'inodorus']
    [[filter97]]
        unique_name = 'is_not_variable_between_t111_and_inodorus_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['t111', 'inodorus']
        maf = 0.7
        min_num_reads = 6
    [[filter98]]
        unique_name = 'is_not_variable_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['cantalupo']
        maf = 0.7
        min_num_reads = 6
    [[filter99]]
        unique_name = 'is_not_variable_between_momordica_t111_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 't111', 'inodorus']
    [[filter100]]
        unique_name = 'is_not_variable_between_momordica_t111_inodorus_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 't111', 'inodorus']
        maf = 0.7
        min_num_reads = 6
    [[filter101]]
        unique_name = 'is_not_variable_between_momordica_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'cantalupo']
    [[filter102]]
        unique_name = 'is_not_variable_between_momordica_cantalupo_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'cantalupo']
        maf = 0.7
        min_num_reads = 6
    [[filter103]]
        unique_name = 'is_not_variable_between_acidulus_t111_inodorus'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 't111', 'inodorus']
    [[filter104]]
        unique_name = 'is_not_variable_between_acidulus_t111_inodorus_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 't111', 'inodorus']
        maf = 0.7
        min_num_reads = 6
    [[filter105]]
        unique_name = 'is_not_variable_between_acidulus_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo']
    [[filter106]]
        unique_name = 'is_not_variable_between_acidulus_cantalupo_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo']
        maf = 0.7
        min_num_reads = 6
    [[filter107]]
        unique_name = 'is_not_variable_between_acidulus_cantalupo'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo']
    [[filter108]]
        unique_name = 'is_not_variable_between_acidulus_cantalupo_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo']
        maf = 0.7
        min_num_reads = 6
    [[filter109]]
        unique_name = 'is_not_variable_between_momordica_africanos_conomon'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'agrestis_africanos', 'conomon']
    [[filter110]]
        unique_name = 'is_not_variable_between_momordica_africanos_conomon_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter111]]
        unique_name = 'is_not_variable_between_acidulus_africanos_conomon'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'agrestis_africanos', 'conomon']
    [[filter112]]
        unique_name = 'is_not_variable_between_acidulus_africanos_conomon_m&m'
        name = 'is_not_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter113]]
        unique_name = 'is_variable_between_momordica_t111_inodorus_africanos_conomon'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 't111', 'inodorus', 'agrestis_africanos', 'conomon']
    [[filter114]]
        unique_name = 'is_variable_between_momordica_t111_inodorus_africanos_conomon_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 't111', 'inodorus', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter115]]
        unique_name = 'is_variable_between_momordica_cantalupo_africanos_conomon'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'cantalupo', 'agrestis_africanos', 'conomon']
    [[filter116]]
        unique_name = 'is_variable_between_momordica_cantalupo_africanos_conomon_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['momordica_dudaim', 'cantalupo', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
     [[filter117]]
        unique_name = 'is_variable_between_acidulus_t111_inodorus_africanos_conomon'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 't111', 'inodorus', 'agrestis_africanos', 'conomon']
    [[filter118]]
        unique_name = 'is_variable_between_acidulus_t111_inodorus_africanos_conomon_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 't111', 'inodorus', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6
    [[filter119]]
        unique_name = 'is_variable_between_acidulus_cantalupo_africanos_conomon'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo', 'agrestis_africanos', 'conomon']
    [[filter120]]
        unique_name = 'is_variable_between_acidulus_cantalupo_africanos_conomon_m&m'
        name = 'is_variable'
        use = True
        group_kind = 'libraries'
        groups = ['agrestis_acidulus', 'cantalupo', 'agrestis_africanos', 'conomon']
        maf = 0.7
        min_num_reads = 6