def create_sa_sample_args(fofns=[], fast5_dirs=[], positions_file=None, motifs=None, alignment_file=None,
                          bwa_reference=None, fw_reference=None, bw_reference=None, name=None,
                          number_of_kmer_assignments=10, probability_threshold=0.8, kmers_from_reference=False,
                          quality_threshold=7, recursive=False, workers=4, assignments_dir=None, readdb=None,
                          ambig_model=None):
    """Create sample arguments for SignalAlignSample. Parameters are explained in SignalAlignmentSample"""
    sample_args = {
        "fofns": fofns,
        "fast5_dirs": fast5_dirs,
        "positions_file": positions_file,
        "motifs": motifs,
        "bwa_reference": bwa_reference,
        "fw_reference": fw_reference,
        "bw_reference": bw_reference,
        "name": name,
        "number_of_kmer_assignments": number_of_kmer_assignments,
        "probability_threshold": probability_threshold,
        "kmers_from_reference": kmers_from_reference,
        'alignment_file': alignment_file,
        'quality_threshold': quality_threshold,
        'recursive': recursive,
        'workers': workers,
        "assignments_dir": assignments_dir,
        "readdb": readdb,
        "ambig_model": ambig_model
    }
    return sample_args