phasing.py 文件源码

def __init__(self, ploidy: int, copy_from: 'HaplotypeSet'=None):
        self.ploidy = ploidy

        # Nodes spelling each haplotype
        self.haplotypes = []  # type: List[List[Node]]

        # Also keep a set of reads used for each haplotype, useful for
        # relative likelihood calculation
        self.read_sets = []  # type: List[Set[OrientedRead]]

        if isinstance(copy_from, HaplotypeSet):
            for i in range(ploidy):
                self.haplotypes.append(deque(copy_from.haplotypes[i]))
                self.read_sets.append(set(copy_from.read_sets[i]))
        else:
            for i in range(ploidy):
                self.haplotypes.append(deque())
                self.read_sets.append(set())

        self.log_rl = float('-inf')
        self.from_large_bubble = False