sam.py 文件源码

def __init__(self, bins, mapq_thresh=30, clip_thresh=1):
        # set parameters
        self.bins = bins
        self.mapQT = mapq_thresh
        self.clip_thresh = clip_thresh

        # initialise data structures
        self.depth_stats = DepthStats(bins, mapq_thresh=mapq_thresh, dtype=np.intc)
        self.aln_stats = np.zeros((bins.num, len(AlignStats.aln_stats_cols)), dtype=np.intc)
        self.fwd_inserts = np.empty(bins.num, dtype=list)
        self.rvs_inserts = np.empty(bins.num, dtype=list)
        for j in range(0, bins.num):
            self.fwd_inserts[j] = []
            self.rvs_inserts[j] = []