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] = []
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