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def __init__(
self, output_fo, tree_index, kmer_lca=False, tie_lca=False, annotate=False, mask_unmatched_bases=False
):
self.output_fo = output_fo
self.tree_index = tree_index
self.k = self.tree_index.k
self.kmer_lca = kmer_lca
self.annotate = annotate
self.tie_lca = tie_lca
self.mask_unmatched_bases = mask_unmatched_bases
self.krakline_parser = KraklineParser()
self.hitmasks_dict = {}
self.covmasks_dict = {}
self.ass_dict = {}
self.max_nodenames = []
self.max_val = 0
def __init__(self, output_fo, tree_index, kmer_lca=False, tie_lca=False, annotate=False):
self.output_fo = output_fo
self.tree_index = tree_index
self.k = self.tree_index.k
self.kmer_lca = kmer_lca
self.annotate = annotate
self.tie_lca = tie_lca
self.krakline_parser = KraklineParser()
self.hitmasks_dict = {}
self.covmasks_dict = {}
self.ass_dict = {}
self.max_nodenames = []
self.max_val = 0