INNER CODE UNIT · Python

Bam2Pat

nloyfer/wgbs_tools · src/python/bam2pat.py:270

class Bam2Pat:
    def __init__(self, args, bam):
        self.args = args
        self.tmp_dir = None
        self.verbose = args.verbose
        self.out_dir = args.out_dir
        self.bam_path = bam
        self.gr = GenomicRegion(args)
        self.PE = None
        if not self.args.nanopore:
            if detect_nanopore(self.bam_path, self.gr.genome.genome_path):
                eprint('[wt bam2pat] Auto-detected modification-aware BAM — enabling --nanopore mode')
                self.args.nanopore = True
        self.start_threads()
        tmpdir_cleanup(self.tmp_dir)

    def set_lists(self):
        # black/white lists:

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