labels.py 文件源码

def bam_to_alignments(truth_bam, ref_name, start=None, end=None):
        """Create list of TruthAlignment objects from a bam of Truth aligned to ref.

        :param truth_bam: (sorted indexed) bam with true sequence aligned to reference
        :param ref: name of reference to process
        :param start: starting position within reference
        :param end: ending position within reference
            (all alignments with any overlap with the interval start:end will be retrieved)
        :returns: tuple(positions, encoded_label_array)

            - positions: numpy structured array with 'ref_major'
              (reference position index) and 'ref_minor'
              (trailing insertion index) fields.

            - feature_array: 1D numpy array of encoded labels
        """
        with pysam.AlignmentFile(truth_bam, 'rb') as bamfile:
            aln_reads = bamfile.fetch(reference=ref_name, start=start, end=end)
            alignments = [TruthAlignment(r) for r in aln_reads if not (r.is_unmapped or r.is_secondary)]
            alignments.sort(key=attrgetter('start'))
        return alignments