Function __init__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, filepath_or_object, mode="rb", max_cache=128, index_filename=None,
                 filename=None, check_header=False, check_sq=True, reference_filename=None,
                 filepath_index=None, require_index=False, duplicate_filehandle=None,
                 ignore_truncation=False):
        """Initialize the class.

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Function __init__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def __init__(self, _io):
        """Instantiating the read parser just needs access to the BGZF io.object

        Args:
            io (BgzfReader): parser for processing BGZF files

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Function mate has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def mate(self, AlignedSegment):
        """ Gets the mate to a given AlignedSegment.

        Note:
            Slow, when compared to the C-API. Not meant for high-throughput analysis.

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Function _range_popper has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def _range_popper(self, interval_start, interval_stop=None, front=True):
        """Simple pop method that accepts a range instead of a single value. Modifies the original bytearray by removing items

        Note:
            Pops from the front of the list by default. If `front` is set to `False`, it

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Function get_ref has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def get_ref(self, ref_id=None, idx=False):
        """Interatively unpacks all the bins, linear intervals, and chunks for a given reference

        A reference is comprised of 2 things: 1) a series of bins that reference chunks of aligned
        reads that are grouped within that bin. 2) a series of virtual offsets of the first read of a

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Function _init_index has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def _init_index(self):
        """Initialize the index file (BAI)"""

        if self._check_idx:
            # self._index = bamnostic.bai.Bai(self._index_path)

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Avoid deeply nested control flow statements.

Open

                        if len(split_field) > 2:
                            tag = split_field[0]
                            value = split_field[2]
                        else:
                            tag, value = split_field

Avoid deeply nested control flow statements.

Open

                    if seg_qual[index] >= base_qual_thresh:
                        yield base, start_pos
                else:

Function _cross_check_header_refs has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def _cross_check_header_refs(reads, header="", referencenames = None, referencelengths = None):
    """Modified code from Peter Cock's [BamWriter](https://github.com/peterjc/biopython/blob/SamBam2015/Bio/Sequencing/SamBam/__init__.py#L1714)
    """
    if not header:
        # If the reads argument is a SamIterator or BamIterator this works:

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Avoid deeply nested control flow statements.

Open

                        if start <= index < stop:
                            if base == 'A':
                                adenine[index - start if index-start > 0 else 0] += 1
                            elif base == 'G':
                                guanine[index - start if index-start > 0 else 0] += 1

Avoid deeply nested control flow statements.

Open

                    if qualities is not None:
                        if seg_qual[index] >= base_qual_thresh:
                            yield base, start_pos
                    else:
                        yield base, start_pos

Function get_ref has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def get_ref(self, ref_id=None, idx=False):
        """Iteratively unpacks all the bins, linear intervals, and chunks for a given reference

        A reference is comprised of 2 things: 1) a series of bins that reference chunks of aligned
        reads that are grouped within that bin. 2) a series of virtual offsets of the first read of a

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Function md_changes has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def md_changes(seq, md_tag):
    """Recreates the reference sequence of a given alignment to the extent that the
    MD tag can represent.

    Note:

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Function reg2bins has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def reg2bins(rbeg, rend):
    """Generates bin ids which overlap the specified region.

    Args:
        rbeg (int): inclusive beginning position of region

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Function update has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def update(self, others):
        """ Same as a regular `dict.update`, however, since pypy's `dict.update`
        doesn't go through `dict.__setitem__`, this is used to ensure it does

        Args:

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Function cigar_changes has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

def cigar_changes(seq, cigar):
    """Recreates the reference sequence to the extent that the CIGAR string can
        represent.

    Args:

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Avoid too many return statements within this function.

Open

                    return

Avoid too many return statements within this function.

Open

            return

Avoid too many return statements within this function.

Open

                return data

Avoid too many return statements within this function.

Open

                    return