Unverified Commit 7229cf0b authored by Wolfgang Maier's avatar Wolfgang Maier Committed by mvdbeek
Browse files

Improve display chunk generation for BAMs 

The new version is faster even for lines containing multiple tabs and
optimizes the no or one tag cases.
It also fixes a subtle bug that would drop a line at chunk boundaries.
parent 85df98a7

lib/galaxy/datatypes/binary.py

+17 −13
Original line number Diff line number Diff line
@@ -607,30 +607,34 @@ class BamNative(CompressedArchive, _BamOrSam): 
            try:

                with pysam.AlignmentFile(dataset.file_name, "rb", check_sq=False) as bamfile:

                    ck_size = 300  # 300 lines

                    ck_data = ""

                    header_line_count = 0

                    if offset == 0:

                        ck_data = bamfile.text.replace("\t", " ")  # type: ignore[attr-defined]

                        header_line_count = bamfile.text.count("\n")  # type: ignore[attr-defined]

                        offset = bamfile.tell()

                        ck_lines = bamfile.text.strip().replace("\t", " ").splitlines()  # type: ignore[attr-defined]

                    else:

                        bamfile.seek(offset)

                    for line_number, alignment in enumerate(bamfile):

                        ck_lines = []

                    for line_number, alignment in enumerate(bamfile, len(ck_lines)):

                        # return only Header lines if 'header_line_count' exceeds 'ck_size'

                        # FIXME: Can be problematic if bam has million lines of header

                        offset = bamfile.tell()

                        if (line_number + header_line_count) > ck_size:

                        if line_number > ck_size:

                            break

                        else:



                        offset = bamfile.tell()

                        bamline = alignment.tostring(bamfile)

                            # Galaxy display each tag as separate column because 'tostring()' funcition put tabs in between each tag of tags column.

                            # Below code will remove spaces between each tag.

                            bamline_modified = ("\t").join(bamline.split()[:11] + [(" ").join(bamline.split()[11:])])

                            ck_data = f"{ck_data}\n{bamline_modified}"

                        # With multiple tags, Galaxy would display each as a separate column

                        # because the 'tostring()' function uses tabs also between tags.

                        # Below code will turn these extra tabs into spaces.

                        n_tabs = bamline.count('\t')

                        if n_tabs > 11:

                            bamline, *extra_tags = bamline.rsplit('\t', maxsplit=n_tabs - 11)

                            bamline = f"{bamline} {' '.join(extra_tags)

                        ck_lines.append(f"{bamline} {' '.join(extra_tags)}")

                    else:

                        # Nothing to enumerate; we've either offset to the end

                        # of the bamfile, or there is no data. (possible with

                        # header-only bams)

                        offset = -1

                    ck_data = "\n".join(ck_lines)

            except Exception as e:

                offset = -1

                ck_data = f"Could not display BAM file, error was:\n{e}"