Example #1
0
def _maybe_add_alignment(algorithm, sample, out):
    if _has_alignment_file(algorithm,
                           sample) and dd.get_phenotype(sample) != "germline":
        for (fname, ext, isplus) in [(sample.get("work_bam"), "ready", False),
                                     (sample.get("umi_bam"), "umi", False),
                                     (sample.get("bigwig"), "ready", False),
                                     (dd.get_disc_bam(sample), "disc", True),
                                     (dd.get_sr_bam(sample), "sr", True)]:
            if fname and os.path.exists(fname):
                if fname.endswith("bam"):
                    ftype, fext = "bam", ".bai"
                elif fname.endswith("cram"):
                    ftype, fext = "cram", ".crai"
                elif fname.endswith("bw"):
                    ftype, fext = "bw", ".bw"
                else:
                    raise ValueError("Unexpected alignment file type %s" %
                                     fname)
                out.append({
                    "path": fname,
                    "type": ftype,
                    "plus": isplus,
                    "ext": ext
                })
                if utils.file_exists(fname + fext):
                    out.append({
                        "path": fname + fext,
                        "type": ftype + fext,
                        "plus": isplus,
                        "index": True,
                        "ext": ext
                    })
    return out
Example #2
0
def _maybe_add_alignment(algorithm, sample, out):
    if _has_alignment_file(algorithm, sample) and dd.get_phenotype(sample) != "germline":
        for (fname, ext, isplus) in [(sample.get("work_bam"), "ready", False),
                                     (sample.get("umi_bam"), "umi", False),
                                     (sample.get("bigwig"), "ready", False),
                                     (dd.get_disc_bam(sample), "disc", True),
                                     (dd.get_sr_bam(sample), "sr", True)]:
            if fname and os.path.exists(fname):
                if fname.endswith("bam"):
                    ftype, fext = "bam", ".bai"
                elif fname.endswith("cram"):
                    ftype, fext = "cram", ".crai"
                elif fname.endswith("bw"):
                    ftype, fext = "bw", ".bw"
                else:
                    raise ValueError("Unexpected alignment file type %s" % fname)
                out.append({"path": fname,
                            "type": ftype,
                            "plus": isplus,
                            "ext": ext})
                if utils.file_exists(fname + fext):
                    out.append({"path": fname + fext,
                                "type": ftype + fext,
                                "plus": isplus,
                                "index": True,
                                "ext": ext})
    return out
Example #3
0
def find_existing_split_discordants(data):
    """Check for pre-calculated split reads and discordants done as part of alignment streaming.
    """
    in_bam = dd.get_align_bam(data)
    sr_file = "%s-sr.bam" % os.path.splitext(in_bam)[0]
    disc_file = "%s-disc.bam" % os.path.splitext(in_bam)[0]
    if utils.file_exists(sr_file) and utils.file_exists(disc_file):
        return sr_file, disc_file
    else:
        sr_file = dd.get_sr_bam(data)
        disc_file = dd.get_disc_bam(data)
        if sr_file and utils.file_exists(sr_file) and disc_file and utils.file_exists(disc_file):
            return sr_file, disc_file
        else:
            return None, None
Example #4
0
def _find_existing_inputs(data):
    """Check for pre-calculated split reads and discordants done as part of alignment streaming.
    """
    in_bam = dd.get_align_bam(data)
    sr_file = "%s-sr.bam" % os.path.splitext(in_bam)[0]
    disc_file = "%s-disc.bam" % os.path.splitext(in_bam)[0]
    if utils.file_exists(sr_file) and utils.file_exists(disc_file):
        return in_bam, sr_file, disc_file
    else:
        sr_file = dd.get_sr_bam(data)
        disc_file = dd.get_disc_bam(data)
        if sr_file and utils.file_exists(sr_file) and disc_file and utils.file_exists(disc_file):
            return in_bam, sr_file, disc_file
        else:
            return None, None, None