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
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
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
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