def _run_wham(inputs, background_bams):
"""Run WHAM on a defined set of inputs and targets.
"""
out_file = os.path.join(_sv_workdir(inputs[0]), "%s-wham.vcf.gz" % dd.get_sample_name(inputs[0]))
if not utils.file_exists(out_file):
with file_transaction(inputs[0], out_file) as tx_out_file:
coords = chromhacks.autosomal_or_x_coords(dd.get_ref_file(inputs[0]))
parallel = {"type": "local", "cores": dd.get_cores(inputs[0]), "progs": []}
rs = run_multicore(_run_wham_coords,
[(inputs, background_bams, coord, out_file)
for coord in coords],
inputs[0]["config"], parallel)
rs = {coord: fname for (coord, fname) in rs}
vcfutils.concat_variant_files([rs[c] for c in coords], tx_out_file, coords,
dd.get_ref_file(inputs[0]), inputs[0]["config"])
return out_file
def _run_wham(inputs, background_bams):
"""Run WHAM on a defined set of inputs and targets.
"""
out_file = os.path.join(_sv_workdir(inputs[0]), "%s-wham.vcf.gz" % dd.get_sample_name(inputs[0]))
if not utils.file_exists(out_file):
with file_transaction(inputs[0], out_file) as tx_out_file:
coords = chromhacks.autosomal_or_x_coords(dd.get_ref_file(inputs[0]))
parallel = {"type": "local", "cores": dd.get_cores(inputs[0]), "progs": []}
rs = run_multicore(_run_wham_coords,
[(inputs, background_bams, coord, out_file)
for coord in coords],
inputs[0]["config"], parallel)
rs = {coord: fname for (coord, fname) in rs}
vcfutils.concat_variant_files([rs[c] for c in coords], tx_out_file, coords,
dd.get_ref_file(inputs[0]), inputs[0]["config"])
return out_file
def _run_wham(inputs, background_bams):
"""Run WHAM on a defined set of inputs and targets.
"""
out_file = os.path.join(_sv_workdir(inputs[0]), "%s-wham.bedpe" % dd.get_sample_name(inputs[0]))
if not utils.file_exists(out_file):
with file_transaction(inputs[0], out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
coords = chromhacks.autosomal_or_x_coords(dd.get_ref_file(inputs[0]))
parallel = {"type": "local", "cores": dd.get_cores(inputs[0]), "progs": ["wham"]}
rs = run_multicore(_run_wham_coords,
[(inputs, background_bams, coord, out_file)
for coord in coords],
inputs[0]["config"], parallel)
rs = {coord: fname for (coord, fname) in rs}
for coord in coords:
with open(rs[coord]) as in_handle:
shutil.copyfileobj(in_handle, out_handle)
return out_file
def _run_wham(inputs, background_bams):
"""Run WHAM on a defined set of inputs and targets.
"""
out_file = os.path.join(_sv_workdir(inputs[0]),
"%s-wham.bedpe" % dd.get_sample_name(inputs[0]))
if not utils.file_exists(out_file):
with file_transaction(inputs[0], out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
coords = chromhacks.autosomal_or_x_coords(
dd.get_ref_file(inputs[0]))
parallel = {
"type": "local",
"cores": dd.get_cores(inputs[0]),
"progs": ["wham"]
}
rs = run_multicore(_run_wham_coords,
[(inputs, background_bams, coord, out_file)
for coord in coords], inputs[0]["config"],
parallel)
rs = {coord: fname for (coord, fname) in rs}
for coord in coords:
with open(rs[coord]) as in_handle:
shutil.copyfileobj(in_handle, out_handle)
return out_file
