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Re-enable GPU features in racon_wrapper #53

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Re-enable GPU features in racon_wrapper #53

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12 changes: 6 additions & 6 deletions scripts/racon_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,9 @@ def __init__(self, sequences, overlaps, target_sequences, split, subsample,
self.mismatch = mismatch
self.gap = gap
self.threads = threads
# self.cudaaligner_batches = cudaaligner_batches
# self.cudapoa_batches = cudapoa_batches
# self.cuda_banded_alignment = cuda_banded_alignment
self.cudaaligner_batches = cudaaligner_batches
self.cudapoa_batches = cudapoa_batches
self.cuda_banded_alignment = cuda_banded_alignment
self.work_directory = os.getcwd() + '/racon_work_directory_' + str(time.time())

def __enter__(self):
Expand Down Expand Up @@ -119,16 +119,16 @@ def run(self):
racon_params = [RaconWrapper.__racon]
if (self.include_unpolished == True): racon_params.append('-u')
if (self.fragment_correction == True): racon_params.append('-f')
# if (self.cuda_banded_alignment == True): racon_params.append('-b')
if (self.cuda_banded_alignment == True): racon_params.append('-b')
racon_params.extend(['-w', str(self.window_length),
'-q', str(self.quality_threshold),
'-e', str(self.error_threshold),
'-m', str(self.match),
'-x', str(self.mismatch),
'-g', str(self.gap),
'-t', str(self.threads),
# '--cudaaligner-batches', str(self.cudaaligner_batches),
# '-c', str(self.cudapoa_batches),
'--cudaaligner-batches', str(self.cudaaligner_batches),
'-c', str(self.cudapoa_batches),
self.subsampled_sequences, self.overlaps, ""])

for target_sequences_part in self.split_target_sequences:
Expand Down