From 4f5affed7321c7d88368a90792d04b6725a80ed6 Mon Sep 17 00:00:00 2001 From: Sam Chorlton <10245822+schorlton@users.noreply.github.com> Date: Tue, 25 May 2021 19:32:29 -0700 Subject: [PATCH] Reenable GPU params in wrapper --- scripts/racon_wrapper.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/scripts/racon_wrapper.py b/scripts/racon_wrapper.py index 4eda76d..a8b0cf4 100644 --- a/scripts/racon_wrapper.py +++ b/scripts/racon_wrapper.py @@ -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): @@ -119,7 +119,7 @@ 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), @@ -127,8 +127,8 @@ def run(self): '-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: