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add lastal -P0 option for multithreading
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lastal uses a single thread by default, but can be set to use multiple
threads. Passing ‘-P0’ tells it to use all available cores. See:
http://last.cbrc.jp/doc/last-parallel.html
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tomkinsc committed Jun 16, 2016
1 parent a46f204 commit 5be1d3b
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion taxon_filter.py
Expand Up @@ -193,7 +193,7 @@ def lastal_chunked_fastq(

lastal_out = mkstempfname('.lastal')
with open(lastal_out, 'wt') as outf:
cmd = [lastal_path, '-Q1']
cmd = [lastal_path, '-Q1', '-P0']
cmd.extend(
[
'-n', max_gapless_alignments_per_position, '-l', min_length_for_initial_matches, '-L',
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