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Minor tweaks to CLI args #347

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merged 1 commit into from
Jul 19, 2024
Merged

Minor tweaks to CLI args #347

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13 changes: 5 additions & 8 deletions vamb/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1611,7 +1611,7 @@ def add_help_arguments(parser: argparse.ArgumentParser):

def add_general_arguments(subparser: argparse.ArgumentParser):
add_help_arguments(subparser)
reqos = subparser.add_argument_group(title="Output (required)", description=None)
reqos = subparser.add_argument_group(title="Output", description=None)
reqos.add_argument(
"--outdir",
metavar="",
Expand Down Expand Up @@ -1639,10 +1639,7 @@ def add_general_arguments(subparser: argparse.ArgumentParser):
metavar="",
type=int,
default=DEFAULT_THREADS,
help=(
"number of threads to use when parsing BAM"
"[min(" + str(DEFAULT_THREADS) + ", nbamfiles)]"
),
help=f"number of threads to use where customizable [{DEFAULT_THREADS}]",
)
general.add_argument(
"--norefcheck",
Expand Down Expand Up @@ -1926,8 +1923,8 @@ def add_clustering_arguments(subparser):
dest="max_clusters",
metavar="",
type=int,
default=None,
help="stop after c clusters [None = infinite]",
default=None, # meaning: do not stop
help=argparse.SUPPRESS,
)

return subparser
Expand Down Expand Up @@ -2068,7 +2065,7 @@ def main():
Version: {vamb.__version_str__}

Default use, good for most datasets:
vamb bin default --outdir out --fasta my_contigs.fna --bamdir bam_dir -o C
vamb bin default --outdir out --fasta my_contigs.fna --bamdir bam_dir

Find the latest updates and documentation at https://github.com/RasmussenLab/vamb"""
logger.add(sys.stderr, format=format_log)
Expand Down
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