jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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detect: --max-reads default #129

Open nick-youngblut opened 2 years ago

nick-youngblut commented 2 years ago

The cli docs for Atropos version 1.1.31 state:

  --max-reads N         Maximum number of reads/pairs to process (no max)

... but the max is actually set to 10000 instead of no max:

        parser.set_defaults(
            max_reads=10000,
            counter_magnitude="K")

So, a atropos detect run with default parameters (and --progress bar):

2022-01-16 07:27:14,174 INFO: Detecting adapters and other potential contaminant sequences based on 12-mers in 10000 reads
  0%|                                                | 10/10000 [00:00<08:54, 18.70it/s]
nick-youngblut commented 2 years ago

...also the progress bar doesn't seem to work for detect. The entire progress bar output for default parameters is:

0%|                                                | 10/10000 [00:00<07:31, 22.14it/s]

The bar never progresses beyond 0%.