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Ambiguous default value for cap-BQ in demuxlet #71

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mvochteloo opened this issue Nov 21, 2023 · 0 comments
Open

Ambiguous default value for cap-BQ in demuxlet #71

mvochteloo opened this issue Nov 21, 2023 · 0 comments

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@mvochteloo
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mvochteloo commented Nov 21, 2023 •
edited

I noticed a discrepancy in the default value for the cap-BQ parameter between the documentation and implementation of demuxlet.

The README.md states that demuxlet defaults to a maximum base quality (cap-BQ) of 40:

Read filtering Options
   --cap-BQ [INT: 40] : Maximum base quality (higher BQ will be capped)

while the actual implementation cmd_cram_demuxlet.cpp seems to default to 20:

int32_t capBQ = 20;

Which one is correct?
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