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?
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:
while the actual implementation cmd_cram_demuxlet.cpp seems to default to 20:
int32_t capBQ = 20;Which one is correct?