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s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
https://s4hts.github.io/HTStream/
Apache License 2.0
49 stars 9 forks source link

fixes ntrimmer bug basepair output growing in size #234

Closed joe-angell closed 3 years ago

joe-angell commented 4 years ago

Problem was empty reads were causing ntrimmer to set rcut 1 on empty sequence making Read::getLengthTrue return 0-1 or max size_t.

joe-angell commented 4 years ago

This still doesn't address the issue of how the empty reads are getting output.

joe-angell commented 4 years ago

@msettles I recommend we merge this before making the change preventing trimming of all bases.