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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

-m (minLength) option removed from hts_QWindowTrim, but does not exist in hts_CutTrim #232

Closed marade closed 4 years ago

marade commented 4 years ago

Commit 86c939a9095bc19c6053efd689da7635dbd001ce removes the option from hts_QWindowTrim, because we're now supposed to use hts_CutTrim instead, but hts_CutTrim does not have a minLength option, so we can now no longer filter by minimum length with the pipeline?

samhunter commented 4 years ago

Hi @marade, there is now a new tool called hts_LengthFilter (https://github.com/s4hts/HTStream/tree/master/hts_LengthFilter) to take care of this step.

marade commented 4 years ago

Ah good. Thanks for the assistance.

samhunter commented 4 years ago

No problem, thanks for feedback!

The idea is that all length filtering can be handled by a single tool, so that statistics for this type of filtering are in the same place instead of spread across many different tools.