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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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insert size hackersonly override #372

Closed eaton-lab closed 3 years ago

eaton-lab commented 4 years ago

Currently it seems that the hackersonly max_insert_size arg is only used if it fails to estimate the insert size from the data itself. We should change it so that if the user sets a hacker value then it overrides the estimated value.

Sandra and I are doing some testing on a digested genome with known size selection mapped back to the genome and it seems we are throwing away a fair number of read pairs b/c of the max_insert_size.

isaacovercast commented 3 years ago

Near as I can tell this was fixed some time ago.