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recommit v0.5.0

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@genomematt genomematt released this 23 Mar 09:33
v0.5.0
cf516b6 
Note that due to a commit error between branches v0.4.0 will not correctly process paired end files.  Read pairs will only be assigned based on the AS score of the reverse read.  For most uses this bug is conservative, but all users should update to v0.5.0
v0.5.0 refactors the score comparison logic and adds the ability to filter on minimum alignment score
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