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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
309 stars 118 forks source link

use some cram decode stuff to reduce run-time of lumpy_filter for cram #269

Closed brentp closed 6 years ago

brentp commented 6 years ago

this reduces the run-time of lumpy_filter on my test-case from 9m16s to 5m10s with identical results.

it simply avoids decoding the base sequence and qualities.

also removes unneeded index stuff.

brentp commented 6 years ago

the tests are failing on master for me.

brentp commented 6 years ago

cc @ryanlayer