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hall-lab / svtyper

Bayesian genotyper for structural variants
MIT License
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improve svtyper speed by ~30% #96

Closed brentp closed 6 years ago

brentp commented 6 years ago

avoids use of CRAM sequence and base-quals which otherwise do not need to be decoded.

This changes the run-time of one test-case from

20.8 seconds to 14.9

ernfrid commented 6 years ago

Does this bump the minimum version of pysam?

ernfrid commented 6 years ago

Probably v0.15.0?

brentp commented 6 years ago

hard to tell, but looks like 0.14.0 might be sufficient.