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Drop chains #718

Merged
merged 11 commits into from
Mar 13, 2017
Merged

Drop chains #718

merged 11 commits into from
Mar 13, 2017

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ekg
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@ekg ekg commented Mar 12, 2017

Implement this option from bwa mem:

       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]

This improves performance by removing clusters (chains of MEMs) which are unlikely to yield useful results.

ekg added 3 commits March 12, 2017 10:59
@ekg
change reseed max MEM length to a factor of 1.5 rather than 2
9392375
@ekg
adjust mapper parameter settings to improve sensitivity
dd6ce9b
@ekg
implement cluster drop filter
e2c3f2e 
When a chain/cluster is less than this fraction of the longest overlapping
cluster, drop it. Tends to keep reads when we have a fair chance of finding a
better alternative, and not try to when it's unlikely.
@ekg ekg merged commit 37f68b6 into master Mar 13, 2017
@ekg ekg removed the in progress label Mar 13, 2017
@adamnovak adamnovak deleted the drop-chains branch March 13, 2019 19:13
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