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maickrau / GraphAligner

MIT License
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Equivalent alignment handling #32

Closed jnvaughn closed 2 years ago

jnvaughn commented 3 years ago

How does GraphAligner handle equivalent alignments at two position in the graph: random placement, etc? Also, is there a way to report mapping quality information? Thanks!

maickrau commented 3 years ago

By default equivalent alignments are randomly placed and there is no mapping quality. In the latest commit in master you can use a hidden experimental parameter "--multiseed-DP 1" which reports all equivalent alignments and also has mapping qualities, but that's still experimental so it might give unexpected results in some cases.

jnvaughn commented 3 years ago

Great. We use this parameter quite heavily but will keep a look out for odd behavior and post here. Thank you again and great tool.

maickrau commented 2 years ago

Versions 1.0.14 and later have mapping qualities and report all equivalently good alignments