Miloš Marić comments

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Miloš Marić

[cudamapper] Add anchor chain output functions to chainer_utils.cuh.

rerun tests

[cudamapper] Do not do self-mapping of reads

@tijyojwad @vellamike FYI

SketchElementImpl::ReadidPositionDirection became new SketchElement

Point 1 is definitely still relevant, not really sure about point 2

Possibly not calculating s array in ksw_extd2_see() correctly

I went into more details on this. All line numbers are based on this file versions: https://github.com/lh3/ksw2/blob/4e0a1ccba8c6ccc87e0342c9712531bde783bf90/ksw2_extd2_sse.c On L99 memory buffer is allocated with `(tlen_ * 8 + qlen_ +...

AMG_Level::Aoriginal not intuitive

One way to have this a bit more readable would be to have a `bool using_internal_A` instead of `Matrix* Aoriginal`. That way it's clear that the intention is to track...