synchronization with vgteam's fork #3
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Allow max gap length to be different on different alignments
Add base-quality adjusted alignments
Fix memory alignment bug for packing quality scores
Fix bugs in DP and traceback
Dozeu already depends on the SSE4.1 API, this wasn't doing any good.
The latter in unavailable on many compilers.
Fix small bug in dynamic programming
Enable non-X86 compatibility
Fully implement the full length bonus
Use a simde that builds on Clang 11
Avoid complaints about extern C templates from simde
Handle an X-drop in between non-X-drop vectors correctly
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For my part, I've done:
As I recall, the reason we were keeping the vgteam fork slightly upstream of the master branch here is that the option to have different insertion and deletion scores did not appear to be complete. Moreover, this is not a functionality that we had particular need for in VG. |
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The commits from myself and @nemequ enable building dozeu for non-x86 and on x86 CPUs that lack SSE4.1. This will enable VG to build on arm64/aarch64 like the upcoming Apple Silicon, the well priced Graviton Amazon AWS servers, or the number 1 ranked supercomputer |
Allow full length bonus to be selected on a per read basis
Fix traceback over X-dropped vectors
Maintain two separate ranges in each forefront
Speed up score matrix look up in quality-adjusted alignments
…f reservations are wrong
Fix allocation to support longer problems
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There is a lot going on here, but my understanding is that a number of issues have been resolved.
I think it's important to synchronize things. Upstream dozeu continues to get improvements and other fixes.
@jeizenga @mr-c @nemequ and @adamnovak might be able to describe relevant things.