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torognes
Smith-Waterman database searches with inter-sequence SIMD parallelisation
Clunky way of solving the request that I wrote about in this issue: https://github.com/torognes/swipe/issues/37 Not suggesting this as the actual solution, but rather showing it so that it is clear...
SWIPE is great but I am running into to issues when aligning sequences that have many hits with the same alignment score. I want all these to appear in the...
Dear swipe team, I am wondering whether this could be also run on Apple ARM64/aarch64 CPUs, which is a different SIMD idea. There are sse2neon.h here: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/blob/master/src/sse2neon.h Thanks, Jianshu
This would be a really useful enhancement. Currently it appears to ignore the -M flag when used with "-p 0".
The raw alignment scores are not shown unless including alignments in the default output format. An option to include the raw alignment scores will be useful in some cases.
``` gcc (GCC) 7.1.0 Copyright (C) 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or...
Especially `db_getsequence` returns the true sequence length + 1. That is compensated in all referencing functions by a substraction of -1 but should be corrected in the function itself. Other...
Adapt SWIPE to AVX2 and the 256-bit registers available in the new Intel Haswell CPUs to become available in June. Should allow 32-way SIMD parallelisation.