[DOC, FEATURE] Improve dna4 complement performance and add documentation. #3026
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Codecov ReportBase: 98.24% // Head: 98.25% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #3026 +/- ##
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Coverage 98.24% 98.25%
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Files 275 276 +1
Lines 12318 12344 +26
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+ Hits 12102 12128 +26
Misses 216 216
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I played around a bit: https://quick-bench.com/q/RtiW9XqNDG_O9BzGo8gUzKAZQNo constexpr uint8_t rank(char c) noexcept
{
uint8_t rank = static_cast<uint8_t>(c);
rank |= (rank & 0b0001'0000) >> 1;
rank += 1u;
rank >>= 2;
rank &= 0b0000'0011;
return rank;
}rank |= (rank & 0b0001'0000) >> 1; // Set 4th bit to one if 5th bit is set (t and T)
rank += 1u; // Luckily flips the bits we need to flip
rank >>= 2; // Drop lowest 2 bits
rank &= 0b0000'0011; // Mask other bits
return rank;Works for both lower and upper case chars. I still need to test it with this PR and auto-vectorization. |
Still needs a few things to be fully dna4-compatible. As a side note, if we were to do the complement in constexpr simdifyable_dna4 & assign_char(char_type const c) noexcept
{
char_type const upper_char = c & 0b0101'1111; // to_upper
rank_type rank = (upper_char == 'A') * 3 + (upper_char == 'C') * 2 + (upper_char == 'G');
return assign_rank(rank);
} |
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eseiler
approved these changes
Oct 19, 2022
SGSSGene
requested changes
Oct 20, 2022
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| allocator(allocator &&) = default; | ||
| allocator & operator=(allocator &&) = default; |
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Can you delete these?
Their usage will lead to double free of forward and reverse
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Why? I get it for the copy ctor/assignment.
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I believe the default implementation of the move operator looks something like this:
allocator & operator=(allocator && other) {
forward = std::move(other.forward);
reverse = std::move(other.reverse);
}
If I have to allocator a1 and a2 and now move one into the other a1 = std::move(a2)
the original memory of a1.forward and a1.reverse is lost and not freed.
But when a1 and a2 go out of scope, they point to the same memory and there will be a double free on the same memory.
Co-authored-by: Enrico Seiler <enrico.seiler@hotmail.de>
Co-authored-by: Enrico Seiler <enrico.seiler@hotmail.de>
Co-authored-by: Enrico Seiler <enrico.seiler@hotmail.de>
Co-authored-by: Enrico Seiler <enrico.seiler@hotmail.de>
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SGSSGene
approved these changes
Oct 21, 2022
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(Aims to) Resolves #1970