Fix reversing seq with unused data #128
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@@ Coverage Diff @@
## master #128 +/- ##
==========================================
+ Coverage 83.18% 83.21% +0.03%
==========================================
Files 44 44
Lines 2949 2949
==========================================
+ Hits 2453 2454 +1
+ Misses 496 495 -1
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|
cjprybol
reviewed
Jan 14, 2021
| @@ -69,7 +69,7 @@ Base.reverse(seq::LongSequence{<:Alphabet}) = _reverse(seq, BitsPerSymbol(seq)) | |||
| @inline function _reverse(seq::LongSequence{A}, B::BT) where {A <: Alphabet, | |||
| BT <: Union{BitsPerSymbol{2}, BitsPerSymbol{4}, BitsPerSymbol{8}}} | |||
| cp = LongSequence{A}(unsigned(length(seq))) | |||
| reverse_data_copy!(identity, cp.data, seq.data, B) | |||
| reverse_data_copy!(identity, cp.data, seq.data, seq_data_len(seq) % UInt, B) | |||
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Taking the remainder like this is a clever way of converting an integer to an unsigned integer. Didn't realize what was going on here until I tried it
julia> x = 1
1
julia> UInt(x)
0x0000000000000001
julia> x % UInt
0x0000000000000001
julia> UInt(x) == (x % UInt)
true
julia> BenchmarkTools.@benchmark UInt($(rand(Int)))
BenchmarkTools.Trial:
memory estimate: 0 bytes
allocs estimate: 0
--------------
minimum time: 0.059 ns (0.00% GC)
median time: 0.070 ns (0.00% GC)
mean time: 0.074 ns (0.00% GC)
maximum time: 0.539 ns (0.00% GC)
--------------
samples: 10000
evals/sample: 1000
julia> BenchmarkTools.@benchmark $(rand(Int)) % UInt
BenchmarkTools.Trial:
memory estimate: 0 bytes
allocs estimate: 0
--------------
minimum time: 0.040 ns (0.00% GC)
median time: 0.040 ns (0.00% GC)
mean time: 0.045 ns (0.00% GC)
maximum time: 15.710 ns (0.00% GC)
--------------
samples: 10000
evals/sample: 1000
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MWE to reproduce bug:
What happened was that the reversing functions assumed that
length(seq.data) == seq_data_len(typeof(Alphabet(seq)), length(seq), which is not a valid guarantee (i.e:LongSequencesare allowed to have noncoding elements at the end of theirdatavector).