getindex not defined for arrays

[diegozea]

I was trying to create a sequence without some index and I've found that getindex using arrays isn't supported:

using BioSequences
seq = dna"CCTAGGAGG"
seq[[1,2,3,7,8,9]] # MethodError
seq[[true, true, true, false, false, false, true, true, true]] # MethodError

[TransGirlCodes]

Thanks for pointing this out @diegozea, perhaps we can include this method in version 2.0.

[ardakdemir]

I have been going over the source code to get familiar and to add this functionality. I could not understand how the decode function call in indexing.jl properly decodes the given Int representation. I could not find a decode function in the source code. Below is the corresponding code from indexing.jl:

@inline function inbounds_getindex(seq::BioSequence{A}, i::Integer) where {A}
    j = bitindex(seq, i)
    @inbounds return decode(A, (seq.data[index(j)] >> offset(j)) & mask(A))
end

[TransGirlCodes]

@ardakdemir The definitions for encode and decode are found here in the body of this loop

BioSequences.jl/src/alphabet.jl

Line 127 in e54ee6b

for A in (DNAAlphabet, RNAAlphabet)

. How encoding and decoding is done, depends on the alphabet parameter A of the BioSequence{A}, and so A is the first argument to the decode method, so as Julia's compiler can select the correct decode method at compile time.

[ardakdemir]

@benjward Thanks for the explanation. @diegozea I have added a trivial implementation of subsequencing functionality on the "subsequencing" branch. Maybe you can give it a try.

[jakobnissen]

This appears to be fixed on master, so closing it