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Update SAM.sequence to return BioSequences.LongDNA{4}

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BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nucleotides in a SAM file, so use the larger
LongDNA variant. The method signatures are also simplified, so simplify
their calls, accordingly.
This commit is contained in:
Thomas A. Christensen II 2022-07-07 09:18:26 -05:00
parent e560681afa
commit 1660a24a0f
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 2 additions and 2 deletions
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4
src/sam/record.jl
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@ -387,7 +387,7 @@ function hastemplength(record::Record)
end end
""" """
sequence(record::Record)::BioSequences.LongDNASeq sequence(record::Record)::BioSequences.LongDNA{4}
Get the segment sequence of `record`. Get the segment sequence of `record`.
""" """
@ -398,7 +398,7 @@ function sequence(record::Record)
return nothing return nothing
end end
seqlen = length(record.seq) seqlen = length(record.seq)
ret = BioSequences.LongDNASeq(seqlen) ret = BioSequences.LongDNA{4}(undef, seqlen)
copyto!(ret, 1, record.data, first(record.seq), seqlen) copyto!(ret, 1, record.data, first(record.seq), seqlen)
return ret return ret
end end