Sequence Orienting Functions
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NextGenSeqUtils.orient_strands — Function.
orient_strands(seqs::Array{String}, phreds::Union{Array{Vector{Phred},1},Void},
names::Union{Array{String,1},Void}, ref::String; k::Int=6)
Orients sequences (with phreds and names, which may be nothing) relative to a reference sequence. k is kmer size for computing kmer vectors.
orient_strands(seqs::Array{String}, ref::String; k::Int=6)
Orients sequences relative to a reference sequence. k is kmer size for computing kmer vectors.
orient_strands(seqs::Array{String,1}, phreds::Union{Array{Vector{Phred},1},Void}, names::Union{Array{String,1},Void},
ref::String, kmers::Array{Array{T,1},1}, ref_kmer::Array{T,1}, rev_ref_kmer::Array{T,1}) where {T <: Real}
Orients sequences with given kmer vectors relative to a reference sequence with given kmer vector.
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NextGenSeqUtils.orient_to_refs — Function.
orient_to_refs(seqs::Array{String,1}, phreds::Union{Array{Vector{Phred},1},Void},
names::Union{Array{String,1},Void}, refs::Array{String,1}; k::Int = 6)
Orients each sequence in seqs to nearest reference sequence in panel of references (refs). Distance determined by amino acid similarity (kmer vector dot prod).