Comparing variations in sequences

Checking for variations in a known haplotype

Looking for a known Variation within a Haplotype is efficiently accomplished using the in operator.

println("\tOvis aires\tHomo sapiens")
for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
    is_sheep = v in bos_ovis_haplotype
    is_human = v in bos_human_haplotype
    println("$v\t$is_sheep\t\t$is_human")
end

	Ovis aires	Homo sapiens
C22T	true		false
G29A	true		false
C4A	false		true
T13C	false		true
C14A	false		true
G17A	false		true
C19A	false		true
T20G	false		true
G25T	false		true

Constructing new haplotypes based on other variations

New haplotypes can be constructed using variations. This might be useful to pool variations found on different reads or to filter variations from a haplotype that aren't validated by another haplotype.

julia> sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
julia> Haplotype(bovine, sheeple)Haplotype{BioSequences.LongSequence{BioSequences.DNAAlphabet{4}}, BioSymbols.DNA} with 9 edits:
  C4A
  T13C
  C14A
  G17A
  C19A
  T20G
  C22T
  G25T
  G29A
julia> reconstruct!(bovine, ans)ERROR: UndefVarError: reconstruct! not defined