Private API Reference

FASTX.FASTA.Record(ps::Pseudoread; prefix::AbstractString="", is_consensus::Bool=false)

Specialized constructor for outputting Pseudoreads to FASTA.Records that can be written to files.

Arguments

• ps::Pseudoread: The modified sequence and read window to be converted into the sequence of the new record

Keywords

• prefix::AbstractString="": A string to start the sequence identifier with, usually based on the reference sequence of ps
• is_consensus::Bool=false: Normally, the new identifier of the record is a combination of the prefix and the SHA1 hash of the alternate sequence. Set is_consensus to true to instead use the word "CONSENSUS" in place of the hash

SequenceVariation.Haplotype(
    query::Union{SAM.Record,BAM.Record}, reference::NucleotideSeq
) -> SequenceVariation.Haplotype

Specialized constructor that allows converting the alignment in a XAM.Record into a Haplotype.

_cigar(var::Variation{S,T}) where {S,T}

Returns a CIGAR operation for var. Only supports insertions and deletions.

See also _cigar_between

_cigar_between(x::Variation{S,T}, y::Variation{S,T}) where {S,T}

Returns a CIGAR operation for the (assumed) matching bases between x and y.

See also _cigar

_indexed_reader(bam::Union{AbstractPath,AbstractString}, int::Interval)

Provides an iterator over records in bam that overlap with int. Note that if no index file is available for bam, then the return value will fall back to an iterator of all records in bam.

_lendiff(ps::Pseudoread)

Gets the difference between the number of bases within the read window of ps on the reference sequence from the number of bases within the read window on the mutated sequence, taking into account insertions and deletions.

_phrederror(quality::Number)

Converts a PHRED33-scaled error number into the expected fractional error of basecall

_pos_to_edge(pos::Number)

Converts pos from a number between 0 (beginning) and 1 (end) to a number ranging from 0 (beginning) to 1 (middle) to 0 (end), i.e. convert a relative position to a relative distance from the edge.

_posin(ps::Pseudoread, v::Variation)

Determines if the positions that make up v are wholly contained by ps

_push_filter!(
    vc::VariationCall,
    label::Char,
    value::Union{Nothing,Number},
    filter::Function=(var, val) -> true,
)

Adds a FILTER entry to vc of the form "$label$value" if filter returns true.

Arguments

• vc::VariationCall: The VariationCall to annotate
• label::Char: The first character of the filter text to add
• value::Union{Nothing,Number}: The value to compare vc against, and to append to the filter text. If set to nothing, _push_filter! will return without evaluating or adding any filters, which may be useful for processing multiple inputs
• filter::Function=(var, val) -> true: A function handle to determine if a filter should be applied or not. Note that this function must return true if and only if the filter should be added to vc. The function will be passed vc and value. Defaults to always applying filters regardless of the values of vc and value.

comonicon_install(;kwargs...)

Install the CLI manually. This will use the default configuration in Comonicon.toml, if it exists. For more detailed reference, please refer to Comonicon documentation.

comonicon_install_path(;[yes=false])

Install the PATH and FPATH to your shell configuration file. You can use comonicon_install_path(;yes=true) to skip interactive prompt. For more detailed reference, please refer to Comonicon documentation.

magnitude(x::UnitRange)

Gets the difference between the last and first elements of x

Example

julia> using HapLink: magnitude

julia> magnitude(0:10)
10

overlap(x::UnitRange{S}, y::UnitRange{S}) where {S}

Finds the inclusive overlap interval of x and y

Example

julia> using HapLink: overlap

julia> overlap(1:5, 3:10)
3:5

julia> overlap(2:4, 6:8)
6:5

julia> overlap(1:10, 2:9)
2:9

variations(vs::AbstractVector{Haplotype})

Extracts all SequenceVariation.Variations from vs.

findset(lst::AbstractArray{T}, comparator::Function) where {T}

Finds every possible set of items in lst where comparator returns true for the set.

Example

function divisible_by_same_number(x, i)
    for j in 2:i
        if all(y -> y % j == 0, x)
            return true
        end
    end
    return false
end
findset(1:12, x -> divisible_by_same_number(x, 5))

# output
6-element Vector{Vector{Int64}}:
 [2, 4, 6, 8, 10, 12]
 [6, 3, 9, 12]
 [5, 10]
 [1]
 [7]
 [11]