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Phred / Probability Conversion Functions

# NextGenSeqUtils.phred_to_log_p — Function.

phred_to_log_p(x)

Conversion from phred value to log probability value.

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# NextGenSeqUtils.phred_to_p — Function.

phred_to_p(q::Phred)

Conversion from phred value to real probability value.

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phred_to_p(x::Vector{Phred})

Conversion from phred values to real probability values in vector.

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# NextGenSeqUtils.p_to_phred — Function.

p_to_phred(p::Prob)

Conversion from real probability value to phred value.

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p_to_phred(p::Prob)

Conversion from real probability values to phred values in vector.

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# NextGenSeqUtils.error_probs_to_phreds — Function.

error_probs_to_phreds(eps::Vector{Float64})

Conversion from error probability values to phred values in vector.

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# NextGenSeqUtils.quality_filter — Function.

quality_filter(infile, outfile=join(split(infile, ".")[1:end-1], ".") * ".filt.fasta"; 
               errorRate = 0.01, minLength = 100, labelPrefix = "seq", errorOut = true)

Writes file with sequences from input file that have all sites within error rate margin.

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quality_filter(seqs::Array{String, 1}, scores::Array, names::Array{String, 1}; errorRate=0.01, minLength=0)

Returns sub arrays with sequences that have site-wise error all within given margin.

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# NextGenSeqUtils.length_vs_qual — Function.

length_vs_qual(fasta_path; plot_title = "Length Vs Errors")

Creates plot of lengths of sequences vs. mean error rates of sequences.

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# NextGenSeqUtils.qual_hist — Function.

qual_hist(fasta_path; plot_title = "Quality Hist")

Creates histogram of mean quality scores per sequence.

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