varity.vcf-to-hgvs.common — varity 0.11.0

alt-sequence clj

(alt-sequence ref-seq seq-start pos ref alt)

Returns sequence a variant applied.

apply-3'-rule clj

(apply-3'-rule variant seq*)

(apply-3'-rule {:keys [pos ref alt] :as variant} seq* direction)

Apply the 3’ rule to the VCF-style variant based on the surrounding sequence.

For example, {:pos 7, :ref T, :alt TAGT} on ...CAGTAGTAGTC... is equivalent to {:pos 13, :ref T, :alt TAGT}. The latter is a normalized variant.

This function can be applied to both nucleotide sequence and amino acid sequence. If you want to normalize the variant as reverse strand, supply :backward to the third argument.

backward-shift clj

(backward-shift seq* pos bases)

diff-bases clj

(diff-bases s1 s2)

(diff-bases s1 s2 offset)

Compares VCF-style base(s) s1 and s2, returning a vector of [bases-only-in-s1 bases-only-in-s2 left-common-len right-common-len].

forward-shift clj

(forward-shift seq* pos bases)

max-repeat-unit-size clj

normalization-read-sequence-step clj

normalize-variant clj

(normalize-variant variant seq-rdr rg)

Normalizes the VCF-style variant based on the surrounding sequence and the ref-gene with the 3’ rule.

read-sequence-stepwise clj

(read-sequence-stepwise seq-rdr {:keys [chr start end]} step)

read-sequence-stepwise-backward clj

(read-sequence-stepwise-backward seq-rdr {:keys [chr start end]} step)

repeat-info clj

(repeat-info seq* pos alt type)