(alt-sequence ref-seq seq-start pos ref alt)
Returns sequence a variant applied.
Returns sequence a variant applied.
(diff-bases s1 s2)
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].
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].
(normalize-variant variant seq-rdr rg)
Normalizes a VCF-style variant based on surrounding sequence. For example, {:pos 7, :ref T, :alt TAGT} on ...CAGTAGTAGTC... is equivalent to {:pos 13, :ref T, :alt TAGT}. The latter is normalized. e.g. ...CAGTAGTAGTC... 7 T TAGT => 13 T TAGT
Normalizes a VCF-style variant based on surrounding sequence. For example, {:pos 7, :ref T, :alt TAGT} on ...CAGTAGTAGTC... is equivalent to {:pos 13, :ref T, :alt TAGT}. The latter is normalized. e.g. ...CAGTAGTAGTC... 7 T TAGT => 13 T TAGT
(read-sequence-stepwise-backward seq-rdr {:keys [chr start end]} step)
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