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SEQVARNOMJS

Javascript parser for Sequence Variant Nomenclature.

This library interprets SVN strings such as:

• simple variants NC00001_1.11:g.111T>G
• wild type NC00001_1.11:g.111=
• compound cis variants NC0001_1.11:g.[111T>G;222A>G]
  • 111T>G and 222A>G are on the same chromosome copy
• trans variants NC0001_1.11:g.[111T>G];[222A>G]
  • 111T>G and 222A>G are on different chromosome copies
• variants with uncertain phasing NC0001_1.11:g.[111T>G](;)[222A>G]
  • 111T>G and 222A>G may be on same chromosome copy or different ones
• complex variants NC0001_1.11:g.[111T>G;222A>G];[333=](;)[444T>A];[555G>A]

We add extensions to the existing standard which allows us to perform pattern matching using logic operators:

• OR operator ^
• AND operator &
• NOT operator !
• GROUPING operator {}

Logic operators can be used throughout the expression E.g.,

• match either simple variant 111T>G or 222A>G NC0001_1.11:g.[111T>G^222A>G]
• match one or another sequence variant {NC0001_1.11:g.111T>G}^{NC0002_2.11:g.222T>G}
• match a complex condition ((111 or 222) and (333 or 444)) on one cis variant NC0001_1.11:g.[{111T>G^222T>G}&{333>T>G^444T>G}]
• match either one transvariant pattern or another NC0001_1.11:g.{[111T>G];[222T>G]}^{[333T>G];[444T>G]}
• match either one unphased variant pattern or another NC0001_1.11:g.{[111T>G](;)[222T>G]}^{[333T>G](;)[444T>G]}
• use nested logical operators {NC0001_1.11:g.111T>G}^{NC0002_2.11:g.{[111T>G]^[222T>G]}^{[333T>G];[444T>G]}}

API

WIP

var svn = require('seqvarnomjs');

var pattern = svn.parse('NC0001_1.11:g.[111T>G^222A>G]');
var genotype = svn.parse('NC0001_1.11:g.111T>G');

svn.match(pattern, genotype); // => true