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API

new BED(opts?)

option type meaning
autoSql string an autoSql declaration to parse lines with
type string one of the builtin schemas
columnNames string[] column names, e.g. from a #chrom start end ... header

At most one option applies; with none, the parser falls back on the standard BED schema and handles a line that doesn't look like BED12 as described in Without a schema. An unknown type throws Type not found: <type>, and a malformed autoSql throws an error that names the line and column where parsing failed.

parser.autoSql holds the parsed schema.

parseLine(line, opts?)

  • line: string | string[] — a tab-delimited line, or the columns already split. Pass an array to parse the space-delimited form UCSC also allows.
  • opts.uniqueId: string — the parser sets the feature's uniqueId field to this value. Use it to give a feature an id when the line has none.

Returns a Feature: a plain object keyed by schema field name.

const p = new BED({ type: 'bigNarrowPeak' })
p.parseLine('chr1\t0\t100\tpeak1\t100\t+\t1.5\t2.5\t3.5\t50', {
  uniqueId: 'peak-1',
})
// { chrom: 'chr1', chromStart: 0, chromEnd: 100, name: 'peak1', score: 100,
//   strand: 1, signalValue: 1.5, pValue: 2.5, qValue: 3.5, peak: 50,
//   uniqueId: 'peak-1' }

Every call is independent, so one parser instance serves a whole file, and every file that shares its schema.

Types

import type {
  Feature,
  AutoSqlField,
  AutoSqlPreSchema,
  AutoSqlSchema,
} from '@gmod/bed'

type Feature = Record<string, string | number | string[] | number[]>
  • AutoSqlField: one declared field, with name, type, comment, plus size for arrays and vals for enum/set.
  • AutoSqlPreSchema: a declaration before type detection, with fields: AutoSqlField[] and, unless built from columnNames, the declaration's type (table, simple or object), name and comment.
  • AutoSqlSchema: the same after type detection, where each field also has isNumeric, isArray and arrayIsNumeric. parser.autoSql is an AutoSqlSchema.

Exports

The package's default export is the BED class, plus the types above.