High performance streaming VCF parser in pure JavaScript
This module is best used when combined with some easy way of retrieving the header and individual lines from a VCF, like the @gmod/tabix module.
const { TabixIndexedFile } = require('@gmod/tabix')
const VCF = require('@gmod/vcf')
const tbiIndexed = new TabixIndexedFile({ path: '/path/to/my.vcf.gz' })
async function doStuff() {
const headerText = await tbiIndexed.getHeader()
const tbiVCFParser = new VCF({ header: headerText })
const variants = []
await tbiIndexed.getLines('ctgA', 200, 300, line =>
variants.push(tbiVCFParser.parseLine(line)),
)
console.log(variants)
}Given a VCF with a single variant line
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
contigA 3000 rs17883296 G T,A 100 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:AP 0|0:0.000,0.000
The variant object returned by parseLine() would be
{
CHROM: 'contigA',
POS: 3000,
ID: ['rs17883296'],
REF: 'G',
ALT: ['T', 'A'],
QUAL: 100,
FILTER: 'PASS',
INFO: {
NS: '3',
DP: '14',
AF: '0.5',
DB: null,
H2: null,
},
}The variant object will also have a lazy attribute called "SAMPLES" that
will not be evaluated unless it is called. This can save time if you only want
the variant information and not the sample-specific information, especially if
your VCF has a lot of samples in it. In the above case the variant.SAMPLES
object would look like
{
HG00096: {
GT: '0|0',
AP: '0.000,0.000',
},
},The parser will try to use metadata from the header if present to convert INFO and FORMAT values to their proper type (int, float) or split them into an array if they represent multiple values.
Metadata can be accessed with the getMetadata() method. With no paramters it
will return all the data. Any parameters passed will further filter the
metadata. For example, a VCF with this header:
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
#CHROM POS ID REF ALT QUAL FILTER INFO
you can access the metadata like this:
> console.log(this.getMetadata())
{ INFO:
{ NS:
{ Number: 1,
Type: 'Integer',
Description: 'Number of Samples With Data' },
DP: { Number: 1, Type: 'Integer', Description: 'Total Depth' },
AF: { Number: NaN, Type: 'Float', Description: 'Allele Frequency' },
AA: { Number: 1, Type: 'String', Description: 'Ancestral Allele' },
DB:
{ Number: 0,
Type: 'Flag',
Description: 'dbSNP membership, build 129' },
H2: { Number: 0, Type: 'Flag', Description: 'HapMap2 membership' } },}
> console.log(this.getMetadata('INFO'))
{ NS:
{ Number: 1,
Type: 'Integer',
Description: 'Number of Samples With Data' },
DP: { Number: 1, Type: 'Integer', Description: 'Total Depth' },
AF: { Number: NaN, Type: 'Float', Description: 'Allele Frequency' },
AA: { Number: 1, Type: 'String', Description: 'Ancestral Allele' },
DB:{ Number: 0,
Type: 'Flag',
Description: 'dbSNP membership, build 129' },
H2: { Number: 0, Type: 'Flag', Description: 'HapMap2 membership' } }
> console.log(this.getMetadata('INFO', 'DP'))
{ Number: 1, Type: 'Integer', Description: 'Total Depth' }
> console.log(this.getMetadata('INFO', 'DP', 'Number'))
1Samples are also available.
> console.log(this.samples)
[ 'HG00096' ]Class representing a VCF parser, instantiated with the VCF header.
Parse a VCF metadata line (i.e. a line that starts with "##") and add its properties to the object.
linestring A line from the VCF. Supports both LF and CRLF newlines.
Parse a VCF header structured meta string (i.e. a meta value that starts with "<ID=...")
metaValstring The VCF metadata value
Returns Array Array with two entries, 1) a string of the metadata ID and 2) an object with the other key-value pairs in the metadata
Get metadata filtered by the elements in args. For example, can pass ('INFO', 'DP') to only get info on an metadata tag that was like "##INFO=<ID=DP,...>"
args...string List of metadata filter strings.
Returns any An object, string, or number, depending on the filtering
Sometimes VCFs have key-value strings that allow the separator within the value if it's in quotes, like: 'ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"'
Parse this at a low level since we can't just split at "," (or whatever separator). Above line would be parsed to: {ID: 'DB', Number: '0', Type: 'Flag', Description: 'dbSNP membership, build 129'}
strstring Key-value pairs in a stringpairSeparatorstring? A string that separates sets of key-value pairs (optional, default';')
Returns object An object containing the key-value pairs
Decode any of the eight percent-encoded values allowed in a string by the VCF spec.
strstring A string that may contain percent-encoded characters
Returns string A string with any percent-encoded characters decoded
Parse a VCF line into an object like { CHROM POS ID REF ALT QUAL FILTER INFO } with SAMPLES optionally included if present in the VCF
linestring A string of a line from a VCF. Supports both LF and CRLF newlines.