Module org.phenopackets.phenopackettools.builder

Package org.phenopackets.phenopackettools.builder.builders

Class VcfRecordBuilder

java.lang.Object

org.phenopackets.phenopackettools.builder.builders.VcfRecordBuilder

public class VcfRecordBuilder
extends Object

Method Summary

Modifier and Type	Method	Description
org.ga4gh.vrsatile.v1.VcfRecord	build()
static VcfRecordBuilder	builder(String assembly, String chromosome, int position, String ref, String alt)
VcfRecordBuilder	filter(String filter)
VcfRecordBuilder	id(String id)	Identifier: Semicolon-separated list of unique identifiers where available If this is a dbSNP/dbVAR variant these rsID/nsvID(s) should be used.
VcfRecordBuilder	info(String info)
static org.ga4gh.vrsatile.v1.VcfRecord	of(String assembly, String chromosome, int position, String ref, String alt)
VcfRecordBuilder	pass()	If this method is called, "PASS" is added to the FILTER column
VcfRecordBuilder	qual(String qual)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

of

public static org.ga4gh.vrsatile.v1.VcfRecord of(String assembly,
 String chromosome,
 int position,
 String ref,
 String alt)

builder

public static VcfRecordBuilder builder(String assembly,
 String chromosome,
 int position,
 String ref,
 String alt)

id

public VcfRecordBuilder id(String id)

Identifier: Semicolon-separated list of unique identifiers where available If this is a dbSNP/dbVAR variant these rsID/nsvID(s) should be used.

Parameters:

id - identifier for this variant

qual

public VcfRecordBuilder qual(String qual)

Parameters:

qual - : Phred-scaled quality score for the assertion made in ALT.

pass

public VcfRecordBuilder pass()

If this method is called, "PASS" is added to the FILTER column

filter

public VcfRecordBuilder filter(String filter)

Parameters:

filter - FILTER field of VCF. calling pass() is equivant to calling filter("PASS)

info

public VcfRecordBuilder info(String info)

Parameters:

info - Additional information: Semicolon-separated series of additional information fields

build

public org.ga4gh.vrsatile.v1.VcfRecord build()