pro.parseq.vcf.utils

Interface VcfParser

All Known Implementing Classes:

VcfParserImpl

public interface VcfParser

Interface for parsing VCF files

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Method Summary

Modifier and Type	Method and Description
VcfFile	parse(VcfReader reader, FaultTolerance mode) Parses input VCF file

Method Detail

parse

VcfFile parse(VcfReader reader,
              FaultTolerance mode)
       throws InvalidVcfFileException

Parses input VCF file

Parameters:

reader - VCF file reader

mode - Parsing mode (can be switched to fail fast or fail safe)

Returns:

VcfFile representing VCF file data

Throws:

InvalidVcfFileException - if input VCF file is malformed