Package org.pharmgkb.parser.vcf

Class VcfParser

java.lang.Object

org.pharmgkb.parser.vcf.VcfParser

All Implemented Interfaces:

Closeable, AutoCloseable

public class VcfParser
extends Object
implements Closeable

This class parses a VCF file.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	VcfParser.Builder

Method Summary

Modifier and Type	Method	Description
void	close()
int	getLineNumber()
VcfMetadata	getMetadata()	Gets VCF metadata (if it has already been parsed).
void	parse()	Parses the entire VCF file (including the metadata).
VcfMetadata	parseMetadata()	Parses metadata only.
boolean	parseNextLine()	Parses just the next data line available, also reading all the metadata if it has not been read.

Methods inherited from class java.lang.Object

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

Method Details

parseMetadata

@Nonnull
public VcfMetadata parseMetadata()
                          throws IOException

Parses metadata only. This method should be if only the metadata is needed; otherwise, parse() is preferred.

Throws:

IOException

getMetadata

@Nullable
public VcfMetadata getMetadata()

Gets VCF metadata (if it has already been parsed).

parse

public void parse()
           throws IOException

Parses the entire VCF file (including the metadata).

This is the preferred way to read a VCF file.

Throws:

IOException

parseNextLine

public boolean parseNextLine()
                      throws IOException,
VcfFormatException

Parses just the next data line available, also reading all the metadata if it has not been read. This is a specialized method; in general calling parse() to parse the entire stream is preferred.

Returns:

Whether another line may be available to read; false only if and only if this is the last line available

Throws:

IllegalStateException - If the stream was already fully parsed

VcfFormatException - If a VCF formatting error is found

IOException

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

getLineNumber

public int getLineNumber()