org.pharmgkb.parser.vcf

Class VcfWriter

java.lang.Object

org.pharmgkb.parser.vcf.VcfWriter

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class VcfWriter
extends java.lang.Object
implements java.io.Closeable

Writes to VCF format from a VcfSample, VcfPositions, and VcfMetadata. For now, this class performs little validation of its own, relying on VcfParser instead. For that reason, it is currently package-accessible only.

See Also:

TransformingVcfLineParser - a read-transform-write streamer that is publically accessible

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VcfWriter.Builder

Method Summary

Modifier and Type	Method and Description
void	close()
void	writeHeader(VcfMetadata metadata)
void	writeLine(VcfMetadata metadata, VcfPosition position, java.util.List<VcfSample> samples)

Methods inherited from class java.lang.Object

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

Method Detail

writeHeader

public void writeHeader(@Nonnull
                        VcfMetadata metadata)

writeLine

public void writeLine(@Nonnull
                      VcfMetadata metadata,
                      @Nonnull
                      VcfPosition position,
                      @Nonnull
                      java.util.List<VcfSample> samples)

close

public void close()

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable