Package org.snpeff.outputFormatter

Class VcfOutputFormatter

java.lang.Object

org.snpeff.outputFormatter.OutputFormatter

org.snpeff.outputFormatter.VcfOutputFormatter

public class VcfOutputFormatter
extends OutputFormatter

Formats output as VCF

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	debug
static java.lang.String	VCF_INFO_OICR_NAME

Constructor Summary

Constructors

Constructor	Description
VcfOutputFormatter()
VcfOutputFormatter(java.util.List<VcfEntry> vcfEntries)	Add all vcf entries to a list (used only for debugging and test-cases)

Method Summary

Modifier and Type	Method	Description
protected void	addHeader()	Add header
protected void	addInfo(VcfEntry vcfEntry)	Add effects to INFO field
OutputFormatter	clone()
java.lang.String	endSection(Marker marker)	Finish up section
java.util.List<java.lang.String>	getNewHeaderLines()	New lines to be added to header
void	setFormatVersion(EffFormatVersion formatVersion)
void	setGatk(boolean gatk)
void	setLossOfFunction(boolean lossOfFunction)
void	setOutOffset(int outOffset)
void	startSection(Marker marker)	Starts a new section
java.lang.String	toString()
protected java.lang.String	toStringHeader()	Show header

Methods inherited from class org.snpeff.outputFormatter.OutputFormatter

add, close, print, printSection, setChrStr, setCommandLineStr, setConfig, setOutputFile, setShowHeader, setSupressOutput, setUseGeneId, setUseHgvs, setUseOicr, setUseSequenceOntology, setVariantEffectResutFilter, setVersion

Methods inherited from class java.lang.Object

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

Field Detail

debug

public static boolean debug

VCF_INFO_OICR_NAME

public static final java.lang.String VCF_INFO_OICR_NAME

See Also:

Constant Field Values

Constructor Detail

VcfOutputFormatter

public VcfOutputFormatter()

VcfOutputFormatter

public VcfOutputFormatter(java.util.List<VcfEntry> vcfEntries)

Add all vcf entries to a list (used only for debugging and test-cases)

Method Detail

addHeader

protected void addHeader()

Add header

addInfo

protected void addInfo(VcfEntry vcfEntry)

Add effects to INFO field

clone

public OutputFormatter clone()

Overrides:

clone in class OutputFormatter

endSection

public java.lang.String endSection(Marker marker)

Finish up section

Overrides:

endSection in class OutputFormatter

getNewHeaderLines

public java.util.List<java.lang.String> getNewHeaderLines()

New lines to be added to header

setFormatVersion

public void setFormatVersion(EffFormatVersion formatVersion)

setGatk

public void setGatk(boolean gatk)

setLossOfFunction

public void setLossOfFunction(boolean lossOfFunction)

setOutOffset

public void setOutOffset(int outOffset)

Overrides:

setOutOffset in class OutputFormatter

startSection

public void startSection(Marker marker)

Description copied from class: OutputFormatter

Starts a new section

Overrides:

startSection in class OutputFormatter

toString

public java.lang.String toString()

Overrides:

toString in class OutputFormatter

toStringHeader

protected java.lang.String toStringHeader()

Show header

Specified by:

toStringHeader in class OutputFormatter