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 final String

VCF_INFO_OICR_NAME
Constructor Summary

Constructors

Constructor

Description

VcfOutputFormatter()

VcfOutputFormatter(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()

String

endSection(Marker marker)

Finish up section

List<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

String

toString()

protected 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 Details
- debug
  
  public static boolean debug
- VCF_INFO_OICR_NAME
  
  public static final String VCF_INFO_OICR_NAME
  See Also:
  
  Constant Field Values
Constructor Details
- VcfOutputFormatter
  
  public VcfOutputFormatter()
- VcfOutputFormatter
  
  public VcfOutputFormatter(List<VcfEntry> vcfEntries)
  
  Add all vcf entries to a list (used only for debugging and test-cases)
Method Details
- 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 String endSection(Marker marker)
  
  Finish up section
  
  Overrides:
  
  endSection in class OutputFormatter
- getNewHeaderLines
  
  public List<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 String toString()
  
  Overrides:
  
  toString in class OutputFormatter
- toStringHeader
  
  protected String toStringHeader()
  
  Show header
  
  Specified by:
  
  toStringHeader in class OutputFormatter

Class VcfOutputFormatter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.outputFormatter.OutputFormatter

Methods inherited from class java.lang.Object

Field Details

debug

VCF_INFO_OICR_NAME

Constructor Details

VcfOutputFormatter

VcfOutputFormatter

Method Details

addHeader

addInfo

clone

endSection

getNewHeaderLines

setFormatVersion

setGatk

setLossOfFunction

setOutOffset

startSection

toString

toStringHeader