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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addHeader()
Add headerprotected void
addInfo(VcfEntry vcfEntry)
Add effects to INFO fieldOutputFormatter
clone()
java.lang.String
endSection(Marker marker)
Finish up sectionjava.util.List<java.lang.String>
getNewHeaderLines()
New lines to be added to headervoid
setFormatVersion(EffFormatVersion formatVersion)
void
setGatk(boolean gatk)
void
setLossOfFunction(boolean lossOfFunction)
void
setOutOffset(int outOffset)
void
startSection(Marker marker)
Starts a new sectionjava.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
-
-
-
-
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 classOutputFormatter
-
endSection
public java.lang.String endSection(Marker marker)
Finish up section- Overrides:
endSection
in classOutputFormatter
-
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 classOutputFormatter
-
startSection
public void startSection(Marker marker)
Description copied from class:OutputFormatter
Starts a new section- Overrides:
startSection
in classOutputFormatter
-
toString
public java.lang.String toString()
- Overrides:
toString
in classOutputFormatter
-
toStringHeader
protected java.lang.String toStringHeader()
Show header- Specified by:
toStringHeader
in classOutputFormatter
-
-