htsjdk.variant.vcf

Class VCFEncoder

java.lang.Object

htsjdk.variant.vcf.VCFEncoder

public class VCFEncoder
extends java.lang.Object

Functions specific to encoding VCF records.

Field Summary

Fields

Modifier and Type	Field and Description
static java.nio.charset.Charset	VCF_CHARSET The encoding used for VCF files: ISO-8859-1

Constructor Summary

Constructors

Constructor and Description
VCFEncoder(VCFHeader header, boolean allowMissingFieldsInHeader, boolean outputTrailingFormatFields) Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally allowing missing fields in the header.

Method Summary

Modifier and Type	Method and Description
void	addGenotypeData(VariantContext vc, java.util.Map<Allele,java.lang.String> alleleMap, java.util.List<java.lang.String> genotypeFormatKeys, java.lang.StringBuilder builder)
java.util.Map<Allele,java.lang.String>	buildAlleleStrings(VariantContext vc)
java.lang.String	encode(VariantContext context)
static java.lang.String	formatVCFDouble(double d) Takes a double value and pretty prints it to a String for display Large doubles => gets %.2f style formatting Doubles < 1 / 10 but > 1/100 => get %.3f style formatting Double < 1/100 => %.3e formatting
void	setAllowMissingFieldsInHeader(boolean allow) Deprecated.
void	setVCFHeader(VCFHeader header) Deprecated.

Methods inherited from class java.lang.Object

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

Field Detail

VCF_CHARSET

public static final java.nio.charset.Charset VCF_CHARSET

The encoding used for VCF files: ISO-8859-1

Constructor Detail

VCFEncoder

public VCFEncoder(VCFHeader header,
                  boolean allowMissingFieldsInHeader,
                  boolean outputTrailingFormatFields)

Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally allowing missing fields in the header.

Method Detail

setVCFHeader

@Deprecated
public void setVCFHeader(VCFHeader header)

Deprecated.

Please see the notes in the default constructor

setAllowMissingFieldsInHeader

@Deprecated
public void setAllowMissingFieldsInHeader(boolean allow)

Deprecated.

Please see the notes in the default constructor

encode

public java.lang.String encode(VariantContext context)

formatVCFDouble

public static java.lang.String formatVCFDouble(double d)

Takes a double value and pretty prints it to a String for display Large doubles => gets %.2f style formatting Doubles < 1 / 10 but > 1/100 => get %.3f style formatting Double < 1/100 => %.3e formatting

Parameters:

d -

Returns:

addGenotypeData

public void addGenotypeData(VariantContext vc,
                            java.util.Map<Allele,java.lang.String> alleleMap,
                            java.util.List<java.lang.String> genotypeFormatKeys,
                            java.lang.StringBuilder builder)

buildAlleleStrings

public java.util.Map<Allele,java.lang.String> buildAlleleStrings(VariantContext vc)