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)
static java.util.Map<Allele,java.lang.String>	buildAlleleStrings(VariantContext vc) return a Map containing Allele -> String(allele position) for all Alleles in VC (as well as NO_CALL) ex: A,T,TC -> { A:0, T:1, TC:2, NO_CALL:EMPTY_ALLELE} This may be efficient when looking up values for many genotypes per VC
java.lang.String	encode(VariantContext context) encodes a VariantContext as a VCF line Depending on the use case it may be more efficient to write(Appendable, VariantContext) directly instead of creating an intermediate string.
static java.lang.String	encodeGtField(VariantContext vc, Genotype g) Easy way to generate the GT field for a Genotype.
static java.lang.String	formatVCFDouble(double d) Takes a double value and pretty prints it to a String for display
void	setAllowMissingFieldsInHeader(boolean allow) Deprecated. since 10/24/13 use the constructor
void	setVCFHeader(VCFHeader header) Deprecated. since 10/24/13 use the constructor
void	write(java.lang.Appendable vcfOutput, VariantContext context) encodes a VariantContext context as VCF, and writes it directly to an Appendable This may be more efficient than calling encode(VariantContext) and then writing the result since it avoids creating an intermediate string.
static void	writeGtField(java.util.Map<Allele,java.lang.String> alleleMap, java.lang.Appendable vcfoutput, Genotype g) write the encoded GT field for a Genotype

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. When writing VCF4.3 is implemented, this should change to UTF-8.

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. since 10/24/13 use the constructor

setAllowMissingFieldsInHeader

@Deprecated
public void setAllowMissingFieldsInHeader(boolean allow)

Deprecated. since 10/24/13 use the constructor

encode

public java.lang.String encode(VariantContext context)

encodes a VariantContext as a VCF line Depending on the use case it may be more efficient to write(Appendable, VariantContext) directly instead of creating an intermediate string.

Returns:

the VCF line

write

public void write(java.lang.Appendable vcfOutput,
                  VariantContext context)
           throws java.io.IOException

encodes a VariantContext context as VCF, and writes it directly to an Appendable This may be more efficient than calling encode(VariantContext) and then writing the result since it avoids creating an intermediate string.

Parameters:

vcfOutput - the Appendable to write to

context - the variant

Throws:

java.io.IOException

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)

writeGtField

public static void writeGtField(java.util.Map<Allele,java.lang.String> alleleMap,
                                java.lang.Appendable vcfoutput,
                                Genotype g)
                         throws java.io.IOException

write the encoded GT field for a Genotype

Parameters:

alleleMap - a mapping of Allele -> GT allele value (from this#buildAlleleStrings(VariantContext)

vcfoutput - the appendable to write to, to avoid inefficiency due to string copying

g - the genotoype to encode

Throws:

java.io.IOException - if appending fails with an IOException

encodeGtField

public static java.lang.String encodeGtField(VariantContext vc,
                                             Genotype g)

Easy way to generate the GT field for a Genotype. This will be less efficient than using this#writeGtField(Map, Appendable, Genotype) because of redundant Map initializations

Parameters:

vc - a VariantContext which must contain g or the results are likely to be incorrect

g - a Genotype in vc

Returns:

a String containing the encoding of the GT field of g

buildAlleleStrings

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

return a Map containing Allele -> String(allele position) for all Alleles in VC (as well as NO_CALL) ex: A,T,TC -> { A:0, T:1, TC:2, NO_CALL:EMPTY_ALLELE} This may be efficient when looking up values for many genotypes per VC