public class VCFEncoder
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.nio.charset.Charset |
VCF_CHARSET
The encoding used for VCF files: ISO-8859-1
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Constructor and Description |
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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.
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Modifier and Type | Method and Description |
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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
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void |
setAllowMissingFieldsInHeader(boolean allow)
Deprecated.
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void |
setVCFHeader(VCFHeader header)
Deprecated.
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public static final java.nio.charset.Charset VCF_CHARSET
public VCFEncoder(VCFHeader header, boolean allowMissingFieldsInHeader, boolean outputTrailingFormatFields)
@Deprecated public void setVCFHeader(VCFHeader header)
@Deprecated public void setAllowMissingFieldsInHeader(boolean allow)
public java.lang.String encode(VariantContext context)
public static java.lang.String formatVCFDouble(double d)
d
- public void addGenotypeData(VariantContext vc, java.util.Map<Allele,java.lang.String> alleleMap, java.util.List<java.lang.String> genotypeFormatKeys, java.lang.StringBuilder builder)
public java.util.Map<Allele,java.lang.String> buildAlleleStrings(VariantContext vc)