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A

AlignmentToSamRecord - Class in org.bdgenomics.convert.htsjdk

Convert Alignment to htsjdk SAMRecord.

AlignmentToSamRecord(SAMFileHeader) - Constructor for class org.bdgenomics.convert.htsjdk.AlignmentToSamRecord

Create a new Alignment to htsjdk SAMRecord converter with the specified header.

AlignmentToSamRecordFactory - Interface in org.bdgenomics.convert.htsjdk

Factory for creating Alignment to htsjdk SAMRecord converters, which require late binding for a SAMFileHeader.

C

configure() - Method in class org.bdgenomics.convert.htsjdk.HtsjdkModule

convert(SAMFileHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamHeaderToProcessingSteps

convert(SAMFileHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamHeaderToReadGroups

convert(SAMFileHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamHeaderToReferences

convert(SAMProgramRecord, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamProgramRecordToProcessingStep

convert(SAMReadGroupRecord, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamReadGroupRecordToReadGroup

convert(SAMRecord, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamRecordToAlignment

convert(SAMSequenceRecord, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.SamSequenceRecordToReference

convert(VariantContext, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VariantContextToGenotypes

convert(VariantContext, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VariantContextToVariants

convert(VCFHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VcfHeaderToReferences

convert(VCFHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VcfHeaderToSamples

convert(VCFHeader, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VcfHeaderToVcfHeaderLines

convert(List<Genotype>, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.GenotypesToVariantContext

convert(Alignment, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.AlignmentToSamRecord

convert(Variant, ConversionStringency, Logger) - Method in class org.bdgenomics.convert.htsjdk.VariantToVariantContext

create(SAMFileHeader) - Method in interface org.bdgenomics.convert.htsjdk.AlignmentToSamRecordFactory

Create a new Alignment to htsjdk SAMRecord converter with the specified header.

create(VCFHeader) - Method in interface org.bdgenomics.convert.htsjdk.GenotypesToVariantContextFactory

Create a new list of Genotypes to VariantContext converter with the specified header.

create(VCFHeader) - Method in interface org.bdgenomics.convert.htsjdk.VariantContextToGenotypesFactory

Create a new VariantContext to list of Genotypes converter with the specified header.

create(VCFHeader) - Method in interface org.bdgenomics.convert.htsjdk.VariantContextToVariantsFactory

Create a new VariantContext to list of Variants converter with the specified header.

create(VCFHeader) - Method in interface org.bdgenomics.convert.htsjdk.VariantToVariantContextFactory

Create a new Variant to VariantContext converter with the specified header.

G

GenotypesToVariantContext - Class in org.bdgenomics.convert.htsjdk

Convert a list of Genotypes to a VariantContext.

GenotypesToVariantContext(VCFHeader) - Constructor for class org.bdgenomics.convert.htsjdk.GenotypesToVariantContext

Create a new list of Genotypes to VariantContext converter with the specified header.

GenotypesToVariantContextFactory - Interface in org.bdgenomics.convert.htsjdk

Factory for creating list of Genotypes to VariantContext converters, which require late binding for a VCFHeader.

H

HtsjdkModule - Class in org.bdgenomics.convert.htsjdk

Guice module for the org.bdgenomics.convert.htsjdk package.

HtsjdkModule() - Constructor for class org.bdgenomics.convert.htsjdk.HtsjdkModule

O

org.bdgenomics.convert.htsjdk - package org.bdgenomics.convert.htsjdk

Convert between htsjdk and bdg-formats data models.

S

SamHeaderToProcessingSteps - Class in org.bdgenomics.convert.htsjdk

Convert a SAMFileHeader to a list of ProcessingSteps.

SamHeaderToProcessingSteps() - Constructor for class org.bdgenomics.convert.htsjdk.SamHeaderToProcessingSteps

Create a new SAMFileHeader to a list of ProcessingSteps converter.

SamHeaderToReadGroups - Class in org.bdgenomics.convert.htsjdk

Convert a SAMFileHeader to a list of ReadGroups.

SamHeaderToReadGroups() - Constructor for class org.bdgenomics.convert.htsjdk.SamHeaderToReadGroups

Create a new SAMFileHeader to a list of ReadGroups converter.

SamHeaderToReadGroups(Converter<SAMReadGroupRecord, ReadGroup>) - Constructor for class org.bdgenomics.convert.htsjdk.SamHeaderToReadGroups

Create a new SAMFileHeader to a list of ReadGroups converter.

SamHeaderToReferences - Class in org.bdgenomics.convert.htsjdk

Convert a SAMFileHeader to a list of References.

SamHeaderToReferences() - Constructor for class org.bdgenomics.convert.htsjdk.SamHeaderToReferences

Create a new SAMFileHeader to a list of References converter.

SamProgramRecordToProcessingStep - Class in org.bdgenomics.convert.htsjdk

Convert a SAMProgramRecord to a ProcessingStep.

SamProgramRecordToProcessingStep() - Constructor for class org.bdgenomics.convert.htsjdk.SamProgramRecordToProcessingStep

Create a new SAMProgramRecord to a ProcessingStep converter.

SamReadGroupRecordToReadGroup - Class in org.bdgenomics.convert.htsjdk

Convert a SAMReadGroup to a ReadGroup.

SamReadGroupRecordToReadGroup() - Constructor for class org.bdgenomics.convert.htsjdk.SamReadGroupRecordToReadGroup

Create a new SAMReadGroupRecord to a ReadGroup converter.

SamRecordToAlignment - Class in org.bdgenomics.convert.htsjdk

Convert htsjdk SAMRecord to Alignment.

SamRecordToAlignment() - Constructor for class org.bdgenomics.convert.htsjdk.SamRecordToAlignment

Create a new htsjdk SAMRecord to Alignment converter.

SamSequenceRecordToReference - Class in org.bdgenomics.convert.htsjdk

Convert a SAMSequenceRecord to a Reference.

SamSequenceRecordToReference() - Constructor for class org.bdgenomics.convert.htsjdk.SamSequenceRecordToReference

Create a new SAMSequenceRecord to a Reference converter.

V

VariantContextToGenotypes - Class in org.bdgenomics.convert.htsjdk

Convert VariantContext to a list of Genotypes.

VariantContextToGenotypes(VCFHeader) - Constructor for class org.bdgenomics.convert.htsjdk.VariantContextToGenotypes

Create a new VariantContext to list of Genotypes converter with the specified header.

VariantContextToGenotypesFactory - Interface in org.bdgenomics.convert.htsjdk

Factory for creating VariantContext to list of Genotypes converters, which require late binding for a VCFHeader.

VariantContextToVariants - Class in org.bdgenomics.convert.htsjdk

Convert VariantContext to a list of Variants.

VariantContextToVariants(VCFHeader) - Constructor for class org.bdgenomics.convert.htsjdk.VariantContextToVariants

Create a new VariantContext to list of Variants converter with the specified header.

VariantContextToVariantsFactory - Interface in org.bdgenomics.convert.htsjdk

Factory for creating VariantContext to list of Variants converters, which require late binding for a VCFHeader.

VariantToVariantContext - Class in org.bdgenomics.convert.htsjdk

Convert a Variant to a VariantContext.

VariantToVariantContext(VCFHeader) - Constructor for class org.bdgenomics.convert.htsjdk.VariantToVariantContext

Create a new Variant to VariantContext converter with the specified header.

VariantToVariantContextFactory - Interface in org.bdgenomics.convert.htsjdk

Factory for creating Variant to VariantContext converters, which require late binding for a VCFHeader.

VcfHeaderToReferences - Class in org.bdgenomics.convert.htsjdk

Convert a VCFHeader to a list of References.

VcfHeaderToReferences() - Constructor for class org.bdgenomics.convert.htsjdk.VcfHeaderToReferences

Create a new VCFHeader to a list of References converter.

VcfHeaderToSamples - Class in org.bdgenomics.convert.htsjdk

Convert a VCFHeader to a list of Samples.

VcfHeaderToSamples() - Constructor for class org.bdgenomics.convert.htsjdk.VcfHeaderToSamples

Create a new VCFHeader to a list of Samples converter.

VcfHeaderToVcfHeaderLines - Class in org.bdgenomics.convert.htsjdk

Convert a VCFHeader to a list of VCFHeaderLines.

VcfHeaderToVcfHeaderLines() - Constructor for class org.bdgenomics.convert.htsjdk.VcfHeaderToVcfHeaderLines

Create a new VCFHeader to a list of VCFHeaderLines converter.

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