Serialized Form

Package org.bdgenomics.convert.htsjdk

Class org.bdgenomics.convert.htsjdk.AlignmentToSamRecord extends AbstractConverter<org.bdgenomics.formats.avro.Alignment,htsjdk.samtools.SAMRecord> implements Serializable

Serialized Fields

header

htsjdk.samtools.SAMFileHeader header

Header.

Class org.bdgenomics.convert.htsjdk.GenotypesToVariantContext extends AbstractConverter<List<org.bdgenomics.formats.avro.Genotype>,htsjdk.variant.variantcontext.VariantContext> implements Serializable

Serialized Fields

header

htsjdk.variant.vcf.VCFHeader header

Header.

Class org.bdgenomics.convert.htsjdk.SamHeaderToProcessingSteps extends AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.ProcessingStep>> implements Serializable

Serialized Fields

processingStepConverter

Converter<htsjdk.samtools.SAMProgramRecord,org.bdgenomics.formats.avro.ProcessingStep> processingStepConverter

Convert a SAMProgramRecord to a ProcessingStep.

Class org.bdgenomics.convert.htsjdk.SamHeaderToReadGroups extends AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.ReadGroup>> implements Serializable

Serialized Fields

readGroupConverter

Converter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup> readGroupConverter

Convert a SAMReadGroupRecord to a ReadGroup.

Class org.bdgenomics.convert.htsjdk.SamHeaderToReferences extends AbstractConverter<htsjdk.samtools.SAMFileHeader,List<org.bdgenomics.formats.avro.Reference>> implements Serializable

Serialized Fields

referenceConverter

Converter<htsjdk.samtools.SAMSequenceRecord,org.bdgenomics.formats.avro.Reference> referenceConverter

Convert SAMSequenceRecord to Reference.

Class org.bdgenomics.convert.htsjdk.SamProgramRecordToProcessingStep extends AbstractConverter<htsjdk.samtools.SAMProgramRecord,org.bdgenomics.formats.avro.ProcessingStep> implements Serializable

Class org.bdgenomics.convert.htsjdk.SamReadGroupRecordToReadGroup extends AbstractConverter<htsjdk.samtools.SAMReadGroupRecord,org.bdgenomics.formats.avro.ReadGroup> implements Serializable

Class org.bdgenomics.convert.htsjdk.SamRecordToAlignment extends AbstractConverter<htsjdk.samtools.SAMRecord,org.bdgenomics.formats.avro.Alignment> implements Serializable

Class org.bdgenomics.convert.htsjdk.SamSequenceRecordToReference extends AbstractConverter<htsjdk.samtools.SAMSequenceRecord,org.bdgenomics.formats.avro.Reference> implements Serializable

Class org.bdgenomics.convert.htsjdk.VariantContextToGenotypes extends AbstractConverter<htsjdk.variant.variantcontext.VariantContext,List<org.bdgenomics.formats.avro.Genotype>> implements Serializable

Serialized Fields

header

htsjdk.variant.vcf.VCFHeader header

Header.

Class org.bdgenomics.convert.htsjdk.VariantContextToVariants extends AbstractConverter<htsjdk.variant.variantcontext.VariantContext,List<org.bdgenomics.formats.avro.Variant>> implements Serializable

Serialized Fields

header

htsjdk.variant.vcf.VCFHeader header

Header.

Class org.bdgenomics.convert.htsjdk.VariantToVariantContext extends AbstractConverter<org.bdgenomics.formats.avro.Variant,htsjdk.variant.variantcontext.VariantContext> implements Serializable

Serialized Fields

header

htsjdk.variant.vcf.VCFHeader header

Header.

Class org.bdgenomics.convert.htsjdk.VcfHeaderToReferences extends AbstractConverter<htsjdk.variant.vcf.VCFHeader,List<org.bdgenomics.formats.avro.Reference>> implements Serializable

Serialized Fields

referenceConverter

Converter<htsjdk.samtools.SAMSequenceRecord,org.bdgenomics.formats.avro.Reference> referenceConverter

Convert SAMSequenceRecord to Reference.

Class org.bdgenomics.convert.htsjdk.VcfHeaderToSamples extends AbstractConverter<htsjdk.variant.vcf.VCFHeader,List<org.bdgenomics.formats.avro.Sample>> implements Serializable

Class org.bdgenomics.convert.htsjdk.VcfHeaderToVcfHeaderLines extends AbstractConverter<htsjdk.variant.vcf.VCFHeader,List<htsjdk.variant.vcf.VCFHeaderLine>> implements Serializable