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Rename AlignmentRecord to Alignment. #2217

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Oct 1, 2019
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Rename AlignmentRecord to Alignment. #2217

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104 changes: 52 additions & 52 deletions adam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicDatasetConverters.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -26,15 +26,15 @@ import org.bdgenomics.adam.rdd.{
}
import org.bdgenomics.adam.rdd.feature.{ CoverageDataset, FeatureDataset }
import org.bdgenomics.adam.rdd.fragment.FragmentDataset
import org.bdgenomics.adam.rdd.read.{ AlignmentRecordDataset, ReadDataset }
import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, ReadDataset }
import org.bdgenomics.adam.rdd.sequence.{ SequenceDataset, SliceDataset }
import org.bdgenomics.adam.rdd.variant.{
VariantDataset,
GenotypeDataset,
VariantContextDataset
}
import org.bdgenomics.adam.sql.{
AlignmentRecord => AlignmentRecordProduct,
Alignment => AlignmentProduct,
Feature => FeatureProduct,
Fragment => FragmentProduct,
Genotype => GenotypeProduct,
Expand Down Expand Up @@ -62,9 +62,9 @@ trait ToFragmentDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]]
val yTag: TypeTag[FragmentProduct] = typeTag[FragmentProduct]
}

trait ToAlignmentRecordDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
trait ToAlignmentDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Alignment, AlignmentProduct, AlignmentDataset] {

val yTag: TypeTag[AlignmentRecordProduct] = typeTag[AlignmentRecordProduct]
val yTag: TypeTag[AlignmentProduct] = typeTag[AlignmentProduct]
}

trait ToGenotypeDatasetConversion[T, U <: Product, V <: GenomicDataset[T, U, V]] extends GenomicDatasetConversion[T, U, V, Genotype, GenotypeProduct, GenotypeDataset] {
Expand Down Expand Up @@ -109,10 +109,10 @@ final class CoverageToFragmentsDatasetConverter extends ToFragmentDatasetConvers
}
}

final class CoverageToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Coverage, Coverage, CoverageDataset] {
final class CoverageToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Coverage, Coverage, CoverageDataset] {

def call(v1: CoverageDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.coverageToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: CoverageDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.coverageToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -164,10 +164,10 @@ final class FeaturesToFragmentsDatasetConverter extends ToFragmentDatasetConvers
}
}

final class FeaturesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Feature, FeatureProduct, FeatureDataset] {
final class FeaturesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Feature, FeatureProduct, FeatureDataset] {

def call(v1: FeatureDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.featuresToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: FeatureDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.featuresToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -219,10 +219,10 @@ final class FragmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversi
}
}

final class FragmentsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Fragment, FragmentProduct, FragmentDataset] {
final class FragmentsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Fragment, FragmentProduct, FragmentDataset] {

def call(v1: FragmentDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.fragmentsToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: FragmentDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.fragmentsToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -260,57 +260,57 @@ final class FragmentsToVariantsDatasetConverter extends ToVariantDatasetConversi
}
}

final class AlignmentRecordsToCoverageDatasetConverter extends ToCoverageDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
def call(v1: AlignmentRecordDataset, v2: Dataset[Coverage]): CoverageDataset = {
ADAMContext.alignmentRecordsToCoverageDatasetConversionFn(v1, v2)
final class AlignmentsToCoverageDatasetConverter extends ToCoverageDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {
def call(v1: AlignmentDataset, v2: Dataset[Coverage]): CoverageDataset = {
ADAMContext.AlignmentsToCoverageDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToFeaturesDatasetConverter extends ToFeatureDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[FeatureProduct]): FeatureDataset = {
ADAMContext.alignmentRecordsToFeaturesDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[FeatureProduct]): FeatureDataset = {
ADAMContext.AlignmentsToFeaturesDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToFragmentsDatasetConverter extends ToFragmentDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[FragmentProduct]): FragmentDataset = {
ADAMContext.alignmentRecordsToFragmentsDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[FragmentProduct]): FragmentDataset = {
ADAMContext.AlignmentsToFragmentsDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToGenotypesDatasetConverter extends ToGenotypeDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[GenotypeProduct]): GenotypeDataset = {
ADAMContext.alignmentRecordsToGenotypesDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[GenotypeProduct]): GenotypeDataset = {
ADAMContext.AlignmentsToGenotypesDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToReadsDatasetConverter extends ToReadDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToReadsDatasetConverter extends ToReadDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[ReadProduct]): ReadDataset = {
ADAMContext.alignmentRecordsToReadsDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[ReadProduct]): ReadDataset = {
ADAMContext.AlignmentsToReadsDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToSequencesDatasetConverter extends ToSequenceDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToSequencesDatasetConverter extends ToSequenceDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[SequenceProduct]): SequenceDataset = {
ADAMContext.alignmentRecordsToSequencesDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[SequenceProduct]): SequenceDataset = {
ADAMContext.AlignmentsToSequencesDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToSlicesDatasetConverter extends ToSliceDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
final class AlignmentsToSlicesDatasetConverter extends ToSliceDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {

def call(v1: AlignmentRecordDataset, v2: Dataset[SliceProduct]): SliceDataset = {
ADAMContext.alignmentRecordsToSlicesDatasetConversionFn(v1, v2)
def call(v1: AlignmentDataset, v2: Dataset[SliceProduct]): SliceDataset = {
ADAMContext.AlignmentsToSlicesDatasetConversionFn(v1, v2)
}
}

final class AlignmentRecordsToVariantsDatasetConverter extends ToVariantDatasetConversion[AlignmentRecord, AlignmentRecordProduct, AlignmentRecordDataset] {
def call(v1: AlignmentRecordDataset, v2: Dataset[VariantProduct]): VariantDataset = {
ADAMContext.alignmentRecordsToVariantsDatasetConversionFn(v1, v2)
final class AlignmentsToVariantsDatasetConverter extends ToVariantDatasetConversion[Alignment, AlignmentProduct, AlignmentDataset] {
def call(v1: AlignmentDataset, v2: Dataset[VariantProduct]): VariantDataset = {
ADAMContext.AlignmentsToVariantsDatasetConversionFn(v1, v2)
}
}

Expand All @@ -334,10 +334,10 @@ final class GenotypesToFragmentsDatasetConverter extends ToFragmentDatasetConver
}
}

final class GenotypesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Genotype, GenotypeProduct, GenotypeDataset] {
final class GenotypesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Genotype, GenotypeProduct, GenotypeDataset] {

def call(v1: GenotypeDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.genotypesToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: GenotypeDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.genotypesToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -390,10 +390,10 @@ final class ReadsToFragmentsDatasetConverter extends ToFragmentDatasetConversion
}
}

final class ReadsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Read, ReadProduct, ReadDataset] {
final class ReadsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Read, ReadProduct, ReadDataset] {

def call(v1: ReadDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.readsToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: ReadDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.readsToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -446,10 +446,10 @@ final class SequencesToFragmentsDatasetConverter extends ToFragmentDatasetConver
}
}

final class SequencesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Sequence, SequenceProduct, SequenceDataset] {
final class SequencesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Sequence, SequenceProduct, SequenceDataset] {

def call(v1: SequenceDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.sequencesToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: SequenceDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.sequencesToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -502,10 +502,10 @@ final class SlicesToFragmentsDatasetConverter extends ToFragmentDatasetConversio
}
}

final class SlicesToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Slice, SliceProduct, SliceDataset] {
final class SlicesToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Slice, SliceProduct, SliceDataset] {

def call(v1: SliceDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.slicesToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: SliceDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.slicesToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down Expand Up @@ -557,10 +557,10 @@ final class VariantsToFragmentsDatasetConverter extends ToFragmentDatasetConvers
}
}

final class VariantsToAlignmentRecordsDatasetConverter extends ToAlignmentRecordDatasetConversion[Variant, VariantProduct, VariantDataset] {
final class VariantsToAlignmentsDatasetConverter extends ToAlignmentDatasetConversion[Variant, VariantProduct, VariantDataset] {

def call(v1: VariantDataset, v2: Dataset[AlignmentRecordProduct]): AlignmentRecordDataset = {
ADAMContext.variantsToAlignmentRecordsDatasetConversionFn(v1, v2)
def call(v1: VariantDataset, v2: Dataset[AlignmentProduct]): AlignmentDataset = {
ADAMContext.variantsToAlignmentsDatasetConversionFn(v1, v2)
}
}

Expand Down
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