ADAM_2.10: Core 0.23.0 API

CollectingSnps

ComputeCovariates

ComputeQualityScore

ComputingCycleCovariate

ComputingDinucCovariate

ComputingOriginalScores

ConsensusGenerator

consensus

Contig

sql

ContigField

ConvertToSAM

ConvertToSAMRecord

Coverage

CoverageRDD

CreateIndelRealignmentTargets

CreateReferencePositionPair

CreatingKnownSnpsTable

CreatingRecalibrationTable

MdTag AlignmentRecord Contig Dbxref Feature Fragment Genotype NucleotideContigFragment OntologyTerm ProcessingStep TranscriptEffect Variant VariantAnnotation VariantCallingAnnotations

call

GenomicDatasetConversion

canEqual

caseSensitive

Alphabet DNAAlphabet

cdnaLength

cdnaPosition

cdsLength

cdsPosition

DefaultHeaderLines AlignmentRecordField VariantAnnotationField AlignmentRecord VariantAnnotation

cigar

cigarX

cigarY

circular

collapse

commandLine

companion

InFormatter BEDInFormatter GFF3InFormatter GTFInFormatter NarrowPeakInFormatter InterleavedFASTQInFormatter Tab5InFormatter Tab6InFormatter BAMInFormatter FASTQInFormatter SAMInFormatter VCFInFormatter

compare

OptionalReferenceOrdering ReferenceOrdering

compareTo

ReferenceRegion

complement

Symbol

compute

ShuffleRegionJoin

computeMismatchingPositions

AlignmentRecordRDD

conf

VCFInFormatter VCFOutFormatter

consensus

algorithms

contains

ReferenceRegion

containsRefName

SequenceDictionary

contig

rdd

contigLength

ContigField NucleotideContigFragmentField Contig NucleotideContigFragment

contigMD5

ContigField Contig

contigMap

ReferenceContigMap

contigName

Coverage AlignmentRecordField ContigField FeatureField GenotypeField NucleotideContigFragmentField VariantField AlignmentRecord Contig Feature Genotype NucleotideContigFragment Variant

contigsToAlignmentRecordsConversionFn

contigsToAlignmentRecordsDatasetConversionFn

contigsToCoverageConversionFn

contigsToCoverageDatasetConversionFn

contigsToFeaturesConversionFn

contigsToFeaturesDatasetConversionFn

contigsToFragmentsConversionFn

contigsToFragmentsDatasetConversionFn

contigsToGenotypesConversionFn

contigsToGenotypesDatasetConversionFn

contigsToVariantContextConversionFn

contigsToVariantsConversionFn

contigsToVariantsDatasetConversionFn

AlignmentRecordConverter VariantContextConverter

convert

convertFragment

convertSAMTagAndValue

AttributeUtils

convertSecondReadToTab5

convertToFastq

convertToSam

AlignmentRecordRDD

convertToTab5

convertToTab6

AnySAMInFormatter BAMInFormatter SAMInFormatter VCFInFormatter

converter

converters

adam

count

Coverage

countKmers

NucleotideContigFragmentRDD AlignmentRecordRDD

countKmersAsDataset

AlignmentRecordRDD

countOfMismatches

MdTag

coverage

CoverageRDD

coverageToAlignmentRecordsConversionFn

coverageToAlignmentRecordsDatasetConversionFn

coverageToContigsConversionFn

coverageToContigsDatasetConversionFn

coverageToFeaturesConversionFn

coverageToFeaturesDatasetConversionFn

coverageToFragmentsConversionFn

coverageToFragmentsDatasetConversionFn

coverageToGenotypesConversionFn

coverageToGenotypesDatasetConversionFn

coverageToVariantContextConversionFn

coverageToVariantsConversionFn

InterleavedFastqInputFormat SingleFastqInputFormat

coverageToVariantsDatasetConversionFn

covers

coversBy

createPredicate

createRecordReader

createSAMHeader