Package org.broadinstitute.hellbender.tools.copynumber.formats.collections
package org.broadinstitute.hellbender.tools.copynumber.formats.collections
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ClassDescriptionAbstractLocatableCollection<METADATA extends LocatableMetadata,
RECORD extends htsjdk.samtools.util.Locatable> Represents a sequence dictionary, an immutable, coordinate-sorted (with no overlaps allowed) collection of records that extendLocatable(although contigs are assumed to be non-null when writing to file), a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records.RepresentsAbstractRecordCollection(which can be represented as aSAMFileHeader), an immutable collection of records, a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records.AbstractSampleLocatableCollection<RECORD extends htsjdk.samtools.util.Locatable>Represents a sample name, a sequence dictionary, an immutable, coordinate-sorted (with no overlaps allowed) collection of records that extendLocatable(although contigs are assumed to be non-null when writing to file), a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records.AbstractSampleRecordCollection<RECORD>Represents a sample name, an immutable collection of records, a set of mandatory column headers given by aTableColumnCollection, and lambdas for reading and writing records.Simple data structure to pass and read/write a List ofAllelicCountobjects.Represents a collection of intervals annotated withCopyNumberAnnotations.Collection of baseline copy-number states.Represents a CBS-style segmentation to enable IGV-compatible plotting.Collection of integer copy-number posteriors.Represents a sequence dictionary and total coverage over each contig in an ordered set associated with a cohort of named samples.Helper class forSimpleCountCollectionused to read/write HDF5.Represents a collection ofIntegerCopyNumberSegmentfor a sample.Represents a CBS-style segmentation to enable IGV-compatible plotting.Collection of copy ratios in linear space generated byGermlineCNVCallerwith their corresponding intervalsA collection representing a real valued vector generated byGermlineCNVCallerSimple data structure to pass and read/write a List ofSimpleCountobjects.CONTIG, START, END, COUNT Note: Unlike the package-private enums in other collection classes, this enum and itsTableColumnCollectionare public so that they can be accessed bySimpleCountCodec, which must be in org.broadinstitute.hellbender.utils.codecs to be discovered as a codec.Represents a collection ofSimpleInterval.