Class and Description |
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AbstractSAMHeaderRecord
Base class for the various concrete records in a SAM header, providing uniform
access to the attributes.
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AlignmentBlock
Represents the contiguous alignment of a subset of read bases to a reference
sequence.
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BAMFileSpan
An ordered list of chunks, capable of representing a set of discontiguous
regions in the BAM file.
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BAMIndex
A basic interface for querying BAM indices.
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BAMIndexMetaData
Metadata about the bam index contained within the bam index.
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BAMRecord
Wrapper class for binary BAM records.
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BAMRecordCodec
Class for translating between in-memory and disk representation of BAMRecord.
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Bin
An individual bin in a BAM file.
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BinList
Provides a list of all bins which could exist in the BAM file.
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BinningIndexBuilder.FeatureToBeIndexed
coordinates are 1-based, inclusive
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BinningIndexContent
In-memory representation of the binning index for a single reference.
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BinningIndexContent.BinList
This class is used to encapsulate the list of Bins store in the BAMIndexContent
While it is currently represented as an array, we may decide to change it to an ArrayList or other structure
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BrowseableBAMIndex
An index interface with additional functionality for querying and inspecting the structure of a BAM index.
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Chunk
A [start,stop) file pointer pairing into the BAM file, stored
as a BAM file index.
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Cigar
A list of CigarElements, which describes how a read aligns with the reference.
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CigarElement
One component of a cigar string.
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CigarOperator
The operators that can appear in a cigar string, and information about their disk representations.
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CoordinateSortedPairInfoMap.Codec
Client must implement this class, which defines the way in which records are written to and
read from file.
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CRAMFileWriter |
CustomReaderFactory
Factory for creating custom readers for accessing API based resources,
e.g.
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DefaultSAMRecordFactory
Default factory for creating SAM and BAM records used by the SAMFileReader classes.
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DownsamplingIterator
Abstract base class for all DownsamplingIterators that provides a uniform interface for recording
and reporting statistics bout how many records have been kept and discarded.
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DownsamplingIteratorFactory.Strategy
Describes the available downsampling strategies.
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DuplicateScoringStrategy.ScoringStrategy |
DuplicateSet
Stores a set of records that are duplicates of each other.
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LinearIndex
The linear index associated with a given reference in a BAM index.
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QueryInterval
Interval relative to a reference, for querying a BAM file.
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SAMBinaryTagAndValue
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
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SAMException |
SAMFileHeader
Header information from a SAM or BAM file.
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SAMFileHeader.GroupOrder |
SAMFileHeader.SortOrder
Ways in which a SAM or BAM may be sorted.
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SamFileHeaderMerger
Merges SAMFileHeaders that have the same sequences into a single merged header
object while providing read group translation for cases where read groups
clash across input headers.
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SAMFileReader
Deprecated.
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SAMFileSource
Represents the origin of a SAM record.
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SAMFileSpan
A interface representing a collection of (possibly) discontinuous segments in the
BAM file, possibly representing the results of an index query.
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SamFileValidator
Validates SAM files as follows:
checks sam file header for sequence dictionary
checks sam file header for read groups
for each sam record
reports error detected by SAMRecord.isValid()
validates NM (nucleotide differences) exists and matches reality
validates mate fields agree with data in the mate record
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SAMFileWriter
Interface for SAMText and BAM file writers.
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SAMFileWriterFactory
Create a writer for writing SAM, BAM, or CRAM files.
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SAMFileWriterImpl
Base class for implementing SAM writer with any underlying format.
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SAMFlag
SAM flags as enum, to be used in GUI, menu, etc...
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SamIndexes
A helper class to read BAI and CRAI indexes.
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SamInputResource
Describes a SAM-like resource, including its data (where the records are), and optionally an index.
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SamPairUtil.PairOrientation
The possible orientations of paired reads.
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SAMProgramRecord
In-memory representation of @PG SAM header record.
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SamReader
Describes functionality for objects that produce
SAMRecord s and associated information. |
SamReader.Indexing
Facet for index-related operations.
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SamReader.PrimitiveSamReader
The minimal subset of functionality needed for a
SAMRecord data source. |
SamReader.ReaderImplementation
Internal interface for SAM/BAM/CRAM file reader implementations,
as distinct from non-file-based readers.
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SamReader.Type
Describes a type of SAM file.
|
SamReaderFactory
Describes the functionality for producing
SamReader , and offers a
handful of static generators. |
SamReaderFactory.Option
A collection of binary
SamReaderFactory options. |
SAMReadGroupRecord
Header information about a read group.
|
SAMReadGroupRecord.PlatformValue |
SAMRecord
Java binding for a SAM file record.
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SAMRecord.SAMTagAndValue
Tag name and value of an attribute, for getAttributes() method.
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SAMRecordComparator
Interface for comparators that define the various SAM sort orders.
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SAMRecordDuplicateComparator
Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).
|
SAMRecordFactory
Factory interface which allows plugging in of different classes for generating instances of
SAMRecord and BAMRecord when reading from SAM/BAM files.
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SAMRecordIterator
A general interface that adds functionality to a CloseableIterator of
SAMRecords.
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SAMRecordQueryNameComparator
Comparator for "queryname" ordering of SAMRecords.
|
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
SAMSequenceRecord
Header information about a reference sequence.
|
SAMTag
The standard tags for a SAM record that are defined in the SAM spec.
|
SAMTagUtil
Facility for converting between String and short representation of a SAM tag.
|
SAMTestUtil.SanityCheckFailedException
Indicates that a required sanity-check condition was not met.
|
SAMValidationError
Class that encapsulates a validation error message as well as a type code so that
errors can be aggregated by type.
|
SAMValidationError.Severity |
SAMValidationError.Type |
SQTagUtil.SQBase
The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
|
SRAIterator.RecordRangeInfo
Describes record ranges info needed for emulating BAM index
|
ValidationStringency
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Class and Description |
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SAMException |
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
---|
SAMFileHeader
Header information from a SAM or BAM file.
|
SAMRecord
Java binding for a SAM file record.
|
ValidationStringency
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Class and Description |
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SAMBinaryTagAndValue
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
|
SAMRecord
Java binding for a SAM file record.
|
Class and Description |
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ValidationStringency
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Class and Description |
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SAMRecord
Java binding for a SAM file record.
|
Class and Description |
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SAMSequenceRecord
Header information about a reference sequence.
|
Class and Description |
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SAMBinaryTagAndValue
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
|
SAMFileHeader
Header information from a SAM or BAM file.
|
SAMRecord.SAMTagAndValue
Tag name and value of an attribute, for getAttributes() method.
|
ValidationStringency
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Class and Description |
---|
SAMFileHeader
Header information from a SAM or BAM file.
|
SAMRecord
Java binding for a SAM file record.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
---|
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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Chunk
A [start,stop) file pointer pairing into the BAM file, stored
as a BAM file index.
|
Cigar
A list of CigarElements, which describes how a read aligns with the reference.
|
SAMBinaryTagAndValue
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
|
SAMFileHeader
Header information from a SAM or BAM file.
|
SAMRecord
Java binding for a SAM file record.
|
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
SAMValidationError
Class that encapsulates a validation error message as well as a type code so that
errors can be aggregated by type.
|
SRAIterator.RecordRangeInfo
Describes record ranges info needed for emulating BAM index
|
ValidationStringency
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Class and Description |
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Cigar
A list of CigarElements, which describes how a read aligns with the reference.
|
CigarElement
One component of a cigar string.
|
SAMException |
SAMFileHeader
Header information from a SAM or BAM file.
|
SamReader
Describes functionality for objects that produce
SAMRecord s and associated information. |
SAMRecord
Java binding for a SAM file record.
|
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
SAMSequenceRecord
Header information about a reference sequence.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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BinningIndexContent
In-memory representation of the binning index for a single reference.
|
SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
Class and Description |
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SAMSequenceDictionary
Collection of SAMSequenceRecords.
|
SAMSequenceRecord
Header information about a reference sequence.
|