Interface | Description |
---|---|
BAMIndex |
A basic interface for querying BAM indices.
|
BinningIndexBuilder.FeatureToBeIndexed |
coordinates are 1-based, inclusive
|
BrowseableBAMIndex |
An index interface with additional functionality for querying and inspecting the structure of a BAM index.
|
CoordinateSortedPairInfoMap.Codec<KEY,REC> |
Client must implement this class, which defines the way in which records are written to and
read from file.
|
CustomReaderFactory.ICustomReaderFactory |
Interface to be implemented by custom factory classes that register
themselves with this factory and are loaded dynamically.
|
SAMFileSpan |
A interface representing a collection of (possibly) discontinuous segments in the
BAM file, possibly representing the results of an index query.
|
SAMFileWriter |
Interface for SAMText and BAM file writers.
|
SamReader |
Describes functionality for objects that produce
SAMRecord s and associated information. |
SamReader.Indexing |
Facet for index-related operations.
|
SamReader.PrimitiveSamReader |
The minimal subset of functionality needed for a
SAMRecord data source. |
SAMRecordComparator |
Interface for comparators that define the various SAM sort orders.
|
SAMRecordFactory |
Factory interface which allows plugging in of different classes for generating instances of
SAMRecord and BAMRecord when reading from SAM/BAM files.
|
SAMRecordIterator |
A general interface that adds functionality to a CloseableIterator of
SAMRecords.
|
Class | Description |
---|---|
AbstractBAMFileIndex |
Provides basic, generic capabilities to be used reading BAM index files.
|
AbstractSAMHeaderRecord |
Base class for the various concrete records in a SAM header, providing uniform
access to the attributes.
|
AlignmentBlock |
Represents the contiguous alignment of a subset of read bases to a reference
sequence.
|
BamFileIoUtils | |
BAMFileReader |
Class for reading and querying BAM files.
|
BAMFileSpan |
An ordered list of chunks, capable of representing a set of discontiguous
regions in the BAM file.
|
BAMIndexer |
Class for both constructing BAM index content and writing it out.
|
BAMIndexMetaData |
Metadata about the bam index contained within the bam index.
|
BamIndexValidator |
Class to validate (at two different levels of thoroughness) the index for a BAM file.
|
BAMQueryMultipleIntervalsIteratorFilter |
Filters out records that do not match any of the given intervals and query type.
|
BAMRecord |
Wrapper class for binary BAM records.
|
BAMRecordCodec |
Class for translating between in-memory and disk representation of BAMRecord.
|
Bin |
An individual bin in a BAM file.
|
BinaryTagCodec |
Converter between disk and in-memory representation of a SAMRecord tag.
|
BinList |
Provides a list of all bins which could exist in the BAM file.
|
BinningIndexBuilder |
Builder for a BinningIndexContent object.
|
BinningIndexContent |
In-memory representation of the binning index for a single reference.
|
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
|
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.
|
CigarElement |
One component of a cigar string.
|
CoordinateSortedPairInfoMap<KEY,REC> |
Holds info about a mate pair for use when processing a coordinate sorted file.
|
CRAMBAIIndexer |
Class for both constructing BAM index content and writing it out.
|
CRAMContainerStreamWriter |
Class for writing SAMRecords into a series of CRAM containers on an output stream.
|
CRAMCRAIIndexer |
Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.
|
CRAMFileReader |
BAMFileReader analogue for CRAM files. |
CRAMFileWriter | |
CRAMIterator | |
CustomReaderFactory |
Factory for creating custom readers for accessing API based resources,
e.g.
|
Defaults |
Embodies defaults for global values that affect how the SAM JDK operates.
|
DefaultSAMRecordFactory |
Default factory for creating SAM and BAM records used by the
SamReader classes. |
DiskBasedBAMFileIndex |
A class for reading BAM file indices, hitting the disk once per query.
|
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.
|
DownsamplingIteratorFactory |
A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while
meeting various criteria.
|
DuplicateScoringStrategy |
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
during duplicate marking (see MarkDuplicates).
|
DuplicateSet |
Stores a set of records that are duplicates of each other.
|
DuplicateSetIterator |
An iterator of sets of duplicates.
|
FixBAMFile | Deprecated
since 07/2017.
|
GenomicIndexUtil |
Constants and methods used by BAM and Tribble indices
|
LinearIndex |
The linear index associated with a given reference in a BAM index.
|
MergingSamRecordIterator |
Provides an iterator interface for merging multiple underlying iterators into a single
iterable stream.
|
NotPrimarySkippingIterator | Deprecated
use
SecondaryAlignmentSkippingIterator instead. |
QueryInterval |
Interval relative to a reference, for querying a BAM file.
|
ReservedTagConstants |
Constants for tags used in our SAM/BAM files
|
SAMBinaryTagAndUnsignedArrayValue |
Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because
signedness cannot be determined by introspection of value.
|
SAMBinaryTagAndValue |
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
|
SAMFileHeader |
Header information from a SAM or BAM file.
|
SAMFileHeader.PgIdGenerator |
Little class to generate program group IDs
|
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.
|
SamFiles | |
SAMFileSource |
Represents the origin of a SAM record.
|
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
|
SamFileValidator.ValidationMetrics | |
SAMFileWriterFactory |
Create a writer for writing SAM, BAM, or CRAM files.
|
SAMFileWriterImpl |
Base class for implementing SAM writer with any underlying format.
|
SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord> |
Provides ordering based on SAM header records' attribute values.
|
SamInputResource |
Describes a SAM-like resource, including its data (where the records are), and optionally an index.
|
SAMLineParser |
This class enables creation of a SAMRecord object from a String in SAM text format.
|
SamPairUtil |
Utility methods for pairs of SAMRecords
|
SamPairUtil.SetMateInfoIterator |
A class to iterate through SAMRecords and set mate information on the given records, and optionally
set the mate cigar tag (true by default).
|
SAMProgramRecord |
In-memory representation of @PG SAM header record.
|
SamReader.AssertingIterator | |
SamReader.PrimitiveSamReaderToSamReaderAdapter |
Decorator for a
SamReader.PrimitiveSamReader that expands its functionality into a SamReader ,
given the backing SamInputResource . |
SamReader.ReaderImplementation |
Internal interface for SAM/BAM/CRAM file reader implementations,
as distinct from non-file-based readers.
|
SamReader.Type |
Describes a type of SAM file.
|
SamReaderFactory |
Describes the functionality for producing
SamReader , and offers a
handful of static generators. |
SAMReadGroupRecord |
Header information about a read group.
|
SAMRecord |
Java binding for a SAM file record.
|
SAMRecord.SAMTagAndValue |
Tag name and value of an attribute, for getAttributes() method.
|
SAMRecordCoordinateComparator |
Comparator for sorting SAMRecords by coordinate.
|
SAMRecordDuplicateComparator |
Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).
|
SAMRecordQueryHashComparator |
SAMRecord comparator that provides an ordering based on a hash of the queryname.
|
SAMRecordQueryNameComparator |
Comparator for "queryname" ordering of SAMRecords.
|
SAMRecordSetBuilder |
Factory class for creating SAMRecords for testing purposes.
|
SAMSequenceDictionary |
Collection of SAMSequenceRecords.
|
SAMSequenceDictionaryCodec |
"On the fly" codec SAMSequenceDictionaryCodec.
|
SAMSequenceRecord |
Header information about a reference sequence.
|
SAMSortOrderChecker |
Encapsulates simple check for SAMRecord order.
|
SamStreams |
Utilities related to processing of
InputStream s encoding SAM data |
SAMTagUtil |
Facility for converting between String and short representation of a SAM tag.
|
SAMTestUtil |
Misc methods for SAM-related unit tests.
|
SAMTextHeaderCodec |
Parser for a SAM text header, and a generator of SAM text header.
|
SAMTextWriter |
Writer for text-format SAM files.
|
SAMTools | Deprecated
since 07/2017.
|
SAMUtils |
Utilty methods.
|
SAMValidationError |
Class that encapsulates a validation error message as well as a type code so that
errors can be aggregated by type.
|
SecondaryAlignmentSkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary elements.
|
SecondaryOrSupplementarySkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.
|
SQTagUtil |
Utility methods for encoding and decoding the SQ tag value of SAMRecord.
|
SRAFileReader | |
SRAIndex |
Emulates BAM index so that we can request chunks of records from SRAFileReader
Here is how it works:
SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as
a length of all references.
|
SRAIterator |
SRA iterator which returns SAMRecords for requested list of chunks
|
SRAIterator.RecordRangeInfo |
Describes record ranges info needed for emulating BAM index
|
TagValueAndUnsignedArrayFlag |
CVO to use as a method return value.
|
TextCigarCodec |
Convert between String and Cigar class representations of CIGAR.
|
TextTagCodec |
Converter between SAM text representation of a tag, and in-memory Object representation.
|
Enum | Description |
---|---|
BamIndexValidator.IndexValidationStringency | |
CigarOperator |
The operators that can appear in a cigar string, and information about their disk representations.
|
DownsamplingIteratorFactory.Strategy |
Describes the available downsampling strategies.
|
DuplicateScoringStrategy.ScoringStrategy | |
SAMFileHeader.GroupOrder | |
SAMFileHeader.SortOrder |
Ways in which a SAM or BAM may be sorted.
|
SAMFlag |
SAM flags as enum, to be used in GUI, menu, etc...
|
SamFlagField |
This determines how flag fields are represented in the SAM file.
|
SamIndexes |
A helper class to read BAI and CRAI indexes.
|
SamPairUtil.PairOrientation |
The possible orientations of paired reads.
|
SamReaderFactory.Option |
A collection of binary
SamReaderFactory options. |
SAMReadGroupRecord.PlatformValue | |
SAMTag |
The standard tags for a SAM record that are defined in the SAM spec.
|
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.
|
ValidationStringency |
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
Exception | Description |
---|---|
FileTruncatedException |
Thrown when it is possible to detect that a SAM or BAM file is truncated.
|
SAMException | |
SAMFormatException |
Thrown when a SAM file being read or decoded (text or binary) looks bad.
|
SAMTestUtil.SanityCheckFailedException |
Indicates that a required sanity-check condition was not met.
|