AbstractBAMFileIndex |
Provides basic, generic capabilities to be used reading BAM index files.
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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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BamFileIoUtils |
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BAMFileReader |
Class for reading and querying BAM files.
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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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BAMFileWriter |
Concrete implementation of SAMFileWriter for writing gzipped BAM files.
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BAMIndexer |
Class for both constructing BAM index content and writing it out.
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BAMIndexMerger |
Merges BAM index files for (headerless) parts of a BAM file into a single
index file.
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BAMIndexMetaData |
Metadata about the bam index contained within the bam index.
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BamIndexValidator |
Class to validate (at two different levels of thoroughness) the index for a BAM file.
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BAMQueryMultipleIntervalsIteratorFilter |
Filters out records that do not match any of the given intervals and query type.
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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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BAMSBIIndexer |
Writes SBI files for BAM files, as understood by SBIIndex .
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BAMStartingAtIteratorFilter |
A decorating iterator that filters out records that do not match the given reference and start position.
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BAMStreamWriter |
Class for writing SAMRecords in BAM format to an output stream.
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Bin |
An individual bin in a BAM file.
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BinaryTagCodec |
Converter between disk and in-memory representation of a SAMRecord tag.
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BinList |
Provides a list of all bins which could exist in the BAM file.
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BinningIndexBuilder |
Builder for a BinningIndexContent object.
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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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BinWithOffset |
An individual bin of a CSI index for BAM files.
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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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CoordinateSortedPairInfoMap<KEY,REC> |
Holds info about a mate pair for use when processing a coordinate sorted file.
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CRAMBAIIndexer |
Class for both constructing BAM index content and writing it out.
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CRAMContainerStreamWriter |
Class for writing SAMRecords into a series of CRAM containers on an output stream, with an optional index.
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CRAMCRAIIndexer |
Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream.
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CRAMFileReader |
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CRAMFileWriter |
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CRAMIterator |
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CSIIndex |
Implementation of the CSI index for BAM files.
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CustomReaderFactory |
Factory for creating custom readers for accessing API based resources,
e.g.
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Defaults |
Embodies defaults for global values that affect how the SAM JDK operates.
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DefaultSAMRecordFactory |
Default factory for creating SAM and BAM records used by the SamReader classes.
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DiskBasedBAMFileIndex |
A class for reading BAM file indices, hitting the disk once per query.
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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 |
A factory for creating DownsamplingIterators that uses a number of different strategies to achieve downsampling while
meeting various criteria.
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DuplicateScoringStrategy |
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
during duplicate marking (see MarkDuplicates).
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DuplicateSet |
Stores a set of records that are duplicates of each other.
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DuplicateSetIterator |
An iterator of sets of duplicates.
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GenomicIndexUtil |
Constants and methods used by BAM and Tribble indices
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HtsgetBAMFileReader |
Class for reading and querying BAM files from an htsget source
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IndexMerger<T> |
Merges index files for (headerless) parts of a partitioned main file into a single index file.
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LinearIndex |
The linear index associated with a given reference in a BAM index.
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MergingSamRecordIterator |
Provides an iterator interface for merging multiple underlying iterators into a single
iterable stream.
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NotPrimarySkippingIterator |
Deprecated.
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QueryInterval |
Interval relative to a reference, for querying a BAM file.
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ReservedTagConstants |
Constants for tags used in our SAM/BAM files
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SAMBinaryTagAndUnsignedArrayValue |
Simple extension to SAMBinaryTagAndValue in order to distinguish unsigned array values, because
signedness cannot be determined by introspection of value.
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SAMBinaryTagAndValue |
Holds a SAMRecord attribute and the tagname (in binary form) for that attribute.
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SAMFileHeader |
Header information from a SAM or BAM file.
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SAMFileHeader.PgIdGenerator |
Little class to generate program group IDs
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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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SamFiles |
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SAMFileSource |
Represents the origin of a SAM record.
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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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SamFileValidator.ValidationMetrics |
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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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SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord> |
Provides ordering based on SAM header records' attribute values.
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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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SAMLineParser |
This class enables creation of a SAMRecord object from a String in SAM text format.
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SamPairUtil |
Utility methods for pairs of SAMRecords
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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).
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SAMProgramRecord |
In-memory representation of @PG SAM header record.
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SamReader.AssertingIterator |
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SamReader.PrimitiveSamReaderToSamReaderAdapter |
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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.
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SamReaderFactory |
Describes the functionality for producing SamReader , and offers a
handful of static generators.
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SAMReadGroupRecord |
Header information about a read group.
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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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SAMRecordCoordinateComparator |
Comparator for sorting SAMRecords by coordinate.
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SAMRecordDuplicateComparator |
Compares records based on if they should be considered PCR Duplicates (see MarkDuplicates).
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SAMRecordQueryHashComparator |
SAMRecord comparator that provides an ordering based on a hash of the queryname.
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SAMRecordQueryNameComparator |
Comparator for "queryname" ordering of SAMRecords.
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SAMRecordSetBuilder |
Factory class for creating SAMRecords for testing purposes.
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SAMSequenceDictionary |
Collection of SAMSequenceRecords.
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SAMSequenceDictionaryCodec |
"On the fly" codec SAMSequenceDictionaryCodec.
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SAMSequenceRecord |
Header information about a reference sequence.
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SAMSortOrderChecker |
Encapsulates simple check for SAMRecord order.
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SamStreams |
Utilities related to processing of InputStream s encoding SAM data
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SAMTagUtil |
Deprecated.
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SAMTestUtil |
Misc methods for SAM-related unit tests.
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SAMTextHeaderCodec |
Parser for a SAM text header, and a generator of SAM text header.
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SAMTextWriter |
Writer for text-format SAM files.
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SAMUtils |
Utilty methods.
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SAMValidationError |
Class that encapsulates a validation error message as well as a type code so that
errors can be aggregated by type.
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SBIIndex |
SBI is an index into BGZF-compressed data files, which has an entry for the file position of the start of every
nth record.
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SBIIndex.Header |
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SBIIndexMerger |
Merges SBI files for parts of a file that have been concatenated.
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SBIIndexWriter |
Writes SBI files as understood by SBIIndex .
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SecondaryAlignmentSkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary elements.
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SecondaryOrSupplementarySkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.
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SQTagUtil |
Deprecated.
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SRAFileReader |
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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.
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SRAIterator |
SRA iterator which returns SAMRecords for requested list of chunks
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SRAIterator.RecordRangeInfo |
Describes record ranges info needed for emulating BAM index
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TagValueAndUnsignedArrayFlag |
CVO to use as a method return value.
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TextCigarCodec |
Convert between String and Cigar class representations of CIGAR.
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TextTagCodec |
Converter between SAM text representation of a tag, and in-memory Object representation.
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