All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
Class |
Description |
AbstractAsyncWriter<T> |
Abstract class that is designed to be extended and specialized to provide an asynchronous
wrapper around any kind of Writer class that takes an object and writes it out somehow.
|
AbstractBAMFileIndex |
Provides basic, generic capabilities to be used reading BAM index files.
|
AbstractBitCodec<T> |
|
AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE> |
Simple basic class providing much of the basic functionality of codecs
Every concrete subclass must implement FeatureCodec.canDecode(String) to indicate whether it can decode the file.
|
AbstractFeatureReader<T extends Feature,SOURCE> |
jrobinso
|
AbstractFeatureReader.ComponentMethods |
|
AbstractIndex |
An abstract implementation of the index class.
|
AbstractIndex.BlockStats |
|
AbstractIndex.IndexType |
|
AbstractIterator<E> |
Base class of implementing iterators.
|
AbstractJavascriptFilter<HEADER,TYPE> |
Javascript filter with HEADER type containing TYPE records.
|
AbstractLocusInfo<E extends AbstractRecordAndOffset> |
The unit of iteration for AbstractLocusIterator.
|
AbstractLocusIterator<T extends AbstractRecordAndOffset,K extends AbstractLocusInfo<T>> |
Iterator that traverses a SAM File, accumulating information on a per-locus basis.
|
AbstractProgressLogger |
Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing
through a stream of SAM records.
|
AbstractReader |
|
AbstractRecordAndOffset |
Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds
to the base and quality at the genomic position described the containing AbstractLocusInfo.
|
AbstractSAMHeaderRecord |
Base class for the various concrete records in a SAM header, providing uniform
access to the attributes.
|
AbstractVCFCodec |
|
AggregateFilter |
Aggregates multiple filters and provides a method for applying them all to a given record with
one method call.
|
AlignedFilter |
Filter to either include or exclude aligned reads
$Id$
|
AlignmentBlock |
Represents the contiguous alignment of a subset of read bases to a reference
sequence.
|
AlignmentSpan |
A span of reads on a single reference.
|
Allele |
Immutable representation of an allele.
|
AsciiFeatureCodec<T extends Feature> |
A convenience base class for codecs that want to read in features from ASCII lines.
|
AsciiLineReader |
|
AsciiLineReaderIterator |
A class that iterates over the lines and line positions in an AsciiLineReader .
|
AsciiWriter |
Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.
|
AsyncBlockCompressedInputStream |
|
AsyncBufferedIterator<T> |
Iterator that uses a dedicated background thread to perform read-ahead to improve
throughput at the expense of increased latency.
|
AsyncFastqWriter |
Implementation of a FastqWriter that provides asynchronous output.
|
AsyncVariantContextWriter |
AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.
|
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.
|
BAMFileWriter |
Concrete implementation of SAMFileWriter for writing gzipped BAM files.
|
BAMIndex |
A basic interface for querying BAM indices.
|
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.
|
BamIndexValidator.IndexValidationStringency |
|
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.
|
BaseCategory |
|
BaseCategoryType |
|
BaseQualityScore |
A read feature representing a single quality score in a read.
|
Bases |
|
BasicFastqWriter |
In general FastqWriterFactory should be used so that AsyncFastqWriter can be enabled, but there are some
cases in which that behavior is explicitly not wanted.
|
BCF2Codec |
Decode BCF2 files
|
BCF2Codec.LazyData |
|
BCF2Codec.SitesInfoForDecoding |
|
BCF2Decoder |
|
BCF2Encoder |
See #BCFWriter for documentation on this classes role in encoding BCF2 files
|
BCF2FieldEncoder |
See #BCFWriter for documentation on this classes role in encoding BCF2 files
|
BCF2FieldEncoder.AtomicInt |
Specialized int encoder for atomic (non-list) integers
|
BCF2FieldEncoder.Flag |
|
BCF2FieldEncoder.Float |
|
BCF2FieldEncoder.GenericInts |
|
BCF2FieldEncoder.IntArray |
|
BCF2FieldEncoder.StringOrCharacter |
|
BCF2FieldWriter |
See #BCFWriter for documentation on this classes role in encoding BCF2 files
|
BCF2FieldWriter.FTGenotypesWriter |
|
BCF2FieldWriter.GenericSiteWriter |
|
BCF2FieldWriter.GenotypesWriter |
|
BCF2FieldWriter.GTWriter |
|
BCF2FieldWriter.IGFGenotypesWriter |
|
BCF2FieldWriter.IntegerTypeGenotypesWriter |
|
BCF2FieldWriter.SiteWriter |
|
BCF2FieldWriter.StaticallyTypeGenotypesWriter |
|
BCF2FieldWriterManager |
See #BCFWriter for documentation on this classes role in encoding BCF2 files
|
BCF2GenotypeFieldDecoders |
An efficient scheme for building and obtaining specialized
genotype field decoders.
|
BCF2GenotypeFieldDecoders.Decoder |
Decoder a field (implicit from creation) encoded as
typeDescriptor in the decoder object in the GenotypeBuilders
one for each sample in order.
|
BCF2LazyGenotypesDecoder |
Lazy version of genotypes decoder for BCF2 genotypes
|
BCF2Type |
BCF2 types and associated information
|
BCF2Utils |
Common utilities for working with BCF2 files
Includes convenience methods for encoding, decoding BCF2 type descriptors (size + type)
|
BCFVersion |
Simple holder for BCF version information
User: depristo
Date: 8/2/12
Time: 2:16 PM
|
BEDCodec |
Codec for parsing BED file, as described by UCSC
See https://genome.ucsc.edu/FAQ/FAQformat.html#format1
|
BEDCodec.StartOffset |
Indicate whether co-ordinates or 0-based or 1-based.
|
BEDFeature |
|
BetaIntegerEncoding |
|
Bin |
An individual bin in a BAM file.
|
BinaryCodec |
Encapsulates file representation of various primitive data types.
|
BinaryFeatureCodec<T extends Feature> |
|
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.
|
BinningIndexBuilder.FeatureToBeIndexed |
coordinates are 1-based, inclusive
|
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
|
BitCodec<T> |
An interface that defines requirements for serializing/deserializing objects into and from a bit stream.
|
BitInputStream |
An interface to describe the requirements for reading bit data as opposed to bytes.
|
BitOutputStream |
An interface to describe the requirements for writing out bits as opposed to bytes.
|
Block |
Class representing CRAM block concept and some methods to operate with block content.
|
Block |
Represents a contiguous block of bytes in a file, defined by a start position and size (in bytes)
|
BlockCompressedFilePointerUtil |
Static for manipulating virtual file pointers in BGZF files.
|
BlockCompressedIndexedFastaSequenceFile |
A block-compressed FASTA file driven by an index for fast lookups.
|
BlockCompressedInputStream |
Utility class for reading BGZF block compressed files.
|
BlockCompressedInputStream.DecompressedBlock |
|
BlockCompressedInputStream.FileTermination |
|
BlockCompressedOutputStream |
Writer for a file that is a series of gzip blocks (BGZF format).
|
BlockCompressedStreamConstants |
Constants shared by BlockCompressed{Input,Output}Stream classes
|
BlockCompressionMethod |
|
BlockContentType |
|
BlockGunzipper |
Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].
|
BrowseableBAMIndex |
An index interface with additional functionality for querying and inspecting the structure of a BAM index.
|
BufferedLineReader |
Implementation of LineReader that is a thin wrapper around BufferedReader.
|
ByteArrayLenEncoding |
|
ByteArraySeekableStream |
Created by vadim on 23/03/2015.
|
ByteArrayStopEncoding |
|
ByteArrayStopEncoding.ByteArrayStopCodec |
|
ChrIndex |
Represents an index on a specific chromosome
|
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.
|
CigarOperator |
The operators that can appear in a cigar string, and information about their disk representations.
|
CigarUtil |
|
ClassFinder |
Utility class that can scan for classes in the classpath and find all the ones
annotated with a particular annotation.
|
CloseableIterator<T> |
This interface is used by iterators that use releasable resources during iteration.
|
CloseableTribbleIterator<T extends Feature> |
The basic iterator we use in Tribble, which allows closing and basic iteration.
|
CloserUtil |
Utility to close things that implement Closeable
WARNING: This should only be used for Closeable things open for read, because it ignores exceptions, and
the caller will probably want to know about exceptions when closing a file being written to, because
this may indicate a failure to flush.
|
CodecLineParsingException |
Class CodecLineParsingException
a generic exception we use if the codec has trouble parsing the line its given
|
CodeUtil |
Miscellaneous util methods that don't fit anywhere else.
|
CollectionUtil |
Small utility methods for dealing with collection classes.
|
CollectionUtil.DefaultingMap<K,V> |
A defaulting map, which returns a default value when a value that does not exist in the map is looked up.
|
CollectionUtil.DefaultingMap.Factory<V,K> |
|
CollectionUtil.MultiMap<K,V> |
Simple multi-map for convenience of storing collections in map values.
|
CollectionUtil.Partitioner<V,K> |
Deprecated.
|
CommonInfo |
Common utility routines for VariantContext and Genotype
|
ComparableTuple<A extends Comparable<A>,B extends Comparable<B>> |
A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.
|
CompoundFilter |
A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.
|
CompressionHeader |
|
CompressionHeaderFactory |
A class responsible for decisions about which encodings to use for a given set of records.
|
Container |
|
ContainerFactory |
|
ContainerIO |
Methods to read and write CRAM containers.
|
ContainerParser |
|
ContentDigests |
|
ContentDigests.KNOWN_DIGESTS |
|
CoordinateSortedPairInfoMap<KEY,REC> |
Holds info about a mate pair for use when processing a coordinate sorted file.
|
CoordinateSortedPairInfoMap.Codec<KEY,REC> |
Client must implement this class, which defines the way in which records are written to and
read from file.
|
CoordMath |
Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends
inclusive.
|
CoordSpanInputSteam |
An input stream that wraps a SeekableStream to produce only bytes specified within coordinates.
|
CountingInputStream |
An input stream that counts the bytes read from it.
|
CountRecords |
An example of how to index a feature file, and then count all the records in the file.
|
CRAIEntry |
A class representing CRAI index entry: file and alignment offsets for each slice.
|
CRAIIndex |
CRAI index used for CRAM files.
|
CRAIIndex.CRAIIndexException |
|
Cram2SamRecordFactory |
|
CramArray |
Methods to read and write CRAM array of integers data type.
|
CRAMBAIIndexer |
Class for both constructing BAM index content and writing it out.
|
CramCompressionRecord |
|
CramCompressionRecord.BAM_FLAGS |
|
CramContainerHeaderIterator |
Iterate over CRAM containers from an input stream, and unlike CramContainerIterator only
the header of each container is read, rather than the whole stream.
|
CramContainerIterator |
An iterator of CRAM containers read from an InputStream .
|
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.
|
CRAMException |
Created by edwardk on 8/13/15.
|
CRAMFileReader |
|
CRAMFileWriter |
|
CramHeader |
A starting object when dealing with CRAM files.
|
CramInt |
Methods to read and write CRAM int values as given in the file format specification.
|
CramIO |
A collection of methods to open and close CRAM files.
|
CRAMIterator |
|
CramNormalizer |
|
CramRecordReader |
|
CRAMReferenceSource |
Interface used to supply a reference source when reading CRAM files.
|
CramSpanContainerIterator |
|
CramVersionPolicies |
The class provides version-dependant rules and policies for CRAM data.
|
CramVersions |
|
CRC32InputStream |
An input stream that calculates CRC32 of all the bytes passed through it.
|
CRC32OutputStream |
An output stream that calculates CRC32 checksum of all the bytes written through the stream.
|
CustomGzipOutputStream |
Hacky little class used to allow us to set the compression level on a GZIP output stream which, for some
bizarre reason, is not exposed in the standard API.
|
CustomReaderFactory |
Factory for creating custom readers for accessing API based resources,
e.g.
|
CustomReaderFactory.ICustomReaderFactory |
Interface to be implemented by custom factory classes that register
themselves with this factory and are loaded dynamically.
|
DataReader<T> |
A basic interface for reading data.
|
DataReaderFactory |
|
DataReaderFactory.DataReaderWithStats<T> |
|
DataSeries |
An annotation to denote a data series field in a java class.
|
DataSeriesMap |
|
DataSeriesType |
Data series types known to CRAM.
|
DataWriter<T> |
A basic interface defining a writer.
|
DataWriterFactory |
|
DateParser |
NOTE: This code has been taken from w3.org, and modified slightly to handle timezones of the form [-+]DDDD,
and also to fix a bug in the application of time zone to the parsed date.
|
DateParser.InvalidDateException |
|
DefaultBitInputStream |
Must not read from delegate unless no bits left in the buffer!!!
|
DefaultBitOutputStream |
|
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.
|
DeflaterFactory |
|
DelegatingIterator<T> |
Simple iterator class that delegates all method calls to an underlying iterator.
|
DeleteOnExitPathHook |
Class to hold a set of Path to be delete on the JVM exit through a shutdown hook.
|
Deletion |
A read feature representing a deletion of one or more bases similar to CigarOperator.D .
|
DiskBackedQueue<E> |
A single-ended FIFO queue.
|
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.
|
DownsamplingIteratorFactory.Strategy |
Describes the available downsampling strategies.
|
DuplicateReadFilter |
Filter out SAMRecords with DuplicateRead flag set
$Id$
|
DuplicateScoringStrategy |
This class helps us compute and compare duplicate scores, which are used for selecting the non-duplicate
during duplicate marking (see MarkDuplicates).
|
DuplicateScoringStrategy.ScoringStrategy |
|
DuplicateSet |
Stores a set of records that are duplicates of each other.
|
DuplicateSetIterator |
An iterator of sets of duplicates.
|
DynamicIndexCreator |
|
EdgeReadIterator |
Iterator that traverses a SAM File, accumulating information on a per-locus basis.
|
EdgingRecordAndOffset |
Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds
to the base and quality for the start of alignment block at the genomic position described by the AbstractLocusInfo.
|
EdgingRecordAndOffset.Type |
Describes the type of TypedRecordAndOffset , whether it represents the start or the end of
an alignment block.
|
EnaRefService |
|
EnaRefService.GaveUpException |
|
Encoding<T> |
An interface to describe how a data series is encoded.
|
EncodingFactory |
|
EncodingID |
Encoding ID as defined in the CRAM specs.
|
EncodingKey |
|
EncodingParams |
|
ExampleBinaryCodec |
An example binary codec that encodes / decodes contig / start / stop values via DataInputStreams
|
ExampleSamUsage |
|
ExposedByteArrayOutputStream |
|
ExternalByteArrayEncoding |
|
ExternalByteEncoding |
|
ExternalCompression |
Methods to provide CRAM external compression/decompression features.
|
ExternalCompressor |
|
ExternalIntegerEncoding |
|
ExternalLongEncoding |
|
FailsVendorReadQualityFilter |
Filter for filtering out reads that do not pass the quality filter
$Id$
|
FastaSequenceFile |
Implementation of ReferenceSequenceFile for reading from FASTA files.
|
FastaSequenceIndex |
Reads/writes a fasta index file (.fai), as generated by `samtools faidx`.
|
FastaSequenceIndexCreator |
|
FastaSequenceIndexEntry |
Hold an individual entry in a fasta sequence index file.
|
FastGenotype |
This class encompasses all the basic information about a genotype.
|
FastLineReader |
Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding,
in order to improve performance.
|
FastqConstants |
|
FastqConstants.FastqExtensions |
|
FastqEncoder |
Codec for encoding records into FASTQ format.
|
FastqQualityFormat |
Enumeration for FastQ quality score formats formats.
|
FastqReader |
Reads a FASTQ file with four lines per record.
|
FastqReader.LineType |
Enum of the types of lines we see in Fastq.
|
FastqRecord |
Simple representation of a FASTQ record, without any conversion
|
FastqWriter |
Simple interface for a class that can write out fastq records.
|
FastqWriterFactory |
Factory class for creating FastqWriter objects.
|
Feature |
Marker interface for Locatables with Tribble support.
|
FeatureCodec<FEATURE_TYPE extends Feature,SOURCE> |
The base interface for classes that read in features.
|
FeatureCodecHeader |
A class to represent a header of a feature containing file.
|
FeatureReader<T extends Feature> |
the basic interface that feature sources need to match
|
FileAppendStreamLRUCache |
LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams
than resource limits will allow.
|
FileTruncatedException |
Thrown when it is possible to detect that a SAM or BAM file is truncated.
|
FilteringIterator |
Deprecated.
|
FilteringIterator |
Deprecated.
|
FilteringSamIterator |
Filtering Iterator which takes a filter and an iterator and iterates through only those records
which are not rejected by the filter.
|
FilteringVariantContextIterator |
A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.
|
FixBAMFile |
Deprecated.
|
FormatUtil |
Simple class used to format object values into a standard format for printing.
|
FTPClient |
|
FTPHelper |
|
FTPReply |
|
FTPStream |
A "non-seekable" ftp stream.
|
FTPUtils |
|
FullBEDFeature |
Object for full BED file.
|
GammaIntegerEncoding |
|
GeneralUtils |
Constants and utility methods used throughout the VCF/BCF/VariantContext classes
|
GenomicIndexUtil |
Constants and methods used by BAM and Tribble indices
|
Genotype |
This class encompasses all the basic information about a genotype.
|
GenotypeBuilder |
A builder class for genotypes
Provides convenience setter methods for all of the Genotype field
values.
|
GenotypeJEXLContext |
|
GenotypeLikelihoods |
|
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair |
|
GenotypeQualityFilter |
A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).
|
GenotypesContext |
Represents an ordered collection of Genotype objects
|
GenotypeType |
Summary types for Genotype objects
|
GolombIntegerEncoding |
|
GolombLongEncoding |
|
GolombRiceIntegerEncoding |
|
GZIIndex |
Represents a .gzi index of a block-compressed file.
|
GZIIndex.IndexEntry |
Index entry mapping the block-offset (compressed offset) to the uncompressed offset where the
block starts.
|
HardClip |
|
HardyWeinbergCalculation |
This class calculates a HardyWeinberg p-value given three values representing
the observed frequences of homozygous and heterozygous genotypes in the
test population.
|
Header |
A header for a metrics file.
|
HeterozygosityFilter |
A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).
|
Histogram<K extends Comparable> |
Class for computing and accessing histogram type data.
|
Histogram.Bin<K extends Comparable> |
Represents a bin in the Histogram.
|
HTTPHelper |
Simple implementation of URLHelper based on the JDK URL and HttpURLConnection classes.
|
HttpUtils |
User: jrobinso
Date: Sep 23, 2009
|
HuffmanByteEncoding |
|
HuffmanCode |
|
HuffmanIntegerEncoding |
|
HuffmanTree<T> |
|
Index |
Interface for all index implementations.
|
IndexCreator |
An interface for creating indexes
|
IndexedFastaSequenceFile |
A fasta file driven by an index for fast, concurrent lookups.
|
IndexFactory |
Factory class for creating indexes.
|
IndexFactory.IndexBalanceApproach |
We can optimize index-file-creation for different factors.
|
IndexFactory.IndexType |
an enum that contains all of the information about the index types, and how to create them
|
IndexToTable |
|
IndicesAreEqual |
Check with two index files are equal
|
InflaterFactory |
|
InputStreamUtils |
|
InsertBase |
A read feature representing a single insert base.
|
Insertion |
A read feature representing a multi-base insertion.
|
InsertSizeFilter |
Filter things that fall outside a specified range of insert sizes.
|
Interval |
Represents a simple interval on a sequence.
|
Interval |
Quick and dirty interval class
Describes a genomic interval and where in a file information for that
interval can be obtained
|
IntervalFilter |
Filter SAMRecords so that only those that overlap the given list of intervals.
|
IntervalIndexCreator |
Creates interval indexes from a stream of features
|
IntervalKeepPairFilter |
Filter out SAMRecords where neither record of a pair overlaps a given set of
intervals.
|
IntervalList |
Represents a list of intervals against a reference sequence that can be written to
and read from a file.
|
IntervalListReferenceSequenceMask |
Serve up loci of interest based on an interval list.
|
IntervalTree<V> |
A Red-Black tree with intervals for keys.
|
IntervalTree |
An implementation of an interval tree, following the explanation.
|
IntervalTree.Node<V1> |
|
IntervalTree.ValuesIterator<V1> |
|
IntervalTreeIndex |
Index based on an interval tree
|
IntervalTreeIndex.ChrIndex |
|
IntervalTreeMap<T> |
Utility class that implements an interval map.
|
IntervalUtil |
|
IntGenotypeFieldAccessors |
A convenient way to provide a single view on the many int and int[] field values we work with,
for writing out the values.
|
IntGenotypeFieldAccessors.Accessor |
|
IntGenotypeFieldAccessors.ADAccessor |
|
IntGenotypeFieldAccessors.DPAccessor |
|
IntGenotypeFieldAccessors.GQAccessor |
|
IntGenotypeFieldAccessors.PLAccessor |
|
IntHashMap<T> |
A hash map that uses primitive ints for the key rather than objects.
|
IOUtil |
Miscellaneous stateless static IO-oriented methods.
|
ISeekableStreamFactory |
|
Iso8601Date |
Use this type rather than java.util.Date in command-line options in order to get ISO 8601 parsing.
|
IterableAdapter<T> |
Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop.
|
IterableOnceIterator<T> |
Abstract implementation of an iterator that also implements Iterable (to return itself)
so that it can be used if for() loops.
|
Iterables |
|
ITF8 |
Methods to read and write int values as per ITF8 specification in CRAM.
|
JavascriptSamRecordFilter |
javascript based read filter
The script puts the following variables in the script context:
- 'record' a SamRecord (
https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
SAMRecord.java ) - 'header' (
https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
SAMFileHeader.java )
|
JavascriptVariantFilter |
javascript based variant filter The script puts the following variables in
the script context:
- 'header' a htsjdk.variant.vcf.VCFHeader
- 'variant' a htsjdk.variant.variantcontext.VariantContext
|
JexlMissingValueTreatment |
How to treat values that appear in a jexl expression but are missing in the context it's applied to
|
Lazy<T> |
Simple utility for building an on-demand (lazy) object-initializer.
|
Lazy.LazyInitializer<T> |
Deprecated.
|
LazyGenotypesContext |
Lazy-loading GenotypesContext.
|
LazyGenotypesContext.LazyData |
|
LazyGenotypesContext.LazyParser |
Simple lazy parser interface.
|
LiftOver |
Java port of UCSC liftOver.
|
LiftOver.PartialLiftover |
Represents a portion of a liftover operation, for use in diagnosing liftover failures.
|
LinearIndex |
The linear index associated with a given reference in a BAM index.
|
LinearIndex |
Index defined by dividing the genome by chromosome, then each chromosome into bins of fixed width (in
genomic coordinates).
|
LinearIndex.ChrIndex |
Blocks are organized as a simple flat list:
|
LinearIndexCreator |
For creating a LinearIndex from a stream of features.
|
LineIterator |
A very simple descriptor for line-iterables.
|
LineIteratorImpl |
A simple iterator over the elements in LineReader.
|
LineReader |
Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.
|
LineReader |
Interface for line-oriented readers.
|
ListMap<K,V> |
A Map class that holds a list of entries under each key instead of a single entry, and
provides utility methods for adding an entry under a key.
|
LittleEndianInputStream |
Input stream with methods to convert byte arrays to numeric values using "little endian" order.
|
LittleEndianOutputStream |
|
Locatable |
Any class that has a single logical mapping onto the genome should implement Locatable
positions should be reported as 1-based and closed at both ends
|
LocationAware |
Describes API for getting current position in a stream, writer, or underlying file.
|
Locus |
Location info about a locus.
|
LocusComparator<T extends Locus> |
compares first by sequence index then by position
|
LocusImpl |
Simple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations.
|
Log |
A wafer thin wrapper around System.err that uses var-args to make it
much more efficient to call the logging methods in without having to
surround every call site with calls to Log.isXXXEnabled().
|
Log.LogLevel |
Enumeration for setting log levels.
|
LongLineBufferedReader |
A variant of BufferedReader with improved performance reading files with long lines.
|
LTF8 |
Methods to read and write LTF8 as per CRAM specs.
|
MappingQualityFilter |
Filter things with low mapping quality.
|
MathUtils |
a collection of functions and classes for various common calculations
|
MathUtils.RunningStat |
a class for calculating moving statistics - this class returns the
mean, variance, and std dev after accumulating any number of records.
|
Md5CalculatingInputStream |
Class to generate an MD5 string for a file as it is being read
|
Md5CalculatingOutputStream |
Class to generate an MD5 string for a file as it is being read
|
MergingIterator<T> |
An iterator over Iterators that return Ts.
|
MergingSamRecordIterator |
Provides an iterator interface for merging multiple underlying iterators into a single
iterable stream.
|
MetricBase |
A base class from which all Metric classes should inherit.
|
MetricsFile<BEAN extends MetricBase,HKEY extends Comparable> |
Contains a set of metrics that can be written to a file and parsed back
again.
|
Murmur3 |
Provides an implementation of the Murmur3_32 hash algorithm that has desirable properties in terms of randomness
and uniformity of the distribution of output values that make it a useful hashing algorithm for downsampling.
|
MutableIndex |
Some Index implementations can be modified in memory.
|
MutableInt |
|
NameAwareCodec |
Created by IntelliJ IDEA.
|
NotPrimaryAlignmentFilter |
Deprecated.
|
NotPrimarySkippingIterator |
Deprecated.
|
NullEncoding<T> |
|
Options |
Available writer options for VariantContextWriters
|
OverclippedReadFilter |
Filters out reads with very few unclipped bases, likely due to the read coming
from a foreign organism, e.g.
|
OverlapDetector<T> |
Utility class to efficiently do in memory overlap detection between a large
set of mapping like objects, and one or more candidate mappings.
|
Padding |
|
ParsingUtils |
|
PassingVariantFilter |
A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).
|
PeekableIterator<Object> |
Generic Closable Iterator that allows you to peek at the next value before calling next
|
PeekIterator<T> |
Wrapper around an iterator that enables non-destructive peeking at the next element that would
be returned by next()
|
Positional |
Minimal interface for an object at support getting the current position in the stream / writer / file, as well as a handful of other
reader-like features.
|
PositionalBufferedStream |
A wrapper around an InputStream which performs it's own buffering, and keeps track of the position.
|
PositionalOutputStream |
Wraps output stream in a manner which keeps track of the position within the file and allowing writes
at arbitrary points
|
PreservationPolicy |
|
PrintReadsExample |
This is a example program showing how to use SAM readers and (optionally) writers.
|
PrintVariantsExample |
This is a example program showing how to use Feature readers and (optionally) writers.
|
ProcessExecutor |
Utility class that will execute sub processes via Runtime.getRuntime().exec(...) and read
off the output from stderr and stdout of the sub process.
|
ProcessExecutor.ExitStatusAndOutput |
|
ProfileIndexReading |
|
ProgressLogger |
Little progress logging class to facilitate consistent output of useful information when progressing
through a stream of SAM records.
|
ProgressLoggerInterface |
An interface defining the record() methods of the Picard-public ProgressLogger implementation.
|
QualityEncodingDetector |
Utility for determining the type of quality encoding/format (see FastqQualityFormat ) used in a SAM/BAM or Fastq.
|
QualityEncodingDetector.FileContext |
|
QualityScorePreservation |
|
QualityScoreTreatment |
|
QualityScoreTreatmentType |
|
QualityUtil |
Utility class for working with quality scores and error probabilities.
|
QueryInterval |
Interval relative to a reference, for querying a BAM file.
|
RANS |
|
RANS.ORDER |
|
ReadableSeekableStreamByteChannel |
|
ReadBase |
A read feature representing a single base with associated quality score.
|
ReadCategory |
|
ReadCategoryType |
|
ReadFeature |
An interface to capture data in read coordinates.
|
ReadNameFilter |
Filter by a set of specified readnames
|
ReadTag |
|
ReferenceCache |
That is a thread-safe wrapper for a list of cache Reference objects.
|
ReferenceSequence |
Wrapper around a reference sequence that has been read from a reference file.
|
ReferenceSequenceFile |
An interface for working with files of reference sequences regardless of the file format
being used.
|
ReferenceSequenceFileFactory |
Factory class for creating ReferenceSequenceFile instances for reading reference
sequences store in various formats.
|
ReferenceSequenceFileWalker |
Manages a ReferenceSequenceFile.
|
ReferenceSequenceMask |
Interface for specifying loci of interest for genotype calling and other operations.
|
ReferenceSource |
Used to represent a CRAM reference, the backing source for which can either be
a file or the EBI ENA reference service.
|
ReferenceTracks |
|
RefSeqIdReader |
A reader that only keeps track of alignment spans.
|
RefSkip |
|
RelativeIso8601Date |
Like Iso8601Date , but also comes in a "lazy now" flavor.
|
RemoteURLHelper |
Implementation of URLHelper designed for remote resources.
|
ReservedTagConstants |
Constants for tags used in our SAM/BAM files
|
ResourceLimitedMap<Key,Value> |
LRU collection class for managing objects that place some resource burden such that not too many of them
can existing in the VM at one time, but they can be reconstructed ias necessary.
|
ResourceLimitedMapFunctor<Key,Value> |
c.f.
|
RuntimeEOFException |
Thrown by various codecs to indicate EOF without having to clutter the API with throws clauses
|
RuntimeIOException |
Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses
|
RuntimeScriptException |
Thrown by classes handling script engines like the javascript-based filters for SAM/VCF
|
Sam2CramRecordFactory |
|
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.
|
SAMException |
|
SAMFileHeader |
Header information from a SAM or BAM file.
|
SAMFileHeader.GroupOrder |
|
SAMFileHeader.PgIdGenerator |
Little class to generate program group IDs
|
SAMFileHeader.SortOrder |
Ways in which a SAM or BAM may be sorted.
|
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.
|
SAMFileSpan |
A interface representing a collection of (possibly) discontinuous segments in the
BAM file, possibly representing the results of an index query.
|
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 |
|
SAMFileWriter |
Interface for SAMText and BAM file writers.
|
SAMFileWriterFactory |
Create a writer for writing SAM, BAM, or CRAM files.
|
SAMFileWriterImpl |
Base class for implementing SAM writer with any underlying format.
|
SAMFlag |
SAM flags as enum, to be used in GUI, menu, etc...
|
SamFlagField |
This determines how flag fields are represented in the SAM file.
|
SAMFormatException |
Thrown when a SAM file being read or decoded (text or binary) looks bad.
|
SAMHeaderRecordComparator<T extends AbstractSAMHeaderRecord> |
Provides ordering based on SAM header records' attribute values.
|
SamIndexes |
A helper class to read BAI and CRAI indexes.
|
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.
|
SamLocusAndReferenceIterator |
Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.
|
SamLocusAndReferenceIterator.SAMLocusAndReference |
|
SamLocusIterator |
Iterator that traverses a SAM File, accumulating information on a per-locus basis.
|
SamLocusIterator.LocusInfo |
The unit of iteration.
|
SamLocusIterator.RecordAndOffset |
Implementation of AbstractRecordAndOffset class for SamLocusIterator .
|
SamPairUtil |
Utility methods for pairs of SAMRecords
|
SamPairUtil.PairOrientation |
The possible orientations of paired reads.
|
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 |
Describes functionality for objects that produce SAMRecord s and associated information.
|
SamReader.AssertingIterator |
|
SamReader.Indexing |
Facet for index-related operations.
|
SamReader.PrimitiveSamReader |
The minimal subset of functionality needed for a SAMRecord data source.
|
SamReader.PrimitiveSamReaderToSamReaderAdapter |
|
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.
|
SamReaderFactory.Option |
|
SAMReadGroupRecord |
Header information about a read group.
|
SAMReadGroupRecord.PlatformValue |
|
SAMRecord |
Java binding for a SAM file record.
|
SAMRecord.SAMTagAndValue |
Tag name and value of an attribute, for getAttributes() method.
|
SAMRecordComparator |
Interface for comparators that define the various SAM sort orders.
|
SAMRecordCoordinateComparator |
Comparator for sorting SAMRecords by coordinate.
|
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.
|
SamRecordFilter |
API for filtering SAMRecords
$Id$
|
SamRecordIntervalIteratorFactory |
Create an iterator over a SamReader that only returns reads that overlap one of the intervals
in an interval list.
|
SAMRecordIterator |
A general interface that adds functionality to a CloseableIterator of
SAMRecords.
|
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.
|
SamRecordTrackingBuffer<T extends SamRecordWithOrdinal> |
This class stores SAMRecords for return.
|
SamRecordWithOrdinal |
A little class to store the unique index associated with this record.
|
SAMSequenceDictionary |
Collection of SAMSequenceRecords.
|
SAMSequenceDictionaryCodec |
"On the fly" codec SAMSequenceDictionaryCodec.
|
SAMSequenceDictionaryExtractor |
Small class for loading a SAMSequenceDictionary from a file
|
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
|
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 |
Misc methods for SAM-related unit tests.
|
SAMTestUtil.SanityCheckFailedException |
Indicates that a required sanity-check condition was not met.
|
SAMTextHeaderCodec |
Parser for a SAM text header, and a generator of SAM text header.
|
SAMTextWriter |
Writer for text-format SAM files.
|
SAMTools |
Deprecated.
|
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.
|
SAMValidationError.Severity |
|
SAMValidationError.Type |
|
Scores |
A read feature representing a contiguous stretch of quality scores in a read.
|
SecondaryAlignmentFilter |
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
|
SecondaryAlignmentSkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary elements.
|
SecondaryOrSupplementaryFilter |
Filter out SAMRecords with Secondary or Supplementary flag set
This class should be viewed as a replacement for NotPrimarySkippingIterator ,
in that we did not want to change the functionality of NPSI to no longer match its name
$Id$
|
SecondaryOrSupplementarySkippingIterator |
Wrapper around SAMRecord iterator that skips over secondary and supplementary elements.
|
SeekableBufferedStream |
A wrapper class to provide buffered read access to a SeekableStream.
|
SeekableFileStream |
|
SeekableFTPStream |
Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both.
|
SeekableFTPStreamHelper |
|
SeekableHTTPStream |
|
SeekableMemoryStream |
|
SeekablePathStream |
|
SeekableStream |
InputStream with random access support (seek).
|
SeekableStreamFactory |
Singleton class for getting SeekableStream s from URL/paths
Applications using this library can set their own factory
|
SequenceUtil |
|
SequenceUtil.SequenceListsDifferException |
|
SimpleBEDFeature |
Feature from a BED file without exon blocks.
|
SimpleFeature |
A simple concrete Feature.
|
Slice |
CRAM slice is a logical union of blocks into for example alignment slices.
|
SnappyLoader |
Checks if Snappy is available, and provides methods for wrapping InputStreams and OutputStreams with Snappy if so.
|
SnpFilter |
A Predicate on VariantContexts that returns true at sites that are SNPs
|
SoftClip |
|
SolexaNoiseFilter |
Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.
|
SolexaQualityConverter |
Optimized method for converting Solexa ASCII qualities into Phred scores.
|
SortingCollection<T> |
Collection to which many records can be added.
|
SortingCollection.Codec<T> |
Client must implement this class, which defines the way in which records are written to and
read from file.
|
SortingLongCollection |
Accumulate a list of longs that can then be sorted in natural order and iterated over.
|
SortingVariantContextWriter |
Deprecated.
|
SQTagUtil |
Utility methods for encoding and decoding the SQ tag value of SAMRecord.
|
SQTagUtil.SQBase |
The ordinals of these are stored in the high-order 2 bits of each byte of the SQ tag.
|
SRAAccession |
Describes a single SRA accession for SRA read collection
Also provides app string functionality and allows to check if working SRA is supported on the running platform
Important: due to checks performed in SRAAccession.isValid(), we won't recognise any accessions other
than ones that follow the pattern "^[SED]RR[0-9]{6,9}$", e.g.
|
SRAAlignmentIterator |
Iterator for aligned reads.
|
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.
|
SRAIndexedSequenceFile |
Allows reading Reference data from SRA
|
SRAIterator |
SRA iterator which returns SAMRecords for requested list of chunks
|
SRAIterator.RecordRangeInfo |
Describes record ranges info needed for emulating BAM index
|
SRALazyRecord |
Extends SAMRecord so that any of the fields will be loaded only when needed.
|
SRAUnalignmentIterator |
Iterator for unaligned reads.
|
SRAUtils |
Provides some functionality which can be used by other classes
Created by andrii.nikitiuk on 10/28/15.
|
StopWatch |
Utility to help in performance testing.
|
Strand |
Enum for strand, which can be encoded as a string
|
StringHeader |
A simple header who's data type is a single String.
|
StringLineReader |
Deprecated.
|
StringUtil |
Grab-bag of stateless String-oriented utilities.
|
StructuralVariantType |
Type of Structural Variant as defined in the VCF spec 4.2
|
SubexponentialIntegerEncoding |
|
Substitution |
A substitution event captured in read coordinates.
|
SubstitutionMatrix |
|
SynchronousLineReader |
Implementation of LineReader that reads lines directly from the underlying stream or reader.
|
TabixFeatureReader<T extends Feature,SOURCE> |
|
TabixFormat |
The values in a Tabix header that define the format of the file being indexed, e.g.
|
TabixIndex |
This class represent a Tabix index that has been built in memory or read from a file.
|
TabixIndexCreator |
IndexCreator for Tabix.
|
TabixIteratorLineReader |
|
TabixReader |
|
TabixReader.Iterator |
|
TabixReader.TIndex |
|
TabixReader.TPair64 |
|
TabixUtils |
classes that have anything to do with tabix
|
TabixUtils.TIndex |
|
TabixUtils.TIntv |
|
TabixUtils.TPair64 |
|
TagFilter |
Filter class for matching tag attributes in SAMRecords
$Id$
|
TagValueAndUnsignedArrayFlag |
CVO to use as a method return value.
|
TempStreamFactory |
Factory class for wrapping input and output streams for temporary files.
|
TestUtil |
|
TextCigarCodec |
Convert between String and Cigar class representations of CIGAR.
|
TextTagCodec |
Converter between SAM text representation of a tag, and in-memory Object representation.
|
TimeChannel |
|
TimeRandomAccessFile |
|
Tribble |
Common, tribble wide constants and static functions
|
TribbleException |
|
TribbleException.CorruptedIndexFile |
|
TribbleException.FeatureFileDoesntExist |
|
TribbleException.InternalCodecException |
|
TribbleException.InvalidDecodeLine |
|
TribbleException.InvalidHeader |
|
TribbleException.MalformedFeatureFile |
|
TribbleException.TabixReaderFailure |
|
TribbleException.UnableToCreateCorrectIndexType |
|
TribbleException.UnableToReadIndexFile |
|
TribbleIndexCreator |
Base class for Tribble-specific index creators.
|
TribbleIndexedFeatureReader<T extends Feature,SOURCE> |
A reader for text feature files (i.e.
|
TrimmingUtil |
Utility code for performing quality trimming.
|
Tuple<A,B> |
A simple tuple class.
|
UnsortedFileException |
an exception for when we've discovered that an input file is unsorted; sorted files are required by Tribble
|
URLHelper |
Interface defining a helper class for dealing with URL resources.
|
UserPasswordInput |
|
Utils |
|
ValidationStringency |
How strict to be when reading a SAM or BAM, beyond bare minimum validation.
|
VariantContext |
High-level overview
|
VariantContext.Type |
|
VariantContext.Validation |
|
VariantContextBuilder |
Builder class for VariantContext .
|
VariantContextComparator |
A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List
provided at construction time, then by start position with each contig/chromosome.
|
VariantContextFilter |
API for filtering VariantContexts.
|
VariantContextUtils |
|
VariantContextUtils.JexlVCMatchExp |
A simple but common wrapper for matching VariantContext objects using JEXL expressions
|
VariantContextWriter |
this class writes VCF files
|
VariantContextWriterBuilder |
|
VariantContextWriterBuilder.OutputType |
|
VCF3Codec |
A feature codec for the VCF3 specification, to read older VCF files.
|
VCFCodec |
A feature codec for the VCF 4 specification
|
VCFCompoundHeaderLine |
a base class for compound header lines, which include info lines and format lines (so far)
|
VCFCompoundHeaderLine.SupportedHeaderLineType |
|
VCFConstants |
|
VCFContigHeaderLine |
A special class representing a contig VCF header line.
|
VCFEncoder |
Functions specific to encoding VCF records.
|
VCFFileReader |
Simplified interface for reading from VCF/BCF files.
|
VCFFilterHeaderLine |
|
VCFFormatHeaderLine |
|
VCFHeader |
A class to represent a VCF header
|
VCFHeader.HEADER_FIELDS |
|
VCFHeaderLine |
|
VCFHeaderLineCount |
the count encodings we use for fields in VCF header lines
|
VCFHeaderLineTranslator |
A class for translating between vcf header versions
|
VCFHeaderLineType |
the type encodings we use for fields in VCF header lines
|
VCFHeaderReader |
Utility class to read a VCF header without being told beforehand whether the input is VCF or BCF.
|
VCFHeaderVersion |
information that identifies each header version
|
VCFIDHeaderLine |
an interface for ID-based header lines
|
VCFInfoHeaderLine |
|
VCFRecordCodec |
Writes VariantContext instances to an OutputStream without headers or metadata.
|
VCFSimpleHeaderLine |
|
VCFStandardHeaderLines |
Manages header lines for standard VCF
|
VCFUtils |
|
Version |
A class to represent a version information, 3 number: major, minor and build number.
|
VersionHeader |
Header that stores information about the version of some piece of software or
data used to create the metrics file.
|
WholeGenomeReferenceSequenceMask |
Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.
|
WholeReadClippedFilter |
Filter SAMRecords so that only those that have at least one un-clipped base are
returned.
|
Writer |
|