Class and Description |
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BinaryCodec
Encapsulates file representation of various primitive data types.
|
CloseableIterator
This interface is used by iterators that use releasable resources during iteration.
|
LineReader
Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.
|
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
|
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().
|
PeekableIterator
Generic Closable Iterator that allows you to peek at the next value before calling next
|
ProgressLoggerInterface
An interface defining the record() methods of the Picard-public ProgressLogger implementation.
|
SortingCollection.Codec
Client must implement this class, which defines the way in which records are written to and
read from file.
|
Class and Description |
---|
AbstractAsyncWriter
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.
|
Class and Description |
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CloseableIterator
This interface is used by iterators that use releasable resources during iteration.
|
Interval
Represents a simple interval on a sequence.
|
Class and Description |
---|
Interval
Represents a simple interval on a sequence.
|
Class and Description |
---|
Histogram
Class for computing and accessing histogram type data.
|
Class and Description |
---|
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
|
Class and Description |
---|
AbstractProgressLogger
Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing
through a stream of SAM records.
|
BinaryCodec
Encapsulates file representation of various primitive data types.
|
BlockCompressedInputStream.FileTermination |
BlockCompressedOutputStream
Writer for a file that is a series of gzip blocks (BGZF format).
|
CloseableIterator
This interface is used by iterators that use releasable resources during iteration.
|
CollectionUtil.DefaultingMap.Factory |
CollectionUtil.Partitioner |
DateParser.InvalidDateException |
DiskBackedQueue
A single-ended FIFO queue.
|
FastqQualityFormat
Enumeration for FastQ quality score formats formats.
|
Histogram
Class for computing and accessing histogram type data.
|
Interval
Represents a simple interval on a sequence.
|
IntervalList
Represents a list of intervals against a reference sequence that can be written to
and read from a file.
|
IntervalTree
A Red-Black tree with intervals for keys.
|
IntervalTree.Node |
Iso8601Date
Use this type rather than java.util.Date in command-line options in order to get ISO 8601 parsing.
|
IterableOnceIterator
Abstract implementation of an iterator that also implements Iterable (to return itself)
so that it can be used if for() loops.
|
Lazy.LazyInitializer
Describes how to build the instance of the lazy object.
|
LineReader
Interface allows for implementations that read lines from a String, an ASCII file, or somewhere else.
|
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.
|
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.
|
ProcessExecutor.ExitStatusAndOutput |
ProgressLoggerInterface
An interface defining the record() methods of the Picard-public ProgressLogger implementation.
|
QualityEncodingDetector.FileContext |
ReferenceSequenceMask
Interface for specifying loci of interest for genotype calling and other operations.
|
RelativeIso8601Date
Like
Iso8601Date , but also comes in a "lazy now" flavor. |
ResourceLimitedMap
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
c.f.
|
SamLocusIterator.LocusInfo
The unit of iteration.
|
SamLocusIterator.RecordAndOffset
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 LocusInfo.
|
SamRecordWithOrdinal
A little class to store the unique index associated with this record.
|
SolexaQualityConverter
Optimized method for converting Solexa ASCII qualities into Phred scores.
|
SortingCollection
Collection to which many records can be added.
|
SortingCollection.Codec
Client must implement this class, which defines the way in which records are written to and
read from file.
|
Class and Description |
---|
CloseableIterator
This interface is used by iterators that use releasable resources during iteration.
|
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.
|
Class and Description |
---|
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
|
Class and Description |
---|
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
|
Class and Description |
---|
AbstractIterator
Base class of implementing iterators.
|
LocationAware
Describes API for getting current position in a stream, writer, or underlying file.
|
Class and Description |
---|
Lazy
Simple utility for building an on-demand (lazy) object-initializer.
|
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
|
Class and Description |
---|
AbstractAsyncWriter
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.
|
Class and Description |
---|
CloseableIterator
This interface is used by iterators that use releasable resources during iteration.
|
IntervalList
Represents a list of intervals against a reference sequence that can be written to
and read from a file.
|
SortingCollection.Codec
Client must implement this class, which defines the way in which records are written to and
read from file.
|