| Interface | Description |
|---|---|
| CloseableIterator<T> |
This interface is used by iterators that use releasable resources during iteration.
|
| CollectionUtil.DefaultingMap.Factory<V,K> | |
| Lazy.LazyInitializer<T> |
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.
|
| ProgressLoggerInterface |
An interface defining the record() methods of the Picard-public ProgressLogger implementation.
|
| ReferenceSequenceMask |
Interface for specifying loci of interest for genotype calling and other operations.
|
| ResourceLimitedMapFunctor<Key,Value> |
c.f.
|
| SortingCollection.Codec<T> |
Client must implement this class, which defines the way in which records are written to and
read from file.
|
| 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.
|
| AbstractIterator<E> |
Base class of implementing iterators.
|
| 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.
|
| 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.
|
| AsciiWriter |
Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.
|
| AsyncBufferedIterator<T> |
Iterator that uses a dedicated background thread to perform read-ahead to improve
throughput at the expense of increased latency.
|
| BinaryCodec |
Encapsulates file representation of various primitive data types.
|
| BlockCompressedFilePointerUtil |
Static for manipulating virtual file pointers in BGZF files.
|
| BlockCompressedInputStream | |
| BlockCompressedOutputStream |
Writer for a file that is a series of gzip blocks (BGZF format).
|
| BlockCompressedStreamConstants |
Constants shared by BlockCompressed{Input,Output}Stream classes
|
| BlockGunzipper |
Alternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].
|
| BufferedLineReader |
Implementation of LineReader that is a thin wrapper around BufferedReader.
|
| CigarUtil | |
| 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.
|
| 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.MultiMap<K,V> |
Simple multi-map for convenience of storing collections in map values.
|
| CollectionUtil.Partitioner<V,K> | Deprecated
use Collectors.groupingBy instead
|
| ComparableTuple<A extends java.lang.Comparable<A>,B extends java.lang.Comparable<B>> |
A simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.
|
| 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. |
| 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.
|
| 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.
|
| DelegatingIterator<T> |
Simple iterator class that delegates all method calls to an underlying iterator.
|
| DiskBackedQueue<E> |
A single-ended FIFO queue.
|
| 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.
|
| FastLineReader |
Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding,
in order to improve performance.
|
| FileAppendStreamLRUCache |
LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams
than resource limits will allow.
|
| FormatUtil |
Simple class used to format object values into a standard format for printing.
|
| Histogram<K extends java.lang.Comparable> |
Class for computing and accessing histogram type data.
|
| Histogram.Bin<K extends java.lang.Comparable> |
Represents a bin in the Histogram.
|
| HttpUtils |
User: jrobinso
Date: Sep 23, 2009
|
| 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.
|
| IntervalListReferenceSequenceMask |
Serve up loci of interest based on an interval list.
|
| IntervalTree<V> |
A Red-Black tree with intervals for keys.
|
| IntervalTree.Node<V1> | |
| IntervalTree.ValuesIterator<V1> | |
| IntervalTreeMap<T> |
Utility class that implements an interval map.
|
| IntervalUtil | |
| IOUtil |
Miscellaneous stateless static IO-oriented methods.
|
| 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 | |
| Lazy<T> |
Simple utility for building an on-demand (lazy) object-initializer.
|
| 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.
|
| 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().
|
| 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.
|
| 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.
|
| 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.
|
| 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()
|
| PositionalOutputStream |
Wraps output stream in a manner which keeps track of the position within the file and allowing writes
at arbitrary points
|
| 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 | |
| ProgressLogger |
Little progress logging class to facilitate consistent output of useful information when progressing
through a stream of SAM records.
|
| QualityEncodingDetector |
Utility for determining the type of quality encoding/format (see
FastqQualityFormat) used in a SAM/BAM or Fastq. |
| QualityUtil |
Utility class for working with quality scores and error probabilities.
|
| RelativeIso8601Date |
Like
Iso8601Date, but also comes in a "lazy now" flavor. |
| 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.
|
| 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. |
| SamRecordIntervalIteratorFactory |
Create an iterator over a
SamReader that only returns reads that overlap one of the intervals
in an interval list. |
| SamRecordTrackingBuffer<T extends SamRecordWithOrdinal> |
This class stores SAMRecords for return.
|
| SamRecordWithOrdinal |
A little class to store the unique index associated with this record.
|
| SequenceUtil | |
| SnappyLoader |
If Snappy is available, obtain single-arg ctors for SnappyInputStream and SnappyOutputStream.
|
| SolexaQualityConverter |
Optimized method for converting Solexa ASCII qualities into Phred scores.
|
| SortingCollection<T> |
Collection to which many records can be added.
|
| SortingLongCollection |
Accumulate a list of longs that can then be sorted in natural order and iterated over.
|
| StopWatch |
Utility to help in performance testing.
|
| StringLineReader |
Implementation of LineReader that gets its input from a String.
|
| StringUtil |
Grab-bag of stateless String-oriented utilities.
|
| TempStreamFactory |
Factory class for wrapping input and output streams for temporary files.
|
| TestUtil | |
| TrimmingUtil |
Utility code for performing quality trimming.
|
| Tuple<A,B> |
A simple tuple class.
|
| WholeGenomeReferenceSequenceMask |
Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.
|
| Enum | Description |
|---|---|
| BlockCompressedInputStream.FileTermination | |
| EdgingRecordAndOffset.Type |
Describes the type of
TypedRecordAndOffset, whether it represents the start or the end of
an alignment block. |
| FastqQualityFormat |
Enumeration for FastQ quality score formats formats.
|
| Log.LogLevel |
Enumeration for setting log levels.
|
| QualityEncodingDetector.FileContext |
| Exception | Description |
|---|---|
| DateParser.InvalidDateException | |
| 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
|
| SequenceUtil.SequenceListsDifferException |