Package picard.util

Interface Summary

Interface	Description
AdapterPair
AtomicIterator<T>	Describes

Class Summary

Class	Description
AbstractInputParser	Class for parsing text files where each line consists of fields separated by whitespace.
AdapterMarker	Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AsyncIterator<T>	Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
BaitDesigner	Designs baits for hybrid selection!
BasicInputParser	TextFileParser which reads a single text file.
BedToIntervalList
CircularByteBuffer	Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
ClippingUtility	Utilities to clip the adapater sequence from a SAMRecord read
CsvInputParser
DbSnpBitSetUtil	Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil.DbSnpBitSets	Little tuple class to contain one bitset for SNPs and another for Indels.
DelimitedTextFileWithHeaderIterator	Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
FifoBuffer	A program that is designed to act as a large memory buffer between processes that are connected with unix pipes where one or more processes either produce or consume their input or output in bursts.
FileChannelJDKBugWorkAround	Work-around for the following bug http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6503430 Call the method in the main thread before launching threads that do memory-mapping.
IlluminaUtil	Misc utilities for working with Illumina specific files and data
IntervalListScatterer
IntervalListToBed	Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListTools	Little class to aid working with interval lists.
Iterators
LiftOverIntervalList
MathUtil	General math utilities
MathUtil.LogMath	A collection of common math operations that work with log values.
MetricsDoclet	Doclet for use with JavaDoc that will find all classes extending MetricBase and output information about the metrics definitions that go along with the classes.
QuerySortedReadPairIteratorUtil	A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil.ReadPair
RExecutor	Util class for executing R scripts.
ScatterIntervalsByNs	A CLP for breaking up a reference into intervals of Ns and ACGTs bases.
TabbedInputParser	Parser for tab-delimited files
TabbedTextFileWithHeaderParser	Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
TestNGUtil	Small class implementing some utility functions that are useful for test and interfacing with the TestNG framework.
TestNGUtil.SingleTestUnitTest<TestClazz extends TestNGUtil.TestNGParameterizable>
TestNGUtil.TestNGParameterizable	Interface for exposing an implementation for converting an object into a Object[] appropriate for positional parameter-passing as performed by TestNG.
UnsignedTypeUtil	A utility class for dealing with unsigned types.

Enum Summary

Enum	Description
BaitDesigner.DesignStrategy	Set of possible design strategies for bait design.
IlluminaUtil.IlluminaAdapterPair	Describes adapters used on each pair of strands
IntervalListScatterer.Mode
IntervalListTools.Action
VariantType	Enum to hold the possible types of dbSnps.