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.
AlleleSubsettingUtils	Utilities class containing methods for restricting VariantContext and GenotypesContext objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.
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!
BarcodeEditDistanceQuery	A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
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 adapter 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	Summary
GraphUtils	Created by farjoun on 11/2/16.
GraphUtils.Graph<Node extends java.lang.Comparable<Node>>
IlluminaUtil	Misc utilities for working with Illumina specific files and data
IntervalListToBed	Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListTools	Performs various IntervalList manipulations.
Iterators
LiftOverIntervalList	This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
LiftoverUtils
MathUtil	General math utilities
MathUtil.LogMath	A collection of common math operations that work with log values.
PropertyUtils	Utility for loading properties files from resources.
QuerySortedReadPairIteratorUtil	A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil.ReadPair
ReflectionUtil	Class which contains utility functions that use reflection.
RExecutor	Util class for executing R scripts.
ScatterIntervalsByNs	A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
SequenceDictionaryUtils	Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils.SamSequenceRecordsIterator
SingleBarcodeDistanceMetric	A class for finding the distance between a single barcode and a barcode-read (with base qualities)
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.
ThreadPoolExecutorUtil
ThreadPoolExecutorWithExceptions	This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
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
IntervalListTools.Action
VariantType	Enum to hold the possible types of dbSnps.