# 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.
  AccumulateQualityYieldMetrics | Combines multiple Picard QualityYieldMetrics files into a single file.
  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 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.