# 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 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 | 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.
  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.