Package htsjdk.samtools.util
package htsjdk.samtools.util
-
ClassDescriptionAbstract 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.Base class of implementing iterators.AbstractLocusInfo<E extends AbstractRecordAndOffset>The unit of iteration for AbstractLocusIterator.Iterator that traverses a SAM File, accumulating information on a per-locus basis.Abstract implementation of a Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.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.Classifies whether the given event is a match, insertion, or deletion.Fast (I hope) buffered Writer that converts char to byte merely by casting, rather than charset conversion.Asynchronous read-ahead implementation of
BlockCompressedInputStream.Iterator that uses a dedicated background thread to perform read-ahead to improve throughput at the expense of increased latency.Encapsulates file representation of various primitive data types.Static for manipulating virtual file pointers in BGZF files.Utility class for reading BGZF block compressed files.Writer for a file that is a series of gzip blocks (BGZF format).Constants shared by BlockCompressed{Input,Output}Stream classesAlternative to GZIPInputStream, for decompressing GZIP blocks that are already loaded into a byte[].Implementation of LineReader that is a thin wrapper around BufferedReader.This interface is used by iterators that use releasable resources during iteration.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.Miscellaneous util methods that don't fit anywhere else.Small utility methods for dealing with collection classes.A defaulting map, which returns a default value when a value that does not exist in the map is looked up.Simple multi-map for convenience of storing collections in map values.Deprecated.use Collectors.groupingBy insteadA simple extension of the Tuple class that, for comparable Types, allows comparing Tuples of non-null elements.Static methods that encapsulate the standard SAM way of storing ranges: one-based, with both ends inclusive.An input stream that wraps aSeekableStreamto produce only bytes specified within coordinates.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.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.Simple iterator class that delegates all method calls to an underlying iterator.A single-ended FIFO queue.Iterator that traverses a SAM File, accumulating information on a per-locus basis.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.Describes the type ofTypedRecordAndOffset, whether it represents the start or the end of an alignment block.Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance.Enumeration for FastQ quality score formats formats.LRU cache of OutputStreams to handle situation in which it is necessary to have more FileOutputStreams than resource limits will allow.Contains file extension constants for read, alignment, variant and annotation filesSimple class used to format object values into a standard format for printing.Represents a .gzi index of a block-compressed file.Helper class for constructing the GZIindex.Index entry mapping the block-offset (compressed offset) to the uncompressed offset where the block starts.Histogram<K extends Comparable>Class for computing and accessing histogram type data.Histogram.Bin<K extends Comparable>Represents a bin in the Histogram.User: jrobinso Date: Sep 23, 2009Represents a simple interval on a sequence.Comparator that orders intervals based on their sequence index, by coordinate then by strand and finally by name.Represents a list of intervals against a reference sequence that can be written to and read from a file.Serve up loci of interest based on an interval list.Writes out the list of intervals to the supplied file.IntervalTree<V>A Red-Black tree with intervals for keys.Utility class that implements an interval map.Miscellaneous stateless static IO-oriented methods.Use this type rather than java.util.Date in command-line options in order to get ISO 8601 parsing.Provides an adapter to wrap an Iterator with an Iterable, allowing it to be run through a foreach loop.Abstract implementation of an iterator that also implements Iterable (to return itself) so that it can be used if for() loops.Lazy<T>Simple utility for building an on-demand (lazy) object-initializer.Deprecated.since 1/2017 use aSupplierinsteadInterface allows for implementations that read lines from a String, an ASCII file, or somewhere else.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.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 endsDescribes API for getting current position in a stream, writer, or underlying file.Location info about a locus.LocusComparator<T extends Locus>compares first by sequence index then by positionSimple implementation of Locus interface for ease of passing as an arg and comparing with other Locus implementations.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().Enumeration for setting log levels.Class to generate an MD5 string for a file as it is being readClass to generate an MD5 string for a file as it is being readAn iterator over Iterators that return Ts.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.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 nextPeekIterator<T>Wrapper around an iterator that enables non-destructive peeking at the next element that would be returned by next()Wraps output stream in a manner which keeps track of the position within the file and allowing writes at arbitrary pointsUtility class that will execute sub processes via Runtime.getRuntime().exec(...) and read off the output from stderr and stdout of the sub process.Little progress logging class to facilitate consistent output of useful information when progressing through a stream of SAM records.An interface defining the record() methods of the Picard-public ProgressLogger implementation.Utility for determining the type of quality encoding/format (seeFastqQualityFormat) used in a SAM/BAM or Fastq.Utility class for working with quality scores and error probabilities.Interface for specifying loci of interest for genotype calling and other operations.LikeIso8601Date, 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.ResourceLimitedMapFunctor<Key,Value> c.f.Thrown by various codecs to indicate EOF without having to clutter the API with throws clausesThrown by various IO classes to indicate IOException without having to clutter the API with throws clausesThrown by classes handling script engines like the javascript-based filters for SAM/VCFA set of constants defined in the sam-spec (https://github.com/samtools/hts-specs) that need to be referenced in code.Iterator that traverses a SAM File, accumulating information on a per-locus basis.The unit of iteration.Implementation ofAbstractRecordAndOffsetclass forSamLocusIterator.Create an iterator over aSamReaderthat only returns reads that overlap one of the intervals in an interval list.Iterator that uses a dedicated background thread to prefetch SAMRecords, reading ahead by a set number of bases to improve throughput.SamRecordTrackingBuffer<T extends SamRecordWithOrdinal>This class stores SAMRecords for return.A little class to store the unique index associated with this record.Checks if Snappy is available, and provides methods for wrapping InputStreams and OutputStreams with Snappy if so.Optimized method for converting Solexa ASCII qualities into Phred scores.Collection to which many records can be added.Client must implement this class, which defines the way in which records are written to and read from file.Accumulate a list of longs that can then be sorted in natural order and iterated over.Utility to help in performance testing.Deprecated.Grab-bag of stateless String-oriented utilities.Factory class for wrapping input and output streams for temporary files.An extension ofBlockCompressedOutputStreamthat doesn't write an empty BGZF block at the end of the stream.Utility code for performing quality trimming.Tuple<A,B> A simple tuple class.Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.