AbstractInputParser |
Class for parsing text files where each line consists of fields separated by whitespace.
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AdapterMarker |
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
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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.
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AsyncIterator<T> |
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be
efficient.
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BaitDesigner |
Designs baits for hybrid selection!
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BasicInputParser |
TextFileParser which reads a single text file.
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BedToIntervalList |
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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.
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ClippingUtility |
Utilities to clip the adapter sequence from a SAMRecord read
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CsvInputParser |
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DbSnpBitSetUtil |
Utility class to use with DbSnp files to determine is a locus is
a dbSnp site.
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DbSnpBitSetUtil.DbSnpBitSets |
Little tuple class to contain one bitset for SNPs and another for Indels.
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DelimitedTextFileWithHeaderIterator |
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
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FifoBuffer |
Summary
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GraphUtils |
Created by farjoun on 11/2/16.
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GraphUtils.Graph<Node extends Comparable<Node>> |
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IlluminaUtil |
Misc utilities for working with Illumina specific files and data
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IntervalListToBed |
Trivially simple command line program to convert an IntervalList file to a BED file.
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IntervalListTools |
Performs various IntervalList manipulations.
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Iterators |
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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.
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LiftoverUtils |
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MathUtil |
General math utilities
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MathUtil.LogMath |
A collection of common math operations that work with log values.
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PropertyUtils |
Utility for loading properties files from resources.
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QuerySortedReadPairIteratorUtil |
A collection of helper utilities for iterating through reads that are in query-name sorted
read order as pairs
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QuerySortedReadPairIteratorUtil.ReadPair |
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ReflectionUtil |
Class which contains utility functions that use reflection.
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RExecutor |
Util class for executing R scripts.
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ScatterIntervalsByNs |
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
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ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection |
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TabbedInputParser |
Parser for tab-delimited files
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TabbedTextFileWithHeaderParser |
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
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ThreadPoolExecutorUtil |
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ThreadPoolExecutorWithExceptions |
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions
while executing
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UnsignedTypeUtil |
A utility class for dealing with unsigned types.
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