| 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!
|
| 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 |
|
| 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.
|