| Interface | Description |
|---|---|
| AdapterPair | |
| AtomicIterator<T> |
Describes
|
| 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 adapater 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 | |
| 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.
|
| 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 | 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.
|