BwaAlignment: The BwaAlignment class

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Package: aroma.seq
Class BwaAlignment

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractAlignment
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--BwaAlignment

Directly known subclasses:

public static class BwaAlignment
extends AbstractAlignment

...

Usage

BwaAlignment(..., indexSet=NULL, flavor=c("backtracking"))

Arguments

...	Arguments passed to AbstractAlignment.
indexSet	An BwaIndexSet.
flavor	A character string specifying the type of BWA algorithm to use for alignment.

Fields and Methods

Methods:

	getAsteriskTags	-
	process	-

Methods inherited from AbstractAlignment:
as.character, getAcronym, getAsteriskTags, getIndexSet, getOrganism, getOutputDataSet, getRootPath, isPaired

Methods inherited from AromaSeqTransform:
as.character, findFilesTodo, getAcronym, getAsteriskTags, getFlavor, getFullName, getInputDataSet, getName, getOptionalArguments, getOrganism, getOutputDataSet, getParameters, getPath, getRootPath, getTags, isDone, length, process, setTags

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, findRspReportTemplate, asThis

Author(s)

Henrik Bengtsson

References

[1] Li H. and Durbin R., Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 2009.
[2] Li H. and Durbin R., Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics, 2010.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.