Description Usage Arguments Fields and Methods Author(s) References
Package: aroma.seq
Class BwaAlignment
Object
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ParametersInterface
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AromaSeqTransform
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AbstractAlignment
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BwaAlignment
Directly known subclasses:
public static class BwaAlignment
extends AbstractAlignment
...
1 | BwaAlignment(..., indexSet=NULL, flavor=c("backtracking"))
|
... |
Arguments passed to |
indexSet |
An |
flavor |
A |
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
Henrik Bengtsson
[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.
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