SamTransform: The SamTransform class

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

Description

Package: aroma.seq
Class SamTransform

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaSeqTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--SamTransform

Directly known subclasses:
BamMerger, PicardDuplicateRemoval

public abstract static class SamTransform
extends AromaSeqTransform

A SamTransform is an AromaSeqTransform that takes BamDataSet:s (or SamDataSet:s) as input.

Usage

SamTransform(..., .className="BamDataSet")

Arguments

...	Arguments passed to AromaSeqTransform.
.className	A character string specifying what class of data sets to accept.

Fields and Methods

Methods:
No methods defined.

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

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