BamMerger: The BamMerger class

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

Description

Package: aroma.seq
Class BamMerger

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

Directly known subclasses:

public static class BamMerger
extends FileGroupsInterface

A BamMerger takes a BamDataSet as input and merges subsets of BamDataFile:s into single ones. How the grouping is done, can be controlled by a parameter.

Usage

BamMerger(dataSet=NULL, groupBy=NULL, ...)

Arguments

dataSet	An BamDataSet.
groupBy	A character string or an explicit named list, specifying which input files should be processed together.
...	Not used.

Fields and Methods

Methods:

	getOutputDataSet	-
	process	-

Methods inherited from FileGroupsInterface:
getGroupBy, getGroupNames, getGroups, getInputDataSet, nbrOfGroups, validateGroups

Methods inherited from SamTransform:
getRootPath

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

Supported operating systems

This method is available on Linux, macOS, and Windows [1].

Author(s)

Henrik Bengtsson

See Also

Internally mergeBam is used for merging, sorting, and indexing.

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