BwaIndexSet: The BwaIndexSet class

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

Description

Package: aroma.seq
Class BwaIndexSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractIndexSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--SequenceContigsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--BwaIndexSet

Directly known subclasses:

public static class BwaIndexSet
extends SequenceContigsInterface

An BwaIndexSet object represents a set of BwaIndexFile:s.

Usage

BwaIndexSet(...)

Arguments

...	Arguments passed to AbstractIndexSet.

Fields and Methods

Methods:

	as.character	-
	getSeqLengths	-
	isCompatibleWith	-
	isComplete	-
	readAnnData	-

Methods inherited from SequenceContigsInterface:
cleanSeqNames, getSeqGenericSummary, getSeqLengths, getSeqNames, getSeqOrdering, getTotalSeqLength, hasDuplicatedSeqs, hasSeqLengths, isCompatibleWithBySeqLengths, isCompatibleWithBySeqNames, isCompatibleWithBySeqs, nbrOfSeqs

Methods inherited from AbstractIndexSet:
as.character, byPrefix, getDefaultFilePatterns, getFastaReferenceFile, getIndexPrefix, getOrganism, isComplete

Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, directoryItem, directoryItems, directoryStructure, directoryStructure<-, updateDirectoryStructure, getFullNameTranslatorSet, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

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.