BamDataFile: The BamDataFile class

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

Description

Package: aroma.seq
Class BamDataFile

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--SequenceContigsInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPathnameInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AromaSeqDataFile
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--BamDataFile

Directly known subclasses:

public static class BamDataFile
extends AromaSeqDataFile

A BamDataFile object represents a BAM file.

Usage

BamDataFile(...)

Arguments

...	Arguments passed to GenericDataFile.

Fields and Methods

Methods:

	buildIndex	-
	convertToSam	-
	countNucleotides	-
	doQDNAseq	-
	extractReadStartPositions	-
	getChipType	-
	getFlagStat	-
	getHeader	-
	getIndexFile	-
	getIndexStats	-
	getPlatform	-
	getReadCounts	-
	getReadGroup	-
	getReadGroups	-
	getSeqLengths	-
	getTargetLengths	-
	getTargetNames	-
	getTargets	-
	getTotalTargetLength	-
	hasIndex	-
	isPaired	-
	isSorted	-
	mpileup	-
	nbrOfMappedReads	-
	nbrOfReads	-
	nbrOfTargets	-
	nbrOfUnmappedReads	-
	readDataFrame	-
	readReadPositions	-
	replaceAllReadGroups	-
	sort	-
	sortByName	-
	sortByPosition	-
	tview	-

Methods inherited from AromaSeqDataFile:
getDefaultFullName, getDefaultSamReadGroup, getSamReadGroup, isCompatibleWith, setSamReadGroup

Methods inherited from AromaPathnameInterface:
directoryStructure, getOrganism

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

Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, directoryItem, directoryItems, directoryStructure, directoryStructure<-, getDataSetName, getOrganismName, getSampleName, loadCacheFile, loadCacheFileItem, memoizedCall2, saveCacheFile, saveCacheFileItem, 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

References

[1] The SAM Format Specification Working Group, The SAM Format Specification, Sept 7, 2011.

See Also

An object of this class is typically part of an BamDataSet.

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