SamReadGroup: The SamReadGroup class

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

Description

Package: aroma.seq
Class SamReadGroup

logical
~~|
~~+--BasicObject
~~~~~~~|
~~~~~~~+--SamReadGroup

Directly known subclasses:

public static class SamReadGroup
extends BasicObject

A SamReadGroup object represents a SAM Read Group.

Usage

SamReadGroup(id=NULL, sample=NULL, library=NULL, platform=NULL, platformUnit=NULL,
  sequencingCenter=NULL, description=NULL, runDate=NULL, flowOrder=NULL,
  keySequence=NULL, program=NULL, predictedInsertSize=NULL, ...)

Arguments

id	Specifies the ID read group field.
sample	Specifies the SM read group field.
library	Specifies the LB read group field.
platform	Specifies the PL read group field.
platformUnit	Specifies the PU read group field.
sequencingCenter	Specifies the CN read group field.
description	Specifies the DS read group field.
runDate	Specifies the DT read group field.
flowOrder	Specifies the FO read group field.
keySequence	Specifies the KS read group field.
program	Specifies the PG read group field.
predictedInsertSize	Specifies the PI read group field.
...	Additional named arguments, including two-letter read group keys for the above, e.g. 'SM'.

Fields and Methods

Methods:

	asSamList	-
	asString	-
	byScanBamHeader	-
	hasDescription	-
	hasID	-
	hasLibrary	-
	hasPlatform	-
	hasPlatformUnit	-
	hasRunDate	-
	hasSample	-
	hasSequencingCenter	-
	isEmpty	-
	merge	-
	validate	-

Methods inherited from BasicObject:
$, $<-, [[, [[<-, as.character, attach, detach, equals, extend, getFields, getInstantiationTime, hasField, hashCode, isReferable, objectSize, print, asThis

Methods inherited from logical:

Author(s)

Henrik Bengtsson

References

[1] The SAM Format Specification Working Group, The SAM Format Specification, Sept 7, 2011.
[2] Collected FAQs about BAM files: What's the meaning of the standard read group fields?, GATK Forums, Mar 2013. http://goo.gl/PWv8MX

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