rbamtools (version 2.4.0)

refSeqDict-class: Class "refSeqDict"

Description

refSeqDict represents Data contained in the header Section of BAM-files.

Objects from the Class

Objects can be created by calls of the form hl<-new("refSeqDict").

References

The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011. http://www.samtools.sourceforge.net/SAM1.pdf

Examples

bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
reader<-bamReader(bam)
isOpen(reader)
header<-getHeader(reader)
htxt<-getHeaderText(header)
refSeqs<-refSeqDict(htxt)
dim(refSeqs)
ht<-getHeaderText(refSeqs)
df<-as.data.frame(refSeqs)
addSeq(refSeqs,SN="nextSeqName",LN=1000)
removeSeqs(refSeqs,3)
bamClose(reader)