View source: R/duffybamtools.R
bamReader | R Documentation |
The bamReader function constructs and returns an S4 object of class bamReader. The bamReader object represents a connection to an opened BAM-file. When an indexname is given or idx=TRUE, the function tries to load an existing BAM-index.
bamReader(filename,indexname,idx=FALSE,verbose=0)
filename |
Filename of BAM-file to be opened for reading. |
indexname |
Optional: Name of BAM-index file |
idx |
Logical |
verbose |
Numeric: Quantifies the extent of textual feedback (levels: 0,1,2). |
Wolfgang Kaisers
bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam)
align<-getNextAlign(reader)
name(align)
position(align)
bamClose(reader)
# Open reader and initialize BAM-index
reader<-bamReader(bam,idx=TRUE)
index.initialized(reader)
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