bamReader: bamReader: Connection to BAM file for reading access.
In rbamtools: Read and Write BAM (Binary Alignment) Files

Description Usage Arguments Author(s) Examples

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.

1	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)
indexInitialized(reader)