# NOT RUN {
bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
idx<-paste(bam,"bai",sep=".")
# Open BAM file
reader<-bamReader(bam)
# Create empty range and fill with push_back
range<-bamRange()
for(i in 1:10)
{
align<-getNextAlign(reader)
push_back(range,align)
}
size(range)
# Eventually:
# }
# NOT RUN {
createIndex(reader,idx)
# }
# NOT RUN {
# Load BAM index file
loadIndex(reader,idx)
indexInitialized(reader) # Should return 'TRUE'
#----------------------------------------------#
# Find appropriate refid (=ID)
# Returns a data.frame with three columns:
# ID=refid, SN=Sequence Name, LN=Sequence length
#----------------------------------------------#
rdf<-getRefData(reader)
head(rdf)
#----------------------------------------------#
# The sequence length (LN) also determines valid
# range for start and stop coordinates
# Invalid refid-, start- or stop-coordinates will
# release an error.
# coords: refid=0, start=0, stop=249250621
#----------------------------------------------#
coords<-as.integer(c(0,0,249250621))
range<-bamRange(reader,coords)
size(range)
align<-getNextAlign(range)
cigarData(align)
range<-bamRange(reader,coords,complex=TRUE)
size(range)
align<-getNextAlign(range)
cigarData(align)
# }
# NOT RUN {
while(!is.null(align))
{
print(position(align))
align<-getNextAlign(range)
}
# }
# NOT RUN {
bamClose(reader)
# }
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