Dear list,

I have a question regarding processing of large bamfiles (such as reading in via ‚readGAlignemnts‘ or computing the coverage).
I know about the option of iterative processing such as shown in the example below.


mybam = open(Bamfile(„bamfile“, yieldSize = 2000000))

gAln <- GAlignments()

while(length(chunk <- readGAlignmentsFromBam(mybam))){
	gAln <- c(gAln,chunk)
	 }
close(mybam)


Obviously the efficiency of iterating depends on the (i) file-size of the bam file and (ii) the available memory.

Can I somehow pinpoint (e.g. file-size, number of alignments, memory requirements) when it is more efficient ( = faster and memory
requirements are feasible) to process the bam-file in one batch or, alternatively, do it in an iterative manner?


Best,
Stefanie


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