Quickest way for pileup at known position?
ebioman opened this issue · comments
ebioman commented
Hi thanks for this great library!
I am a bit confused currently what the fastest way is to get a pileup at a known position.
Currently I found the only way being from IndexedReader where here bam
would be the IndexedReader:
bam.fetch((chr,start,end)).expect("ERROR: could not fetch region");
for pile in bam.pileup().map(|x| x.expect("ERROR: could not parse BAM file")) {
if pile.pos() as u64 == start {
// here comes the the analysis of that position
}
}
This iterator part and checking the position to match my position of interest is though pretty slow and I am wondering whether I am doing here something very obviously wrong ?
I guess by fetching a 1bp specific position I still can get quite a large range depending on my read length, but still I feel I am missing something here...