> As such is there a specific function in the htsjdk to retrieve the number
> of reads/alignments that cover a specific position i.e. chr2:10,000?
> Or is this something that requires some coding, say iterating through a
> query from a SamReader? If so does any one have any recommendations/code
> snippets for the most efficient way to do this?
>
Hi,
That's a synopsis of how I would do it. If there are better ways I'd like
to know myself!
Dario
public void getDepthAtInterval(){
String chrom= "chr1";
int from= 1000;
int to= 2000;
SamReader samReader = ...// Get a SamRaader obj;
// Loci to sample (could be a single position):
IntervalList il= new IntervalList(samReader.getFileHeader());
il.add(new Interval(chrom, from, to));
// Start iterating through loci:
SamLocusIterator samLocIter= new SamLocusIterator(samReader, il, true);
samLocIter.setSamFilters(filters); // Optional list of List<SamRecordFilter>
Iterator<SamLocusIterator.LocusInfo> iter= samLocIter.iterator();
while(iter.hasNext()){
LocusInfo locusInfo= iter.next();
int depth= locusInfo.getRecordAndPositions().size();
int pos= locusInfo.getPosition();
System.out.println("Depth " + depth + " at position " + pos);
}
samLocIter.close();
}
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