Iterating through BAM file using net.sf.samtools.SAMFileReader

[hpimentel]

Hi all,

I'm new to the Java SAMTools API.

I want to be able to read a BAM file, operate on a the current read (if it is the first of a pair), get the mate, and operate on the mate.

I've tried using a SAMRecordIterator, and then using SAMReader.queryMate(), which throws an exception since it is iterating.

I've also tried using a different SAMReader object, which works but is super slow.

I could do some trickery temporarily saving the first read until the mate is read, but I'd rather not if I don't have to.

Any ideas?



Thanks!