seek to random record in bam file

[Brent Pedersen]

Hi,

I want to sample some characteristics of a bam file, something like
`samtools flagstat` but with, e.g.
$n reads from each of $m random sites in the bam.

Is there a simple way to do this without using the index?


With the index, I guess I could just use `bam.index.Chunks` with a
random genomic region. Is that the best way? I was hoping I could seek
to a random location, find the next bgzf block start and make the
bam.Reader start from there, but it doesn't seem like that's feasible.

thanks,
-Brent

[Dan Kortschak]

You can't seek to a random location in a bgzf stream and expect to be
able to read valid data. You also can't expect to seek to a random
position in the uncompressed data of a bam file and expect to be able
to parse a valid bam record (this precludes starting at a random file
offset and looking for the next bgzf header).

Either use an index or flick Omit on and off depending on what you
need.

[Brent Pedersen]

I'd done this with a tabix/bgzf file before by seeking to a random
location, finding the next bgzf magic, decompressing, discarding til
the first new-line, and reading from there.
I guess there's no way to do this with bam since there's not an end of record.

I'll use the index.