On 8 Dec 2015, at 13:56, Claudio Alberti <claudio.albe...@epfl.ch> wrote:
>
> It seems that bgfz_seek and bgzf_tell can work as well, do you see any issue
> with them?
It would be a similar situation to that noted in that September BCF / VCF.GZ
thread, though you are in a better position due to the legacy existence of a
bam_read1() that takes a raw BGZF*.
If you open a BGZF file with bgzf_open(), you will be able to read BAM records
from it with bam_read1() or SAM.GZ records from it with
bgzf_getline()/sam_parse1(). These operate on the BGZF file handle directly
(thus without further buffering), so bgzf_seek()/bgzf_tell() will cooperate
with them.
But you will be out of luck entirely with SAM and CRAM files, as these do not
have any underlying BGZF structure so can't be opened or read via BGZF routines.
So this is not a general solution, but it may suffice e.g. if for now you are
only interested in BAM files. But note also that bam_read1() and
bgzf_getline() are at the less-supported end of the HTSlib API.
John
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