[Samtools-devel] SAM index files (SAI)

[Peter C. <p.j...@go...>]

Hi all (samtools-devel and igv-help),

I'm aware that IGV supports SAM index files with the extension SAI,
and igvtools can create these:
http://www.broadinstitute.org/igv/BAM
http://www.broadinstitute.org/igv/igvtools

Are these SAI files exactly the same format as BAM index files with the
BAI extension (except that the offsets are simply unsigned 64 bit integers,
rather than BGZF virtual offsets)?

If so, could this be clarified in the SAM/BAM specification? Basically in
Section 5 replace BAM with SAM/BAM, and add this text just after the
opening paragraph:

> Indexes for SAM files are given the file extension "*.sai" while for BAM
> files the index extension is "*.bam". SAM indexes use simple integer
> offsets, while BAM indexes use BGZF virtual file offsets described in
> the previous section.

I'm happy to prepare that change as a patch to the tex file in SVN.

Also (again assuming SAI files are the same structure as BAI files),
is there any technical reason why samtools index doesn't work on
SAM files?

Thanks,

Peter