Re: [Samtools-devel] Reference length limit differs between SAM & BAM spec?

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

On Monday, September 26, 2011, Heng Li <lh...@sa...> wrote:
> The 2^29-1 limit is imposed by BAM indexing, which does not
> work any more given longer genomes.

OK, that confirms my guess.

> Probably a better way to state this is to set a 2^31-1 limit
> in SAM, but say in the indexing section that the current
> strategy has a limitation.

Yes please, that would be an improvement.

> As to the reference sequence, the recommended use
> is to index the fasta with faidx to enable quick access
> to subsequences in any regions. Samtools never
> loads the entire reference into memory.

Does faidx also have a limit on the sequence length?

Peter