Interesting thread!
I like these comments:
"This is twice as long as the longest human chromosome and is
quite adequate for practical use" - Thomas W. Blackwell
"Hopefully 2 Gbp suffices for most species that people are
interested in." - John Marshall.
As already mentioned, bread wheat, which provides ~20% of all the
calories consumed by humans globally, has 6 of it's 27 chromosomes
*assembled* to a length of greater than 537 Mbp [1]...
I won't mention Paris japonica ;-)
[1]
https://docs.google.com/spreadsheet/ccc?key=0Aqs5UFlky_s6dDlmVVFib3FoSm1tS1JIQzMxY0RVb2c
On 18 October 2013 11:50, John Marshall <j...@sanger.ac.uk> wrote:
> On 17 Oct 2013, at 17:08, Thomas W. Blackwell wrote:
>> Chromosome positions beyond 2^29 - 1 = 536,870,911 are not representable
>> in the .bam binary format.
>
> Actually the 2^29 - 1 limitation is in the BAI index format.
>
> BAM files themselves can represent positions up to 2^31 - 1, i.e., 2 billion
> or so. The SAM/BAM specification originally said 2^29 out of sympathy with
> BAI, but this was increased to 2^31 - 1 a couple of years ago [1].
>
> If a BAM file contains reads with positions beyond 2^29 - 1 then you won't be
> able to index it with a .bai index, as the original poster found. HTSlib
> introduces a new index format, "CSI", that is similar to BAI but is more
> flexible about bin size and depth, so can index all the positions
> representable in BAM.
>
> Hopefully 2 Gbp suffices for most species that people are interested in. In
> principle the existing file formats could be compatibly pushed to 4 Gbp, but
> this would require great care with getting signed v. unsigned arithmetic
> correct in the implementations so would likely not really be worthwhile.
>
> John
>
> [1] See
> https://github.com/samtools/hts-specs/commit/28c54abe2d3478eb7ea7c5fea0a268282b087f2b
> and also today's commit that updates a couple of 2^29 figures that were
> previously missed.
>
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