Re: [Samtools-devel] Specification update or disclaimer

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

On Thu, Jul 18, 2013 at 5:24 PM, Nigel Delaney
<nde...@br...> wrote:
> Hi,
>
> I had a request to make about the SAMTools website.  Currently, the SAMTools
> website has a specification file (http://samtools.sourceforge.net/SAM1.pdf)
> which is a very well written explanation of the SAM/BAM/BAI file format.
>
> Unfortunately, it also appears to be out of date.  I am trying to maintain a
> library of SAM/BAM parsing and manipulation tools, and recently lost a lot
> of time tracking down issues caused by the file format of recent SAM files
> being binary incompatible with the specification on the website.  In
> particular, it appears that new files:
>
> -Contain a series of chunks in the index file representing metadata by
> creating a pseudo-bin in the reference.

Are you asking about this issue?
https://github.com/samtools/sam-spec/pull/2

> -May now also include an EOF file block in BAM files.

Yes, that's been asked about before. I was meaning to write a
pull request to add this...

Peter