Re: [Samtools-help] documentation on CSI format

[John M. <jm...@sa...>]

On 21 Feb 2015, at 01:43, Adam Birnbaum <ad...@ed...> wrote:
> I’ve been looking for information and documentation on CSI format, and found only this one page on the record format and binning algorithms:  http://samtools.github.io/hts-specs/CSIv1.pdf.

That CSI document at http://samtools.github.io/hts-specs/ is indeed the spec.  At the moment it's over-brief and needs to be read in conjunction with the description of BAI in the SAM spec.  CSI embodies much the same idea as BAI, so much can be gleaned from the BAI description and the differences shown in the CSI record format.

One of my back-burners has an update to the CSI spec to make it more complete and self-contained.  I guess your question provides motivation to finish it up!

    John

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