[Samtools-devel] CRAM format question

[Michael B. <mi...@ed...>]

My company intends to add CRAM format support to its product. As first step to better understand specification I started working on implementation functionality similar to <cram_dump> with <scramble> as a compression/decompression reference and would appreciate if someone could help me to clear some questions. The CRAM 3.0 June 2015 spec is used.

- I believe sentences after table that explain Encoding (subexponential encoding example on page 3) should be edited to reflect actual table content.
-  cramp_dump handles more keys in preservation map than specified in the spec (MI, UI, PI), the same with data series encoding map as well. What is the general rule of having boolean key? Why even we have to have value for that? In other words: are the missing keys are "false" by default? How about if substitution matrix will be missed for example?
- I have noticed scramble uses BB key which is not part of the specification. Should the source code be used as the "specification"?

Thank you,
Michael