Re: [Samtools-devel] Unspecified bits in SAM FLAG

[James B. <jk...@sa...>]

On Wed, Aug 19, 2015 at 02:57:47PM +0300, Artem Tarasov wrote:
> There's another hack you can use - store information in place of the ending
> '\0' of the read name, setting the byte back to zero before writing out.
> This requires a bit more care but you get 8 bits of space instead of just 4.

That's horrid!  Although it reminds me of an equally horrid hack I did
to read names in io_lib.  For machines without unaligned word access
(eg SPARC) I made the cigar ops aligned by varying the number of
read-name nul termination bytes in the in-memory BAM representation
from 1 to 4. :-)

I'm not advising using it as a way to hide information though!

James

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