[Debian-med-packaging] Bug#753485: Status of samtools

[Aleksandar Zlicic]

Hi, Andreas

Only some parts of the patches were accepted.
https://github.com/samtools/htslib/commit/e8806c71f3408d2cbff8caa8df17eef848d33a02

The pull request (https://github.com/samtools/htslib/pull/99/) contains  two
patches, one dealing with endianness related issues and the other one dealing
with unaligned access issues.

Most of the changes that fix endianness related issues were accepted, except
the ones that fix detection of system endiannes on mips (mips big endian is
not detected). This is still an issue in htslib and consequently in samtools.
I will contact upstream to see if they would be willing to reconsider including
these changes at least.

On the other hand, most of the changes regarding unaligned access issues
weren't accepted and upstream developers suggested this should be fixed in
another way, that is by implementing a standard set of functions for accessing
memory in both cases (where architecture supports unaligned access and for
architectures which don't) and using these functions for accessing memory
throughout the code.

One of the samtools developers has done some work to implement this
(https://github.com/jkbonfield/htslib/tree/SPARC), but changes from this
experimental branch haven't been merged to the main branch yet.

Best Regards
Aleksandar Zlicic
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