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
