I'm glad you're contributing to genomics technology, but I feel compelled to point out that zlib is a terrible algorithm for compressing BAM files. The reason is that over 50% of the compressed BAM file space is spent on encoding the quality scores at full resolution, which is just wasted effort. Quality scores are very hard to compress- they are very close to completely random data- and the best compressed use complex probabilistic models to switch the encoding technology depending on what category quality scores fall into.
I'm all for a replacement for BAM file format and the quality scores. Ideally something that supports delta based encoding to a reference genome similar to CRAM and something that more compactly represents quality of bases sequenced.
In the meantime as a user of BAM I'm very very very grateful for faster zlib as it makes life a lot better with the current large installed base of programs that use BAM and data sets in BAM. These sort of improvements really do make a meaningful difference in the same way that switching to SSDs from magnetic disks didn't improve the implementation of my software but makes my computer a lot faster to boot up and compile things.
