Changes
- #401: The default number of threads is now 1 instead of 3.
- #409: Ensure reference names are unique and conform to the SAM specification.
Contributed by @drtconway in PR #411. - #269, #418: Strobealign scales now much better to systems with many cores. Previously, decompressing gzipped-compressed input files was a bottleneck starting at about 30 threads.
We now use ISA-L for decompression, which is about three times as fast as zlib, and decompression is also done in a separate thread. We tested up to 128 cores, and strobealign was still able to use all cores.
Contributed by @telmin. - #447: Switched to a new way for hashing randstrobes in preparation for the introduction of multi-context seeds. Pre-generated index files (
.stifiles) therefore need to be re-generated. (Strobealign will complain if you try to use an outdated index file.)
Contributors
telmin and drtconway