Release 2.0 (9 July 2020)

This is the first production release of BWA-MEM2.

Changes since the last release:

Made the source code more secure with more than 300 changes all across it.
Added support for memory re-allocations in case the pre-allocated fixed memory is insufficient.
Added support for MC flag in the sam file and support for -5, -q flags in the command line.
The output is now identical to the output of bwa-mem-0.7.17.
Merged index building code with FMI_Search class.
Added support for different ways to input read files, now, it is same as bwa-mem.
Fixed a bug in AVX512 sam processing part, which was leading to incorrect output.

Release 2.0pre2 (4 February 2020)

Miscellaneous changes:

Changed the license from GPL to MIT.
IMPORTANT: the index structure has changed since commit 6743183. Please rebuild the index if you are using a later commit or the new release.
Added charts in README.md comparing the performance of bwa-mem2 with bwa-mem.

Major code changes:

Fixed working for variable length reads.
Fixed a bug involving reads of length greater than 250bp.
Added support for allocation of more memory in small chunks if large pre-allocated fixed memory is insufficient. This is needed very rarely (thus, having no impact on performance) but prevents asserts from failing (code from crashing) in that scenario.
Fixed a memory leak due to not releasing the memory allocated for seeds after smem.
Fixed a segfault due to non-alignment of small allocated memory in the optimized banded Smith-Waterman.
Enabled working with genomes larger than 7-8 billion nucleotides (e.g. Wheat genome).
Fixed a segfault occuring (with gcc compiler) while reading the index.