Release 2.2.1 (17 March 2021)

Hotfix for v2.2: Fixed the bug mentioned in #135.

Release 2.2 (8 March 2021)

Changes since the last release (2.1):

  • Passed the validation test on ~88 billions reads (Credits: Keiran Raine, CASM division, Sanger Institute)
  • Fixed bugs reported in #109 causing mismatch between bwa-mem and bwa-mem2
  • Fixed the issue (# 112) causing crash due to corrupted thread id
  • Using all the SSE flags to create optimized SSE41 and SSE42 binaries

Release 2.1 (16 October 2020)

Release 2.1 of BWA-MEM2.

Changes since the last release (2.0):

  • Smaller index: the index size on disk is down by 8 times and in memory by 4 times due to moving to only one type of FM-index (2bit.64 instead of 2bit.64 and 8bit.32) and 8x compression of suffix array. For example, for human genome, index size on disk is down to ~10GB from ~80GB and memory footprint is down to ~10GB from ~40GB. There is a substantial decrease in index IO time due to the reduction and hardly any performance impact on read mapping.

  • Added support for 2 more execution modes: sse4.2 and avx.

  • Fixed multiple bugs including those reported in Issues #71, #80 and #85.

  • Merged multiple pull requests.

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.