v2.2.1: Hotfix for v2.2

Hotfix: Fixed the bug mentioned in #135.

Bwa-mem2-2.2

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

Bwa-mem2-2.1

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.

Bwa-mem2-2.0

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.

The tool is described in the paper:

• Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.

Bwa-mem2-2.0pre2

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.

Bwa-mem2-2.0pre1

A pre-release.