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Overall improvements in the use of prefetch instructions. (contribution by Igor Sfiligoi)
Made input/output fully asynchronous by using a dedicated thread. (contribution by Igor Sfiligoi)
Added support for AVX2 256-bit instructions with can be enabled by
setting the SSE_AXV2 environment variable at compile time. (contribution by Igor Sfiligoi)
Fixed an issue causing bowtie2 to crash when processing ZSTD
files with high compression ratios.
Changed the way that unique alignments are counted in summary
message to better match up with filters on SAM output