new(github.com/DaehwanKimLab/hisat2): hisat2 2.2.2#13464
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Graph-based read aligner (C++). aarch64 SSE2->sse2neon shim; perl+python wrappers; gcc14 build + libstdcxx runtime.
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Adds HISAT2 — fast graph-based read aligner (bowtie2 lineage). C++/Makefile, x86 SSE2 intrinsics. On aarch64 (incl. darwin arm) the recipe shims
<emmintrin.h>onto a pinned sse2neon, drops-msse2/-m64, setsPOPCNT_CAPABILITY=0+SSE_FLAG=-march=armv8-a+simd(the include-guard must not collide with theEList<T,int S>template param).CC=cc CXX=c++.hisat2/-build/-inspectare perl/python wrappers (/usr/bin/envshebangs) → perl+python runtime deps; gcc 14 build + libstdcxx runtime on linux (darwin = Apple clang). Verified on linux/arm64: builds all 7 binaries,hisat2 --version-> 2.2.2, index+align gives 100% alignment. (Note: upstreamhisat2-inspectwrapperimport impbreaks on py3.12 — unrelated to arch.)