new(github.com/marbl/Mash): mash 2.3#13463
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Genome distance via MinHash (C++). capnp+gsl+zlib; bootstrap (autoconf); 2 aarch64 source patches (cstdint include, x86-only memcpy symver gate); inline fixture.
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Adds Mash — fast genome/metagenome distance estimation via MinHash. C++/autotools. Now that deps landed:
capnproto.org(capnp codegen at build + libcapnp at runtime) +gnu.org/gsl+ zlib. The tag archive ships noconfigure, so./bootstrap.sh(autoconf build dep); flags--with-capnp/--with-gsl. Two aarch64 source fixes (both VM-verified): (1)CXXFLAGS: -include cstdint -include limits— the 2019 code omits transitive includes modern libstdc++ no longer leaks; (2) aMakefile.insed gating Mash'smemcpy@GLIBC_2.2.5symver hack to x86_64 only (that symbol version is x86-only; on aarch64 it fails to link, and a naive neuter recurses → segfault). gcc 14 build + libstdcxx runtime on linux. Verified on linux/arm64: capnp codegen runs,mash --version-> 2.3, sketch+self-dist -> 0 on an inline-fixture FASTA.