Apple Silicon native port (v2) — native arm64 DeepVariant/DeepTrio/DeepSomatic/pangenome

.gitignore

@@ -10,3 +10,36 @@
 bazel-*
 
 **/.ipynb_checkpoints
+
+# v2 — Apple Silicon native port
+build/
+build-*/
+.cache/
+**/__pycache__/
+tools/conversion/venv-*/
+tools/conversion/.cache/
+tools/conversion/models/
+tools/conversion/Generated/
+tools/reference/cache/
+tools/reference/output/
+benchmarks/runs/
+benchmarks/*.log
+testdata/reference/large/
+*.mlpackage
+*.mlmodelc
+*.tfrecord
+*.bam
+*.bai
+*.fa
+*.fai
+*.fa.gz
+*.vcf
+*.vcf.gz
+*.tbi
+*.bed
+.DS_Store
+validation/work/
+validation/output/
+
+# Local Claude Code settings (do not commit)
+.claude/

CMakeLists.txt

@@ -0,0 +1,81 @@
+cmake_minimum_required(VERSION 3.27)
+project(deepvariant VERSION 1.10.0 LANGUAGES CXX OBJCXX C)
+
+# ---------------------------------------------------------------------------
+# Guards: macOS arm64 only.
+# ---------------------------------------------------------------------------
+if(NOT APPLE OR NOT CMAKE_SYSTEM_PROCESSOR STREQUAL "arm64")
+  message(FATAL_ERROR "This build targets macOS arm64 only.")
+endif()
+if(CMAKE_SYSTEM_VERSION VERSION_LESS "23")  # macOS 14 = Darwin 23.x
+  message(FATAL_ERROR "macOS 14 (Sonoma) or newer required.")
+endif()
+
+# ---------------------------------------------------------------------------
+# Language standards
+# ---------------------------------------------------------------------------
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_OBJCXX_STANDARD 17)
+set(CMAKE_OBJCXX_STANDARD_REQUIRED ON)
+
+# Visibility: match TF convention — default hidden.
+set(CMAKE_C_VISIBILITY_PRESET   hidden)
+set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+set(CMAKE_VISIBILITY_INLINES_HIDDEN ON)
+
+# All depedencies built as STATIC.
+set(BUILD_SHARED_LIBS OFF)
+
+# Default build type.
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+endif()
+
+# Build output goes to a single directory for easy inspection.
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
+
+# ---------------------------------------------------------------------------
+# Compiler flags — arm64, Clang (Apple Clang 21+)
+# ---------------------------------------------------------------------------
+add_compile_options(
+  -arch arm64
+  # Target the Apple-M microarchitecture for scheduling + the full ARMv8 ISA
+  # (CRC32/dotprod/etc.). ISA/scheduling only — fast-math stays OFF globally,
+  # so the deterministic conv_serial/conv_kahan/bnns reductions remain
+  # bit-identical (guarded by the determinism microtests in ctest).
+  -mcpu=apple-m1
+  -Wall
+  -Wextra
+  -Wno-unused-parameter
+  -Wno-missing-field-initializers
+)
+
+# ---------------------------------------------------------------------------
+# Module path
+# ---------------------------------------------------------------------------
+list(PREPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+# ---------------------------------------------------------------------------
+# External dependencies (order matters: protos before nucleus)
+# ---------------------------------------------------------------------------
+include(deps)    # FetchContent / find_package for htslib, abseil, protobuf, ssw
+include(protos)  # compile DeepVariant + nucleus + TF-example protos
+
+# ---------------------------------------------------------------------------
+# Core libraries (TF-free)
+# ---------------------------------------------------------------------------
+add_subdirectory(third_party/nucleus)
+add_subdirectory(deepvariant/realigner)
+add_subdirectory(deepvariant)          # upstream C++ libs (Phase 3)
+add_subdirectory(deepvariant/native)   # runtime binary (Phase 2+)
+
+# ---------------------------------------------------------------------------
+# Tests (Phase 1 gate: ctest -V must pass)
+# ---------------------------------------------------------------------------
+enable_testing()
+include(CTest)
+add_subdirectory(tests/native)  # thin wrappers around upstream C++ test code