First attempt at CRF

Author: kvg

BUILD_NOTES.md

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+# Build Notes for hidive
+
+## System Dependencies
+
+### sdsl-lite (vgteam fork)
+
+The `odgi-ffi` dependency requires sdsl-lite, which has known compilation issues with newer Clang versions. The vgteam fork (https://github.com/vgteam/sdsl-lite) includes fixes for these issues.
+
+**Installation:**
+
+```bash
+# Install the vgteam fork of sdsl-lite system-wide
+# This can be done via Homebrew or by building from source:
+git clone https://github.com/vgteam/sdsl-lite.git
+cd sdsl-lite
+mkdir build && cd build
+cmake ..
+make
+sudo make install
+```
+
+### OpenMP (libomp)
+
+OpenMP is required for sdsl-lite compilation.
+
+**Installation on macOS:**
+
+```bash
+brew install libomp
+```
+
+### Build Configuration
+
+When building, ensure the system-installed sdsl-lite and OpenMP are found by setting:
+
+```bash
+export CMAKE_PREFIX_PATH="/opt/homebrew/opt/libomp:$CMAKE_PREFIX_PATH"
+export CFLAGS="-I/opt/homebrew/opt/libomp/include"
+export CXXFLAGS="-I/opt/homebrew/opt/libomp/include"
+export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
+export CMAKE_ARGS="-Dsdsl-lite_ROOT=/usr/local/include -DOpenMP_C_INCLUDE_DIR=/opt/homebrew/opt/libomp/include -DOpenMP_CXX_INCLUDE_DIR=/opt/homebrew/opt/libomp/include -DOpenMP_C_LIB_NAMES=omp -DOpenMP_CXX_LIB_NAMES=omp -DOpenMP_omp_LIBRARY=/opt/homebrew/opt/libomp/lib/libomp.dylib -DCMAKE_C_FLAGS=-I/opt/homebrew/opt/libomp/include -DCMAKE_CXX_FLAGS=-I/opt/homebrew/opt/libomp/include"
+```
+
+Or add these to your shell profile for persistent configuration.
+
+**Note:** The vgteam fork of sdsl-lite fixes the `louds_tree.hpp` compilation issues that occur with newer Clang versions. Make sure you have this version installed system-wide rather than relying on the bundled version in odgi-ffi.
+
+## odgi-ffi Status
+
+The `odgi-ffi` crate is **disabled** due to build issues with Clang 17+ and the `atomic_queue` dependency. Instead, hidive uses a modular approach:
+
+### Design Decision
+
+**Users prepare ODGI graphs externally** using the command-line `odgi` tool. This approach:
+- Avoids build complexity and dependency issues
+- Allows users to use their preferred graph construction tools
+- Makes the workflow more modular and debuggable
+- Enables reuse of graphs across multiple analyses
+
+### Workflow
+
+1. **Build pangenome graph**: `hidive build-pangenome` outputs a GFA file
+2. **Convert to ODGI**: Users run `odgi build -g <gfa> -o <odgi>` (external tool)
+3. **Use ODGI graph**: `hidive train-crf` and `hidive infer-haplotypes` accept ODGI files
+
+See `PANGENOME_WORKFLOW.md` for detailed instructions.
+
+### Dependencies
+
+- **seqwish**: Included as Rust dependency, used by `build-pangenome`
+- **odgi**: Command-line tool, must be installed separately by users
+