diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
new file mode 100644
index 0000000..1bae4be
--- /dev/null
+++ b/.github/workflows/CI.yml
@@ -0,0 +1,120 @@
+# This file is autogenerated by maturin v1.4.0
+# To update, run
+#
+#    maturin generate-ci github
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64, x86]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          architecture: ${{ matrix.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  macos:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/')"
+    needs: [linux, windows, macos, sdist]
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing *
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..c6b68b1
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,73 @@
+/target
+target/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..30a6d37
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,34 @@
+[build-system]
+requires = ["maturin>=1.4,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "scatac_fragment_tools"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "pyBigWig",
+    "polars",
+    "pyarrow",
+    "numba",
+    "rich-argparse"
+]
+
+[tool.maturin]
+features = ["pyo3/extension-module"]
+module-name = "scatac_fragment_tools._rust_scatac_fragment_tools"
+
+[project.optional-dependencies]
+development = [
+    "mypy"
+]
+
+[project.scripts]
+scatac_fragment_tools = "scatac_fragment_tools.cli.main:main"
+
diff --git a/rust/Cargo.lock b/rust/Cargo.lock
new file mode 100644
index 0000000..01c13d9
--- /dev/null
+++ b/rust/Cargo.lock
@@ -0,0 +1,273 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+
+[[package]]
+name = "_rust_scatac_fragment_tools"
+version = "0.1.0"
+dependencies = [
+ "pyo3",
+]
+
+[[package]]
+name = "autocfg"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
+
+[[package]]
+name = "bitflags"
+version = "1.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
+
+[[package]]
+name = "cfg-if"
+version = "1.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+
+[[package]]
+name = "indoc"
+version = "1.0.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfa799dd5ed20a7e349f3b4639aa80d74549c81716d9ec4f994c9b5815598306"
+
+[[package]]
+name = "libc"
+version = "0.2.152"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "13e3bf6590cbc649f4d1a3eefc9d5d6eb746f5200ffb04e5e142700b8faa56e7"
+
+[[package]]
+name = "lock_api"
+version = "0.4.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45"
+dependencies = [
+ "autocfg",
+ "scopeguard",
+]
+
+[[package]]
+name = "memoffset"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5a634b1c61a95585bd15607c6ab0c4e5b226e695ff2800ba0cdccddf208c406c"
+dependencies = [
+ "autocfg",
+]
+
+[[package]]
+name = "once_cell"
+version = "1.19.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
+
+[[package]]
+name = "parking_lot"
+version = "0.12.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f"
+dependencies = [
+ "lock_api",
+ "parking_lot_core",
+]
+
+[[package]]
+name = "parking_lot_core"
+version = "0.9.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "redox_syscall",
+ "smallvec",
+ "windows-targets",
+]
+
+[[package]]
+name = "proc-macro2"
+version = "1.0.76"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "95fc56cda0b5c3325f5fbbd7ff9fda9e02bb00bb3dac51252d2f1bfa1cb8cc8c"
+dependencies = [
+ "unicode-ident",
+]
+
+[[package]]
+name = "pyo3"
+version = "0.19.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e681a6cfdc4adcc93b4d3cf993749a4552018ee0a9b65fc0ccfad74352c72a38"
+dependencies = [
+ "cfg-if",
+ "indoc",
+ "libc",
+ "memoffset",
+ "parking_lot",
+ "pyo3-build-config",
+ "pyo3-ffi",
+ "pyo3-macros",
+ "unindent",
+]
+
+[[package]]
+name = "pyo3-build-config"
+version = "0.19.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "076c73d0bc438f7a4ef6fdd0c3bb4732149136abd952b110ac93e4edb13a6ba5"
+dependencies = [
+ "once_cell",
+ "target-lexicon",
+]
+
+[[package]]
+name = "pyo3-ffi"
+version = "0.19.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e53cee42e77ebe256066ba8aa77eff722b3bb91f3419177cf4cd0f304d3284d9"
+dependencies = [
+ "libc",
+ "pyo3-build-config",
+]
+
+[[package]]
+name = "pyo3-macros"
+version = "0.19.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dfeb4c99597e136528c6dd7d5e3de5434d1ceaf487436a3f03b2d56b6fc9efd1"
+dependencies = [
+ "proc-macro2",
+ "pyo3-macros-backend",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "pyo3-macros-backend"
+version = "0.19.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "947dc12175c254889edc0c02e399476c2f652b4b9ebd123aa655c224de259536"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "quote"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef"
+dependencies = [
+ "proc-macro2",
+]
+
+[[package]]
+name = "redox_syscall"
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+checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa"
+dependencies = [
+ "bitflags",
+]
+
+[[package]]
+name = "scopeguard"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
+
+[[package]]
+name = "smallvec"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4dccd0940a2dcdf68d092b8cbab7dc0ad8fa938bf95787e1b916b0e3d0e8e970"
+
+[[package]]
+name = "syn"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
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+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "target-lexicon"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "69758bda2e78f098e4ccb393021a0963bb3442eac05f135c30f61b7370bbafae"
+
+[[package]]
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+
+[[package]]
+name = "unindent"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c"
+
+[[package]]
+name = "windows-targets"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
+dependencies = [
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
+
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
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+
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.48.5"
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+checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
+
+[[package]]
+name = "windows_i686_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
diff --git a/rust/Cargo.toml b/rust/Cargo.toml
new file mode 100644
index 0000000..7b51c4d
--- /dev/null
+++ b/rust/Cargo.toml
@@ -0,0 +1,12 @@
+[package]
+name = "_rust_scatac_fragment_tools"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "_rust_scatac_fragment_tools"
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = "0.19.0"
diff --git a/rust/src/lib.rs b/rust/src/lib.rs
new file mode 100644
index 0000000..29d82f8
--- /dev/null
+++ b/rust/src/lib.rs
@@ -0,0 +1,8 @@
+use pyo3::prelude::*;
+
+#[pymodule]
+fn _rust_scatac_fragment_tools(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
+    // set version dunder
+    m.add("__version__", env!("CARGO_PKG_VERSION"))?;
+    Ok(())
+}
\ No newline at end of file
diff --git a/src/scatac_fragment_tools/__init__.py b/src/scatac_fragment_tools/__init__.py
new file mode 100644
index 0000000..fc01bf1
--- /dev/null
+++ b/src/scatac_fragment_tools/__init__.py
@@ -0,0 +1,2 @@
+from scatac_fragment_tools import _rust_scatac_fragment_tools
+__version__ = _rust_scatac_fragment_tools.__version__
\ No newline at end of file
diff --git a/src/scatac_fragment_tools/cli/__init__.py b/src/scatac_fragment_tools/cli/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/scatac_fragment_tools/library/__init__.py b/src/scatac_fragment_tools/library/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/scatac_fragment_tools/library/bigwig/__init__.py b/src/scatac_fragment_tools/library/bigwig/__init__.py
new file mode 100644
index 0000000..e69de29