diff --git a/.cargo/config-portable.toml b/.cargo/config-portable.toml
new file mode 100644
index 0000000..8f60b0a
--- /dev/null
+++ b/.cargo/config-portable.toml
@@ -0,0 +1,14 @@
+# inspired by https://curiouscoding.nl/posts/release-flow/#avx2
+
+# .cargo/config-portable.toml
+[target.x86_64-unknown-linux-gnu]
+rustflags = ["-C", "target-cpu=x86-64-v3", "-C", "target-feature=+avx2"]
+
+[target.aarch64-unknown-linux-gnu]
+rustflags = ["-C", "target-cpu=neoverse-n1"]
+
+[target.aarch64-apple-darwin]
+rustflags = ["-C", "target-cpu=apple-a14"]
+
+[target.x86_64-apple-darwin]
+rustflags = ["-C", "target-cpu=x86-64-v3", "-C", "target-feature=+avx2"]
diff --git a/.cargo/config.toml b/.cargo/config.toml
new file mode 100644
index 0000000..cb7e64c
--- /dev/null
+++ b/.cargo/config.toml
@@ -0,0 +1,4 @@
+# taken from https://curiouscoding.nl/posts/release-flow/#avx2
+[build]
+# By default, we want maximum performance rather than portability.
+rustflags = ["-C", "target-cpu=native"]
diff --git a/.github/build-setup.yml b/.github/build-setup.yml
new file mode 100644
index 0000000..e916387
--- /dev/null
+++ b/.github/build-setup.yml
@@ -0,0 +1,19 @@
+- name: Use portable Cargo config for CI builds
+  shell: bash
+  run: |
+    set -euo pipefail
+    cp .cargo/config-portable.toml .cargo/config.toml
+
+- name: Force AVX2 for x86_64 (via RUSTFLAGS)
+  if: contains(join(matrix.targets, ','), 'x86_64-')
+  shell: bash
+  run: |
+    set -euo pipefail
+    echo 'RUSTFLAGS=-C target-cpu=x86-64-v3 -C target-feature=+avx2' >> "$GITHUB_ENV"
+
+- name: Show effective x86_64 rustflags (proof)
+  if: contains(join(matrix.targets, ','), 'x86_64-')
+  shell: bash
+  run: |
+    set -euo pipefail
+    echo "RUSTFLAGS=${RUSTFLAGS-}"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f6b098f..6dc7e9d 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,4 +1,4 @@
-# This file was autogenerated by dist: https://opensource.axo.dev/cargo-dist/
+# This file was autogenerated by dist: https://axodotdev.github.io/cargo-dist
 #
 # Copyright 2022-2024, axodotdev
 # SPDX-License-Identifier: MIT or Apache-2.0
@@ -47,7 +47,7 @@ on:
 jobs:
   # Run 'dist plan' (or host) to determine what tasks we need to do
   plan:
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     outputs:
       val: ${{ steps.plan.outputs.manifest }}
       tag: ${{ !github.event.pull_request && github.ref_name || '' }}
@@ -56,16 +56,17 @@ jobs:
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
       - name: Install dist
         # we specify bash to get pipefail; it guards against the `curl` command
         # failing. otherwise `sh` won't catch that `curl` returned non-0
         shell: bash
-        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.24.1/cargo-dist-installer.sh | sh"
+        run: "curl --proto '=https' --tlsv1.2 -LsSf https://github.com/axodotdev/cargo-dist/releases/download/v0.31.0/cargo-dist-installer.sh | sh"
       - name: Cache dist
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/dist
@@ -81,7 +82,7 @@ jobs:
           cat plan-dist-manifest.json
           echo "manifest=$(jq -c "." plan-dist-manifest.json)" >> "$GITHUB_OUTPUT"
       - name: "Upload dist-manifest.json"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-plan-dist-manifest
           path: plan-dist-manifest.json
@@ -107,6 +108,7 @@ jobs:
       # - N "local" tasks that build each platform's binaries and platform-specific installers
       matrix: ${{ fromJson(needs.plan.outputs.val).ci.github.artifacts_matrix }}
     runs-on: ${{ matrix.runner }}
+    container: ${{ matrix.container && matrix.container.image || null }}
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       BUILD_MANIFEST_NAME: target/distrib/${{ join(matrix.targets, '-') }}-dist-manifest.json
@@ -114,14 +116,39 @@ jobs:
       - name: enable windows longpaths
         run: |
           git config --global core.longpaths true
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
+      - name: Install Rust non-interactively if not already installed
+        if: ${{ matrix.container }}
+        run: |
+          if ! command -v cargo > /dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+            echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          fi
+      - name: "Use portable Cargo config for CI builds"
+        run: |
+          set -euo pipefail
+          cp .cargo/config-portable.toml .cargo/config.toml
+        shell: "bash"
+      - name: "Force AVX2 for x86_64 (via RUSTFLAGS)"
+        if: "contains(join(matrix.targets, ','), 'x86_64-')"
+        run: |
+          set -euo pipefail
+          echo 'RUSTFLAGS=-C target-cpu=x86-64-v3 -C target-feature=+avx2' >> "$GITHUB_ENV"
+        shell: "bash"
+      - name: "Show effective x86_64 rustflags (proof)"
+        if: "contains(join(matrix.targets, ','), 'x86_64-')"
+        run: |
+          set -euo pipefail
+          echo "RUSTFLAGS=${RUSTFLAGS-}"
+        shell: "bash"
       - name: Install dist
-        run: ${{ matrix.install_dist }}
+        run: ${{ matrix.install_dist.run }}
       # Get the dist-manifest
       - name: Fetch local artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
@@ -143,12 +170,12 @@ jobs:
         run: |
           # Parse out what we just built and upload it to scratch storage
           echo "paths<<EOF" >> "$GITHUB_OUTPUT"
-          jq --raw-output ".upload_files[]" dist-manifest.json >> "$GITHUB_OUTPUT"
+          dist print-upload-files-from-manifest --manifest dist-manifest.json >> "$GITHUB_OUTPUT"
           echo "EOF" >> "$GITHUB_OUTPUT"
 
           cp dist-manifest.json "$BUILD_MANIFEST_NAME"
       - name: "Upload artifacts"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-build-local-${{ join(matrix.targets, '_') }}
           path: |
@@ -160,23 +187,24 @@ jobs:
     needs:
       - plan
       - build-local-artifacts
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       BUILD_MANIFEST_NAME: target/distrib/global-dist-manifest.json
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
       - name: Install cached dist
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
       - run: chmod +x ~/.cargo/bin/dist
       # Get all the local artifacts for the global tasks to use (for e.g. checksums)
       - name: Fetch local artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
@@ -194,7 +222,7 @@ jobs:
 
           cp dist-manifest.json "$BUILD_MANIFEST_NAME"
       - name: "Upload artifacts"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: artifacts-build-global
           path: |
@@ -206,26 +234,27 @@ jobs:
       - plan
       - build-local-artifacts
       - build-global-artifacts
-    # Only run if we're "publishing", and only if local and global didn't fail (skipped is fine)
-    if: ${{ always() && needs.plan.outputs.publishing == 'true' && (needs.build-global-artifacts.result == 'skipped' || needs.build-global-artifacts.result == 'success') && (needs.build-local-artifacts.result == 'skipped' || needs.build-local-artifacts.result == 'success') }}
+    # Only run if we're "publishing", and only if plan, local and global didn't fail (skipped is fine)
+    if: ${{ always() && needs.plan.result == 'success' && needs.plan.outputs.publishing == 'true' && (needs.build-global-artifacts.result == 'skipped' || needs.build-global-artifacts.result == 'success') && (needs.build-local-artifacts.result == 'skipped' || needs.build-local-artifacts.result == 'success') }}
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     outputs:
       val: ${{ steps.host.outputs.manifest }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
       - name: Install cached dist
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           name: cargo-dist-cache
           path: ~/.cargo/bin/
       - run: chmod +x ~/.cargo/bin/dist
       # Fetch artifacts from scratch-storage
       - name: Fetch artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: target/distrib/
@@ -238,14 +267,14 @@ jobs:
           cat dist-manifest.json
           echo "manifest=$(jq -c "." dist-manifest.json)" >> "$GITHUB_OUTPUT"
       - name: "Upload dist-manifest.json"
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           # Overwrite the previous copy
           name: artifacts-dist-manifest
           path: dist-manifest.json
       # Create a GitHub Release while uploading all files to it
       - name: "Download GitHub Artifacts"
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v7
         with:
           pattern: artifacts-*
           path: artifacts
@@ -274,10 +303,11 @@ jobs:
     # still allowing individual publish jobs to skip themselves (for prereleases).
     # "host" however must run to completion, no skipping allowed!
     if: ${{ always() && needs.host.result == 'success' }}
-    runs-on: "ubuntu-20.04"
+    runs-on: "ubuntu-22.04"
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
+          persist-credentials: false
           submodules: recursive
diff --git a/.github/workflows/sanitize-cargo.yml b/.github/workflows/sanitize-cargo.yml
new file mode 100644
index 0000000..b9722db
--- /dev/null
+++ b/.github/workflows/sanitize-cargo.yml
@@ -0,0 +1,38 @@
+name: Sanitize Cargo
+on: 
+  push:
+    branches:
+      - main
+
+permissions:
+  "contents": "write"
+
+jobs:
+  sanitize_cargo_file:
+    if: "contains(github.event.head_commit.message, '[do_tag]')"
+    runs-on: ubuntu-latest
+    # This is optional; it exposes the plan to your job as an environment variable
+    #env:
+    #  PLAN: ${{ inputs.plan }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.PAT_TOK }}
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Install cargo-sanitize
+        run: |
+          cargo install cargo-sanitize
+      - name: Sanitize Cargo.toml file
+        run: |
+          cp Cargo.toml Cargo.toml.cs_orig
+          cargo-sanitize -i Cargo.toml.cs_orig -o Cargo.toml
+      - name: Tag and push new commit
+        run: |
+          export VERSION_TAG=`cargo read-manifest | jq ".version" | tr -d '"'`
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add Cargo.toml.cs_orig
+          git add Cargo.toml
+          git commit -m "create sanitized release"
+          git tag --force -a v${VERSION_TAG} -m "version ${VERSION_TAG}"
+          git push --force origin v${VERSION_TAG}
diff --git a/.gitignore b/.gitignore
index 088ba6b..1c0a2c9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,14 @@ Cargo.lock
 
 # These are backup files generated by rustfmt
 **/*.rs.bk
+
+# Local cargo config (contains dev-only [patch] overrides)
+# .cargo/config.toml
+radtk/
+gencode_v49/
+gencode_v49_new/
+piscem-cpp/
+sshash/
+sample_quant_new/
+sample_quant/
+
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 34a485a..0000000
--- a/.gitmodules
+++ /dev/null
@@ -1,8 +0,0 @@
-[submodule "cuttlefish"]
-	path = cuttlefish
-	url = https://github.com/COMBINE-lab/cuttlefish.git
-	branch = develop
-[submodule "piscem-cpp"]
-	path = piscem-cpp
-	url = https://github.com/COMBINE-lab/piscem-cpp.git
-	branch = dev
diff --git a/Cargo.lock b/Cargo.lock
index 8284e23..28aa0dc 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -1,27 +1,70 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
+version = 4
 
 [[package]]
 name = "adler2"
-version = "2.0.0"
+version = "2.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "320119579fcad9c21884f5c4861d16174d0e06250625266f50fe6898340abefa"
+
+[[package]]
+name = "ahash"
+version = "0.8.12"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627"
+checksum = "5a15f179cd60c4584b8a8c596927aadc462e27f2ca70c04e0071964a73ba7a75"
+dependencies = [
+ "cfg-if",
+ "getrandom 0.3.4",
+ "once_cell",
+ "version_check",
+ "zerocopy",
+]
 
 [[package]]
 name = "aho-corasick"
-version = "1.1.3"
+version = "1.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916"
+checksum = "ddd31a130427c27518df266943a5308ed92d4b226cc639f5a8f1002816174301"
 dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "aliasable"
+version = "0.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "250f629c0161ad8107cf89319e990051fae62832fd343083bea452d93e2205fd"
+
+[[package]]
+name = "allocator-api2"
+version = "0.2.21"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923"
+
+[[package]]
+name = "ambassador"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8184c5d23ba3829fb1e93388d776c3469cd9f4162af65250490b4f22d3ecf614"
+dependencies = [
+ "itertools 0.10.5",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.117",
+]
+
+[[package]]
+name = "anes"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299"
+
 [[package]]
 name = "anstream"
-version = "0.6.18"
+version = "0.6.21"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8acc5369981196006228e28809f761875c0327210a891e941f4c683b3a99529b"
+checksum = "43d5b281e737544384e969a5ccad3f1cdd24b48086a0fc1b2a5262a26b8f4f4a"
 dependencies = [
  "anstyle",
  "anstyle-parse",
@@ -34,49 +77,95 @@ dependencies = [
 
 [[package]]
 name = "anstyle"
-version = "1.0.10"
+version = "1.0.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "55cc3b69f167a1ef2e161439aa98aed94e6028e5f9a59be9a6ffb47aef1651f9"
+checksum = "5192cca8006f1fd4f7237516f40fa183bb07f8fbdfedaa0036de5ea9b0b45e78"
 
 [[package]]
 name = "anstyle-parse"
-version = "0.2.6"
+version = "0.2.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3b2d16507662817a6a20a9ea92df6652ee4f94f914589377d69f3b21bc5798a9"
+checksum = "4e7644824f0aa2c7b9384579234ef10eb7efb6a0deb83f9630a49594dd9c15c2"
 dependencies = [
  "utf8parse",
 ]
 
 [[package]]
 name = "anstyle-query"
-version = "1.1.2"
+version = "1.1.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "79947af37f4177cfead1110013d678905c37501914fba0efea834c3fe9a8d60c"
+checksum = "40c48f72fd53cd289104fc64099abca73db4166ad86ea0b4341abe65af83dadc"
 dependencies = [
- "windows-sys 0.59.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
 name = "anstyle-wincon"
-version = "3.0.6"
+version = "3.0.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2109dbce0e72be3ec00bed26e6a7479ca384ad226efdd66db8fa2e3a38c83125"
+checksum = "291e6a250ff86cd4a820112fb8898808a366d8f9f58ce16d1f538353ad55747d"
 dependencies = [
  "anstyle",
- "windows-sys 0.59.0",
+ "once_cell_polyfill",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
 name = "anyhow"
-version = "1.0.93"
+version = "1.0.102"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7f202df86484c868dbad7eaa557ef785d5c66295e41b460ef922eca0723b842c"
+
+[[package]]
+name = "arbitrary-chunks"
+version = "0.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2ad8689a486416c401ea15715a4694de30054248ec627edbf31f49cb64ee4086"
+
+[[package]]
+name = "arrayvec"
+version = "0.7.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7c02d123df017efcdfbd739ef81735b36c5ba83ec3c59c80a9d7ecc718f92e50"
+
+[[package]]
+name = "autocfg"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c08606f8c3cbf4ce6ec8e28fb0014a2c086708fe954eaa885384a6165172e7e8"
+
+[[package]]
+name = "bgzip"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b64fd8980fb64af5951bc05de7772b598150a6f7eac42ec17f73e8489915f99b"
+dependencies = [
+ "flate2",
+ "log",
+ "rayon",
+ "thiserror 1.0.69",
+]
+
+[[package]]
+name = "binout"
+version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4c95c10ba0b00a02636238b814946408b1322d5ac4760326e6fb8ec956d85775"
+checksum = "222fb4925a15bea6a68075021910e03d6aa2d04951d71ff1d956190a551d738f"
 
 [[package]]
 name = "bitflags"
-version = "2.6.0"
+version = "2.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
+checksum = "843867be96c8daad0d758b57df9392b6d8d271134fce549de6ce169ff98a92af"
+
+[[package]]
+name = "bitm"
+version = "0.5.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "31468ea4a856000d83cb61960dfdc2980ecd96b15b61321c8c76cc96aea6e688"
+dependencies = [
+ "dyn_size_of",
+]
 
 [[package]]
 name = "block-buffer"
@@ -87,20 +176,79 @@ dependencies = [
  "generic-array",
 ]
 
+[[package]]
+name = "block-pseudorand"
+version = "0.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2097358495d244a0643746f4d13eedba4608137008cf9dec54e53a3b700115a6"
+dependencies = [
+ "chiapos-chacha8",
+ "nanorand",
+]
+
+[[package]]
+name = "bon"
+version = "3.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2d13a61f2963b88eef9c1be03df65d42f6996dfeac1054870d950fcf66686f83"
+dependencies = [
+ "bon-macros",
+ "rustversion",
+]
+
+[[package]]
+name = "bon-macros"
+version = "3.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d314cc62af2b6b0c65780555abb4d02a03dd3b799cd42419044f0c38d99738c0"
+dependencies = [
+ "darling",
+ "ident_case",
+ "prettyplease",
+ "proc-macro2",
+ "quote",
+ "rustversion",
+ "syn 2.0.117",
+]
+
 [[package]]
 name = "buffer-redux"
-version = "1.0.2"
+version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
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+dependencies = [
+ "zstd-sys",
+]
+
+[[package]]
+name = "zstd-sys"
+version = "2.0.16+zstd.1.5.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "91e19ebc2adc8f83e43039e79776e3fda8ca919132d68a1fed6a5faca2683748"
+dependencies = [
+ "cc",
+ "pkg-config",
+]
+
+[[patch.unused]]
+name = "libradicl"
+version = "0.11.0"
+source = "git+https://github.com/COMBINE-lab/libradicl.git?branch=develop#5a2f8e8aa6973debaad40748d2b9f19ac1a4b6ce"
diff --git a/Cargo.toml b/Cargo.toml
index 0f99ee9..5a39d0f 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,29 +1,39 @@
+[workspace]
+
 [package]
 name = "piscem"
-version = "0.11.0"
-edition = "2021"
+version = "0.16.2"
+edition = "2024"
 build = "build.rs"
+license = "BSD-3-Clause"
+description = "Fast, space-efficient k-mer-based read mapper for bulk RNA-seq, scRNA-seq, and scATAC-seq"
 repository = "https://github.com/COMBINE-lab/piscem"
+homepage = "https://github.com/COMBINE-lab/piscem"
+readme = "README.md"
+keywords = ["bioinformatics", "genomics", "rna-seq", "mapping", "kmer"]
+categories = ["command-line-utilities", "science"]
 
 [build-dependencies]
-cmake = "0.1.52"
-
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+toml = "0.8"
 
 [dependencies]
-num_cpus = "1.16.0"
-anyhow = "1.0.93"
-clap = { version = "4.5.21", features = [
+piscem-rs = "0.1.0"
+cf1-rs = "0.3.1"
+num_cpus = "1.17.0"
+anyhow = "1.0.100"
+clap = { version = "4.5.56", features = [
   "cargo",
   "derive",
   "env",
   "wrap_help",
 ] }
-tracing = "0.1.40"
-tracing-subscriber = { version = "0.3.18", default-features = true, features = [
+tracing = "0.1.44"
+tracing-subscriber = { version = "0.3.22", default-features = true, features = [
   "env-filter",
 ] }
-prepare_fasta = "0.1.0"
+prepare_fasta = { version = "0.2.0" }
+serde_json = "1.0.149"
+mimalloc = "0.1"
 
 [profile.release]
 lto = "thin"
@@ -32,65 +42,3 @@ opt-level = 3
 # generated by 'cargo dist init'
 [profile.dist]
 inherits = "release"
-
-# Config for 'dist'
-[workspace.metadata.dist]
-# The preferred dist version to use in CI (Cargo.toml SemVer syntax)
-cargo-dist-version = "0.24.1"
-# The installers to generate for each app
-installers = ["shell"]
-# Target platforms to build apps for (Rust target-triple syntax)
-targets = [
-  "aarch64-apple-darwin",
-  "x86_64-apple-darwin",
-  "x86_64-unknown-linux-gnu",
-]
-# The archive format to use for non-windows builds (defaults .tar.xz)
-unix-archive = ".tar.gz"
-# CI backends to support
-ci = "github"
-# Which actions to run on pull requests
-pr-run-mode = "plan"
-# Whether to install an updater program
-install-updater = true
-# Generate and dist a source tarball
-source-tarball = false
-# Path that installers should place binaries in
-install-path = "CARGO_HOME"
-## since this is cross-language and 
-## we are not including C++ debug 
-## symbols, this currently doesn't work 
-## and would be of limited utility anyway.
-# debug = true
-# split-debuginfo = "packed"
-
-[[workspace.metadata.dist.extra-artifacts]]
-artifacts = ["source.tar.gz", "source.tar.gz.sha256"]
-build = [
-  "bash",
-  "scripts/git-archive-all.sh",
-  "--format",
-  "tar.gz",
-  "--prefix",
-  "piscem/",
-  "source.tar.gz",
-]
-
-[workspace.metadata.dist.github-custom-runners]
-aarch64-apple-darwin = "macos-14"
-
-[workspace.metadata.dist.dependencies.homebrew]
-autoconf = { version = "2.72", stage = [
-  "build",
-  "run",
-], targets = [
-  "aarch64-apple-darwin",
-] }
-automake = { version = "1.16.5", stage = [
-  "build",
-  "run",
-], targets = [
-  "aarch64-apple-darwin",
-] }
-coreutils = { stage = ["build"] }
-gnu-tar = { stage = ["build"] }
diff --git a/README.md b/README.md
index 7541021..f66fa1a 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,11 @@
 # piscem
 
-`piscem` is a rust wrapper for a next-generation index + mapper tool (still currently written in C++17).
+`piscem` is a rust wrapper for a next-generation index + mapper tool consisting of a compacted de Bruijn graph constructor (with tiling information), and a very efficient index and read mapper.
 
 Notes
 =====
 
- - If you are primarily interested in simply *using* `piscem`, you can obtain pre-compiled binaries from the GitHub [releases](https://github.com/COMBINE-lab/piscem/releases/tag/v0.10.3) page
+ - If you are primarily interested in simply *using* `piscem`, you can obtain pre-compiled binaries from the GitHub [releases](https://github.com/COMBINE-lab/piscem/releases/tag/v0.16.2) page
 for linux x86-64, OSX x86-64, and OSX ARM. Likewise, `piscem` can be installed using [bioconda](https://bioconda.github.io/recipes/piscem/README.html).  The instructions below are 
 primarily for those who need to *build* `piscem` from source.
 
@@ -22,51 +22,18 @@ before running `piscem`.
 Building
 ========
 
-This repository currently pulls in (as submodules) `piscem-cpp` and `cuttlefish`, and then uses cargo + the cmake crate to build the C++ code.  It then calls out to the main C++ function from `main.rs`.  The idea is that in this framework, code can slowly be migrated from C++ -> Rust in a piecemeal fashion, while the overall top-level repo remains a "rust build".  Importantly, `piscem` unifies and simplifies the other tools, making them runnable via a single executable and providing an improved command line interface.
-
 To build `piscem`, first check out this repository **with recursive dependencies**:
 
 ```
-git clone --recursive https://github.com/COMBINE-lab/piscem.git
-```
-
-if you have accidentally checked out the repo without the `--recursive` flag, you can change into the top-level directory and run:
-
-```
-git submodule update --init --recursive
+git clone https://github.com/COMBINE-lab/piscem.git
 ```
 
 Once you have checked out the repository, you can build `piscem` with 
 
 ```
-cargo build --release
+RUSTFLAGS="-C target-cpu=native" cargo build --release
 ```
 
-It is worth noting that the build process respects the `CC` and `CXX` environment flags, so if you wish to use a specific C++ compiler, you can run:
-
-```
-CC=<path_to_c_compiler> CXX=<path_to_cxx_compiler> cargo build --release
-```
-
-Compling this code requires a C++17 capable compiler, so if your default compiler does not have these capabilities, please be sure to pass the appropriate 
-flags along to `cargo build` with a sufficiently capable compiler.
-
-Other details about building
-----------------------------
-
-The build process requries access to static libraries for both `zlib` and `libbz2`. If these are not in your standard path, you can provide them via the `RUSTFLAGS` option as:
-
-```
-RUSTFLAGS='-L <path_to_directory_with_libraries>' cargo build --release
-```
-
-Finally, on some systems, you may get a strange linking error related to relocatable symbols. In that case, you can pass the `NOPIE` option to the build process as follows:
-
-```
-NOPIE=TRUE cargo build --release
-```
-
-Note that the `CC`, `CXX`, `RUSTFLAGS` and `NOPIE` environment variables are all "stackable" and you can provide any subset of them that you need during build.
 
 Usage
 =====
@@ -96,9 +63,6 @@ Info for different sub-commands
 build
 -----
 
-> **Note**
-> Since the build process makes use of [KMC3](https://github.com/refresh-bio/KMC) for a k-mer enumeration step, which, in turn, makes use of intermediate files to keep memory usage low, **you will likely need to increase the default number of file handles that can be open at once**.  Before running the `build` command, you can do this by running `ulimit -n 2048` in the terminal where you execute the `build` command.  You can also put this command in any script that you will use to run `piscem build`, or add it to your shell initalization scripts / profiles so that it is the default for new shells that you start
-
 The build subcommand indexes one or more reference sequences, building a piscem index over them. The usage for the command is as so:
 
 ```
diff --git a/build.rs b/build.rs
index 28e69cf..c10c877 100644
--- a/build.rs
+++ b/build.rs
@@ -1,152 +1,15 @@
-use cmake::Config;
-use std::env;
-
 fn main() {
-    let custom_cc = env::var("CC");
-    let custom_cxx = env::var("CXX");
-    let conda_build = env::var("CONDA_BUILD");
-    let nopie_build = env::var("NOPIE");
-    let nobmi2_var = env::var("NO_BMI2");
-
-    let is_conda_build = match conda_build {
-        Ok(val) => match val.to_uppercase().as_str() {
-            "TRUE" | "1" | "YES" => true,
-            "FALSE" | "0" | "NO" => false,
-            _ => true,
-        },
-        Err(_e) => false,
-    };
-
-    println!("cargo:rerun-if-changed=cuttlefish/CMakeLists.txt");
-    println!("cargo:rerun-if-changed=piscem-cpp/CMakeLists.txt");
-
-    let mut cfg_piscem_cpp = Box::new(Config::new("piscem-cpp"));
-    let mut cfg_cf = Box::new(Config::new("cuttlefish"));
-
-    (*cfg_cf).define("INSTANCE_COUNT", "32");
-    if let Ok(cc_var) = custom_cc {
-        (*cfg_piscem_cpp).define("CMAKE_C_COMPILER", cc_var.clone());
-        (*cfg_cf).define("CMAKE_C_COMPILER", cc_var);
-    }
-
-    if let Ok(cxx_var) = custom_cxx {
-        (*cfg_piscem_cpp).define("CMAKE_CXX_COMPILER", cxx_var.clone());
-        (*cfg_cf).define("CMAKE_CXX_COMPILER", cxx_var);
-    }
-
-    if is_conda_build {
-        (*cfg_cf).define("CONDA_BUILD", "TRUE");
-        (*cfg_cf).define("CMAKE_OSX_DEPLOYMENT_TARGET", "10.15");
-        (*cfg_cf).define("MACOSX_SDK_VERSION", "10.15");
-    }
-
-    if let Ok(nobmi2) = nobmi2_var {
-        match nobmi2.as_str() {
-            "1" | "TRUE" | "true" | "True" => {
-                (*cfg_piscem_cpp).define("NO_BMI2", "TRUE");
-            }
-            _ => {}
-        }
-    }
-
-    (*cfg_piscem_cpp).always_configure(false);
-    (*cfg_cf).always_configure(false);
-
-    let dst_piscem_cpp = (*cfg_piscem_cpp).build();
-    let dst_cf = (*cfg_cf).build();
-
-    if let Ok(nopie) = nopie_build {
-        match nopie.as_str() {
-            "1" | "TRUE" | "true" | "True" => {
-                println!("cargo:rustc-link-arg=-no-pie");
-            }
-            _ => {}
-        }
-    }
-
-    println!(
-        "cargo:rustc-link-search=native={}",
-        dst_cf.join("lib").display()
-    );
-    println!(
-        "cargo:rustc-link-search=native={}",
-        dst_piscem_cpp.join("lib").display()
-    );
-
-    // For some reason, if we are using
-    // *some* linux distros (and on conda) and are
-    // building for the linux target;
-    // things get put in the lib64 directory
-    // rather than lib... So, we add that here
-    println!(
-        "cargo:rustc-link-search=native={}",
-        dst_cf.join("lib64").display()
-    );
-    println!(
-        "cargo:rustc-link-search=native={}",
-        dst_piscem_cpp.join("lib64").display()
-    );
-    let profile = std::env::var("PROFILE").unwrap();
-    match profile.as_str() {
-        "debug" => {
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Debug").join("lib64").display()
-            );
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Debug").join("lib").display()
-            );
-        }
-        "release" => {
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Release").join("lib64").display()
-            );
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Release").join("lib").display()
-            );
-        }
-        _ => (),
-    }
-
-    let profile = std::env::var("PROFILE").unwrap();
-    match profile.as_str() {
-        "debug" => {
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Debug").join("lib64").display()
-            );
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Debug").join("lib").display()
-            );
-        }
-        "release" => {
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Release").join("lib64").display()
-            );
-            println!(
-                "cargo:rustc-link-search=native={}",
-                dst_piscem_cpp.join("Release").join("lib").display()
-            );
-        }
-        _ => (),
-    }
-
-    println!("cargo:rustc-link-lib=static=kmc_core");
-    //println!("cargo:rustc-link-lib=static=pesc_static");
-    //println!("cargo:rustc-link-lib=static=build_static");
-    println!("cargo:rustc-link-lib=static=sshash_static");
-    println!("cargo:rustc-link-lib=static=zcf");
-    println!("cargo:rustc-link-lib=static=bz2");
-    println!("cargo:rustc-link-lib=static=radicl");
-
-    #[cfg(target_os = "linux")]
-    println!("cargo:rustc-link-lib=dylib=stdc++");
-
-    #[cfg(target_os = "macos")]
-    println!("cargo:rustc-link-lib=dylib=c++");
+    // Extract cf1-rs version from Cargo.lock so we can embed it in the version JSON.
+    let lock_contents =
+        std::fs::read_to_string("Cargo.lock").expect("Failed to read Cargo.lock");
+    let lock: toml::Value = lock_contents.parse().expect("Failed to parse Cargo.lock");
+    let version = lock["package"]
+        .as_array()
+        .unwrap()
+        .iter()
+        .find(|p| p["name"].as_str() == Some("cf1-rs"))
+        .and_then(|p| p["version"].as_str())
+        .unwrap_or("unknown");
+    println!("cargo:rustc-env=CF1_RS_VERSION={version}");
+    println!("cargo:rerun-if-changed=Cargo.lock");
 }
diff --git a/clean_build.sh b/clean_build.sh
index 8583f96..d5de79e 100755
--- a/clean_build.sh
+++ b/clean_build.sh
@@ -2,9 +2,5 @@
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 
-echo "cleaning external dependency directories of cuttlefish and piscem-cpp."
-rm -fr ${SCRIPT_DIR}/cuttlefish/external/*
-rm -fr ${SCRIPT_DIR}/piscem-cpp/external/zlib-cloudflare
-
 echo "invoking cargo clean"
 cargo clean --target-dir ${SCRIPT_DIR}/target
diff --git a/cuttlefish b/cuttlefish
deleted file mode 160000
index e24249c..0000000
--- a/cuttlefish
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e24249cfd4566ad74ec02870af5c0a7069f738e2
diff --git a/dist-workspace.toml b/dist-workspace.toml
new file mode 100644
index 0000000..05f0fe0
--- /dev/null
+++ b/dist-workspace.toml
@@ -0,0 +1,41 @@
+[workspace]
+members = ["cargo:."]
+
+# Config for 'dist'
+[dist]
+github-build-setup = "../build-setup.yml"
+# The preferred dist version to use in CI (Cargo.toml SemVer syntax)
+cargo-dist-version = "0.31.0"
+# The installers to generate for each app
+installers = ["shell"]
+# Target platforms to build apps for (Rust target-triple syntax)
+targets = ["aarch64-apple-darwin", "aarch64-unknown-linux-gnu", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
+# CI backends to support
+ci = "github"
+# Whether to install an updater program
+install-updater = true
+# Path that installers should place binaries in
+install-path = "CARGO_HOME"
+## since this is cross-language and 
+## we are not including C++ debug 
+## symbols, this currently doesn't work 
+## and would be of limited utility anyway.
+# debug = true
+# split-debuginfo = "packed"
+
+[[dist.extra-artifacts]]
+artifacts = ["source-full.tar.gz", "source-full.tar.gz.sha256"]
+build = ["bash", "-c", """
+  set -e
+  git archive --format=tar.gz --prefix=piscem/ HEAD > source-full.tar.gz
+  shasum -a 256 source-full.tar.gz > source-full.tar.gz.sha256
+  """]
+
+[dist.github-custom-runners]
+aarch64-apple-darwin = "macos-14"
+x86_64-apple-darwin = "macos-15-intel"
+x86_64-unknown-linux-gnu = "ubuntu-22.04"
+
+[dist.dependencies.homebrew]
+coreutils = { stage = ["build"] }
+gnu-tar = { stage = ["build"] }
diff --git a/piscem-cpp b/piscem-cpp
deleted file mode 160000
index 7be79ee..0000000
--- a/piscem-cpp
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 7be79eee2295ee039c13523bc746114b7d5e1234
diff --git a/release.sh b/release.sh
new file mode 100755
index 0000000..7a3602a
--- /dev/null
+++ b/release.sh
@@ -0,0 +1,48 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ $# -ne 1 ]; then
+    echo "Usage: $0 <version>  (e.g. $0 0.15.0)" >&2
+    exit 1
+fi
+
+VERSION="$1"
+TAG="v${VERSION}"
+CARGO_TOML="Cargo.toml"
+
+# Validate version looks reasonable (digits and dots)
+if ! echo "$VERSION" | grep -qE '^[0-9]+\.[0-9]+\.[0-9]+'; then
+    echo "Error: version '$VERSION' doesn't look like a semver (expected X.Y.Z)" >&2
+    exit 1
+fi
+
+# Check we're in the right directory
+if [ ! -f "$CARGO_TOML" ]; then
+    echo "Error: $CARGO_TOML not found. Run this from the piscem repo root." >&2
+    exit 1
+fi
+
+# Check for uncommitted changes
+if ! git diff --quiet || ! git diff --cached --quiet; then
+    echo "Error: working tree has uncommitted changes. Commit or stash first." >&2
+    exit 1
+fi
+
+# Check tag doesn't already exist
+if git rev-parse "$TAG" >/dev/null 2>&1; then
+    echo "Error: tag '$TAG' already exists." >&2
+    exit 1
+fi
+
+# Update version in Cargo.toml
+sed -i '' "s/^version = \".*\"/version = \"${VERSION}\"/" "$CARGO_TOML"
+
+echo "Updated $CARGO_TOML to version $VERSION"
+
+# Commit, tag, and push
+git add "$CARGO_TOML"
+git commit -m "release ${TAG}"
+git tag "$TAG"
+git push origin main "$TAG"
+
+echo "Released ${TAG} and pushed to origin."
diff --git a/src/main.rs b/src/main.rs
index 79feaae..306d14f 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,33 +1,29 @@
-use std::ffi::CString;
-use std::ffi::{OsStr, OsString};
+use mimalloc::MiMalloc;
 use std::io;
-use std::os::raw::{c_char, c_int};
 use std::path::PathBuf;
 
-use anyhow::{bail, Result};
+#[global_allocator]
+static GLOBAL: MiMalloc = MiMalloc;
+
+use anyhow::{Context, Result, bail};
+use cf1_rs::{CfInput, cf_build as cf1_build};
 use clap::{Parser, Subcommand};
-use tracing::{error, info, warn, Level};
+use serde_json::json;
+use tracing::{Level, error, info, warn};
 
 mod piscem_commands;
 use piscem_commands::*;
 
-#[link(name = "pesc_static", kind = "static")]
-extern "C" {
-    pub fn run_pesc_sc(args: c_int, argsv: *const *const c_char) -> c_int;
-    pub fn run_pesc_bulk(args: c_int, argsv: *const *const c_char) -> c_int;
-    pub fn run_pesc_sc_atac(args: c_int, argsv: *const *const c_char) -> c_int;
-}
-
-#[link(name = "build_static", kind = "static")]
-extern "C" {
-    pub fn run_build(args: c_int, argsv: *const *const c_char) -> c_int;
-    pub fn run_build_poison_table(args: c_int, argsv: *const *const c_char) -> c_int;
-}
-
-#[link(name = "cfcore_static", kind = "static", modifiers = "+whole-archive")]
-extern "C" {
-    pub fn cf_build(args: c_int, argsv: *const *const c_char) -> c_int;
-}
+use piscem_rs::cli::build as rs_build;
+use piscem_rs::cli::poison as rs_poison;
+use piscem_rs::cli::map_bulk;
+use piscem_rs::cli::map_scrna;
+use piscem_rs::cli::map_scatac;
+use piscem_rs::cli::build::BuildArgs;
+use piscem_rs::cli::poison::BuildPoisonArgs;
+use piscem_rs::cli::map_scrna::MapScrnaArgs;
+use piscem_rs::cli::map_bulk::MapBulkArgs;
+use piscem_rs::cli::map_scatac::MapScatacArgs;
 
 /// Indexing and mapping to compacted colored de Bruijn graphs
 #[derive(Debug, Parser)]
@@ -60,16 +56,8 @@ enum Commands {
     MapSCAtac(MapSCAtacOpts),
 }
 
-// from: https://stackoverflow.com/questions/74322541/how-to-append-to-pathbuf
-fn append_to_path(p: impl Into<OsString>, s: impl AsRef<OsStr>) -> PathBuf {
-    let mut p = p.into();
-    p.push(s);
-    p.into()
-}
-
 fn main() -> Result<(), anyhow::Error> {
     let cli_args = Cli::parse();
-    //env_logger::Builder::from_env(Env::default().default_filter_or("warn")).init();
 
     let quiet = cli_args.quiet;
     if quiet {
@@ -99,6 +87,7 @@ fn main() -> Result<(), anyhow::Error> {
             work_dir,
             overwrite,
             no_ec_table,
+            polya_clip_length,
             decoy_paths,
             seed,
         }) => {
@@ -110,8 +99,11 @@ fn main() -> Result<(), anyhow::Error> {
                 );
             }
             if threads > ncpus {
-                bail!("the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
-                    threads, ncpus);
+                bail!(
+                    "the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
+                    threads,
+                    ncpus
+                );
             }
             if mlen >= klen {
                 bail!(
@@ -143,89 +135,100 @@ fn main() -> Result<(), anyhow::Error> {
                 }
             }
 
-            let mut args: Vec<CString> = vec![];
-
-            let cf_out = PathBuf::from(output.as_path().to_string_lossy().into_owned() + "_cfish");
-            let cf_base_path = cf_out.as_path();
-            let seg_file = append_to_path(cf_base_path, ".cf_seg");
-            let seq_file = append_to_path(cf_base_path, ".cf_seq");
-            let struct_file = append_to_path(cf_base_path, ".json");
-            let mut build_ret;
-
-            if overwrite {
-                if struct_file.exists() {
-                    std::fs::remove_file(struct_file.clone())?;
-                }
-                if seg_file.exists() {
-                    std::fs::remove_file(seg_file.clone())?;
-                }
-                if seq_file.exists() {
-                    std::fs::remove_file(seq_file.clone())?;
+            // Ensure the parent directory of the output prefix exists.
+            if let Some(parent) = output.parent() {
+                if !parent.as_os_str().is_empty() && !parent.exists() {
+                    std::fs::create_dir_all(parent)?;
+                    info!(
+                        "created output directory {} (did not previously exist)",
+                        parent.display()
+                    );
                 }
             }
 
-            if struct_file.exists() && (!seq_file.exists() || !seg_file.exists()) {
-                warn!("The prefix you have chosen for output already corresponds to an existing cDBG structure file {:?}.", struct_file.display());
-                warn!("However, the corresponding seq and seg files do not exist. Please either delete this structure file, choose another output prefix, or use the --overwrite flag.");
-                bail!("Cannot write over existing index without the --overwrite flag.");
-            }
-
-            args.push(CString::new("cdbg_builder").unwrap());
-
-            // We can treat the different input options independently
-            // here because the argument parser should have enforced
-            // their exclusivity.
-            let mut has_input = false;
-
-            if let Some(seqs) = ref_seqs {
+            // Build CfInput from CLI args, using native variants where possible.
+            let cf_input = if let Some(ref seqs) = ref_seqs {
                 if !seqs.is_empty() {
                     let out_stem =
                         PathBuf::from(output.as_path().to_string_lossy().into_owned() + ".sigs");
                     let configs = prepare_fasta::RecordParseConfig {
                         input: seqs.clone(),
                         output_stem: out_stem,
-                        polya_clip_length: None,
+                        polya_clip_length,
                     };
                     info!("Computing and recording reference signatures...");
                     prepare_fasta::parse_records(configs)?;
                     info!("done.");
-                    args.push(CString::new("--seq").unwrap());
-                    let reflist = seqs.join(",");
-                    args.push(CString::new(reflist.as_str()).unwrap());
-                    has_input = true;
+                    CfInput::Files(seqs.iter().map(PathBuf::from).collect())
+                } else {
+                    bail!("--ref-seqs provided but empty");
                 }
-            }
-
-            if let Some(lists) = ref_lists {
-                if !lists.is_empty() {
-                    args.push(CString::new("--list").unwrap());
-                    let reflist = lists.join(",");
-                    args.push(CString::new(reflist.as_str()).unwrap());
-                    has_input = true;
+            } else if let Some(ref lists) = ref_lists {
+                if lists.len() == 1 {
+                    CfInput::ListFile(PathBuf::from(&lists[0]))
+                } else {
+                    // Multiple list files — resolve all to individual paths.
+                    let mut files = Vec::new();
+                    for list_path in lists {
+                        let contents = std::fs::read_to_string(list_path)
+                            .with_context(|| format!("reading list file {}", list_path))?;
+                        for line in contents.lines() {
+                            let line = line.trim();
+                            if !line.is_empty() {
+                                files.push(PathBuf::from(line));
+                            }
+                        }
+                    }
+                    CfInput::Files(files)
                 }
-            }
+            } else if let Some(ref dirs) = ref_dirs {
+                if dirs.len() == 1 {
+                    CfInput::Directory(PathBuf::from(&dirs[0]))
+                } else {
+                    // Multiple directories — resolve all to individual file paths.
+                    let mut files = Vec::new();
+                    for dir_path in dirs {
+                        for entry in std::fs::read_dir(dir_path)
+                            .with_context(|| format!("reading directory {}", dir_path))?
+                        {
+                            let path = entry?.path();
+                            if path.is_file() {
+                                files.push(path);
+                            }
+                        }
+                    }
+                    CfInput::Files(files)
+                }
+            } else {
+                bail!("Input (via --ref-seqs, --ref-lists, or --ref-dirs) must be provided.");
+            };
 
-            if let Some(dirs) = ref_dirs {
-                if !dirs.is_empty() {
-                    args.push(CString::new("--dir").unwrap());
-                    let reflist = dirs.join(",");
-                    args.push(CString::new(reflist.as_str()).unwrap());
-                    has_input = true;
+            let cf_out = PathBuf::from(output.as_path().to_string_lossy().into_owned() + "_cfish");
+            let cf_out_str = cf_out.as_path().to_string_lossy();
+            let seg_file = PathBuf::from(format!("{}.cf_seg", cf_out_str));
+            let seq_file = PathBuf::from(format!("{}.cf_seq", cf_out_str));
+            let struct_file = PathBuf::from(format!("{}.json", cf_out_str));
+
+            if overwrite {
+                for f in [&struct_file, &seg_file, &seq_file] {
+                    if f.exists() {
+                        std::fs::remove_file(f)?;
+                    }
                 }
             }
 
-            assert!(
-                has_input,
-                "Input (via --ref-seqs, --ref-lists, or --ref-dirs) must be provided."
-            );
-
-            args.push(CString::new("-k").unwrap());
-            args.push(CString::new(klen.to_string()).unwrap());
-            args.push(CString::new("--track-short-seqs").unwrap());
-            args.push(CString::new("--poly-N-stretch").unwrap());
+            if struct_file.exists() && (!seq_file.exists() || !seg_file.exists()) {
+                warn!(
+                    "The prefix you have chosen for output already corresponds to an existing cDBG structure file {:?}.",
+                    struct_file.display()
+                );
+                warn!(
+                    "However, the corresponding seq and seg files do not exist. Please either delete this structure file, choose another output prefix, or use the --overwrite flag."
+                );
+                bail!("Cannot write over existing index without the --overwrite flag.");
+            }
 
-            // check if the provided work directory exists.
-            // If not, then try and create it.
+            // Ensure work directory exists.
             match work_dir.try_exists() {
                 Ok(true) => {
                     info!(
@@ -234,11 +237,14 @@ fn main() -> Result<(), anyhow::Error> {
                     );
                 }
                 Ok(false) => {
-                    // try to create it
                     match std::fs::create_dir_all(&work_dir) {
                         Ok(_) => {}
                         Err(e) => {
-                            error!("when attempting to create working directory {}, encountered error {:#?}", &work_dir.display(), e);
+                            error!(
+                                "when attempting to create working directory {}, encountered error {:#?}",
+                                &work_dir.display(),
+                                e
+                            );
                             bail!(
                                 "Failed to create working directory {} for index construction : {:#?}",
                                 &work_dir.display(),
@@ -256,11 +262,9 @@ fn main() -> Result<(), anyhow::Error> {
                 }
             }
 
-            // check if the provided output path is more than just a prefix
-            // if so, check if the specified directory exists and create it
-            // if it doesn't.
+            // Ensure the output parent directory exists.
             if let Some(parent_path) = cf_out.parent() {
-                if !parent_path.exists() {
+                if !parent_path.as_os_str().is_empty() && !parent_path.exists() {
                     std::fs::create_dir_all(parent_path)?;
                     info!(
                         "directory {} did not already exist; creating it.",
@@ -269,147 +273,72 @@ fn main() -> Result<(), anyhow::Error> {
                 }
             }
 
-            args.push(CString::new("-o").unwrap());
-            args.push(CString::new(cf_out.as_path().to_string_lossy().into_owned()).unwrap());
-
-            args.push(CString::new("-t").unwrap());
-            args.push(CString::new(threads.to_string()).unwrap());
-            // output format
-            args.push(CString::new("-f").unwrap());
-            args.push(CString::new("3").unwrap());
-            // work directory
-            args.push(CString::new("-w").unwrap());
-            args.push(CString::new(work_dir.as_path().to_string_lossy().into_owned()).unwrap());
-
-            info!("args = {:?}", args);
-            {
-                let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-                let args_len: c_int = args.len() as c_int;
-                build_ret = unsafe { cf_build(args_len, arg_ptrs.as_ptr()) };
-            }
-
-            if build_ret != 0 {
-                bail!(
-                    "cDBG constructor returned exit code {}; failure.",
-                    build_ret
-                );
-            }
-
-            args.clear();
-            args.push(CString::new("ref_index_builder").unwrap());
-
-            args.push(CString::new("-i").unwrap());
-            args.push(CString::new(cf_out.as_path().to_string_lossy().into_owned()).unwrap());
-            args.push(CString::new("-k").unwrap());
-            args.push(CString::new(klen.to_string()).unwrap());
-            args.push(CString::new("-m").unwrap());
-            args.push(CString::new(mlen.to_string()).unwrap()); // minimizer length
-
-            args.push(CString::new("--canonical-parsing").unwrap());
-            if !no_ec_table {
-                args.push(CString::new("--build-ec-table").unwrap());
-            }
-            args.push(CString::new("-o").unwrap());
-            args.push(CString::new(output.as_path().to_string_lossy().into_owned()).unwrap());
-
-            args.push(CString::new("-d").unwrap());
-            args.push(CString::new(work_dir.as_path().to_string_lossy().into_owned()).unwrap());
-
-            args.push(CString::new("-t").unwrap());
-            args.push(CString::new(threads.to_string()).unwrap());
-
-            args.push(CString::new("--seed").unwrap());
-            args.push(CString::new(seed.to_string()).unwrap());
-
-            if quiet {
-                args.push(CString::new("--quiet").unwrap());
-            }
-
-            {
-                println!("{:?}", args);
-                let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-                let args_len: c_int = args.len() as c_int;
-                build_ret = unsafe { run_build(args_len, arg_ptrs.as_ptr()) };
-            }
-
-            if build_ret != 0 {
-                bail!("indexer returned exit code {}; failure.", build_ret);
-            }
+            info!("starting cDBG construction with cf1-rs");
+            let cf_result = cf1_build()
+                .input(cf_input)
+                .output_prefix(cf_out.clone())
+                .k(klen)
+                .threads(threads)
+                .work_dir(work_dir.clone())
+                .call()?;
+
+            info!(
+                "cDBG construction complete: {} unitigs, {} vertices",
+                cf_result.unitig_count, cf_result.vertex_count
+            );
 
-            // now, build the poison table if there are decoys
+            // Build piscem-rs index from cuttlefish output
+            rs_build::run(BuildArgs {
+                input: cf_out.clone(),
+                output: output.clone(),
+                klen,
+                mlen,
+                threads,
+                build_ec_table: !no_ec_table,
+                canonical: true,
+                seed,
+                single_mphf: false,
+            })?;
+
+            // Build poison table if decoys were provided
             if let Some(decoy_pathbufs) = decoy_paths {
-                args.clear();
-                args.push(CString::new("poison_table_builder").unwrap());
-
-                // index is the one we just built
-                args.push(CString::new("-i").unwrap());
-                args.push(CString::new(output.as_path().to_string_lossy().into_owned()).unwrap());
-
-                args.push(CString::new("-t").unwrap());
-                args.push(CString::new(threads.to_string()).unwrap());
-
-                if overwrite {
-                    args.push(CString::new("--overwrite").unwrap());
-                }
-
-                let path_args = decoy_pathbufs
-                    .into_iter()
-                    .map(|x| x.to_string_lossy().into_owned())
-                    .collect::<Vec<String>>()
-                    .join(",");
-                args.push(CString::new("-d").unwrap());
-                args.push(CString::new(path_args).unwrap());
-
-                if quiet {
-                    args.push(CString::new("--quiet").unwrap());
-                }
+                rs_poison::run(BuildPoisonArgs {
+                    index: output.clone(),
+                    decoys: decoy_pathbufs,
+                    threads,
+                })?;
+            }
 
-                {
-                    println!("{:?}", args);
-                    let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-                    let args_len: c_int = args.len() as c_int;
-                    build_ret = unsafe { run_build_poison_table(args_len, arg_ptrs.as_ptr()) };
-                }
-                if build_ret != 0 {
-                    bail!(
-                        "building poison table returned exit code {}; failure.",
-                        build_ret
-                    );
+            if !keep_intermediate_dbg {
+                info!("removing intermediate cdBG files produced by cf1-rs.");
+                for (path, label) in [
+                    (&cf_result.seg_file, "segment"),
+                    (&cf_result.seq_file, "tiling"),
+                ] {
+                    match std::fs::remove_file(path) {
+                        Ok(_) => info!("removed {} file {}", label, path.display()),
+                        Err(e) => warn!("cannot remove {}, error: {:?}", path.display(), e),
+                    }
                 }
+                // Keep the json file — it's small and may contain useful info.
             }
 
-            if !keep_intermediate_dbg {
-                info!("removing intermediate cdBG files produced by cuttlefish.");
+            let piscem_rs_ver = piscem_rs::VERSION;
+            let cf1_rs_ver = env!("CF1_RS_VERSION");
+            let piscem_ver = clap::crate_version!();
 
-                match std::fs::remove_file(seg_file.clone()) {
-                    Ok(_) => {
-                        info!("removed segment file {}", seg_file.display());
-                    }
-                    Err(e) => {
-                        warn!(
-                            "cannot remove {}, encountered error {:?}!",
-                            seg_file.display(),
-                            e
-                        );
-                    }
-                };
+            let version_json = json!({
+                "piscem-rs": piscem_rs_ver,
+                "cf1-rs": cf1_rs_ver,
+                "piscem": piscem_ver
+            });
 
-                match std::fs::remove_file(seq_file.clone()) {
-                    Ok(_) => {
-                        info!("removed tiling file {}", seq_file.display());
-                    }
-                    Err(e) => {
-                        warn!(
-                            "cannot remove {}, encountered error {:?}!",
-                            seq_file.display(),
-                            e
-                        );
-                    }
-                };
-                // for now, let the json file stick around. It's
-                // generally very small and may contain useful information
-                // about the references being indexed.
-            }
+            let mut fname = output.as_path().to_string_lossy().into_owned();
+            fname.push_str("_ver.json");
+
+            let fname = PathBuf::from(fname);
+            let ver_file = std::fs::File::create(fname)?;
+            serde_json::to_writer_pretty(ver_file, &version_json)?;
 
             info!("piscem build finished.");
         }
@@ -422,23 +351,32 @@ fn main() -> Result<(), anyhow::Error> {
                 );
             }
             if sc_opts.threads > ncpus {
-                bail!("the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
-                    sc_opts.threads, ncpus);
-            }
-
-            let mut args = sc_opts.as_argv()?;
-            if quiet {
-                args.push(CString::new("--quiet").unwrap());
+                bail!(
+                    "the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
+                    sc_opts.threads,
+                    ncpus
+                );
             }
 
-            info!("cmd: {:?}", args);
-            let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-            let args_len: c_int = args.len() as c_int;
-
-            let map_ret = unsafe { run_pesc_sc(args_len, arg_ptrs.as_ptr()) };
-            if map_ret != 0 {
-                bail!("mapper returned exit code {}; failure", map_ret);
-            }
+            let args = MapScrnaArgs {
+                index: PathBuf::from(&sc_opts.index),
+                read1: sc_opts.read1.iter().map(PathBuf::from).collect(),
+                read2: sc_opts.read2.iter().map(PathBuf::from).collect(),
+                geometry: sc_opts.geometry,
+                output: sc_opts.output.clone(),
+                threads: sc_opts.threads,
+                skipping_strategy: sc_opts.skipping_strategy,
+                no_poison: sc_opts.no_poison,
+                struct_constraints: sc_opts.struct_constraints,
+                ignore_ambig_hits: sc_opts.ignore_ambig_hits,
+                max_ec_card: sc_opts.max_ec_card,
+                max_hit_occ: sc_opts.max_hit_occ as usize,
+                max_hit_occ_recover: sc_opts.max_hit_occ_recover as usize,
+                max_read_occ: sc_opts.max_read_occ as usize,
+                with_position: sc_opts.with_position,
+                quiet,
+            };
+            map_scrna::run(args)?;
         }
 
         Commands::MapSCAtac(scatac_opts) => {
@@ -449,23 +387,51 @@ fn main() -> Result<(), anyhow::Error> {
                 );
             }
             if scatac_opts.threads > ncpus {
-                bail!("the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
-                    scatac_opts.threads, ncpus);
+                bail!(
+                    "the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
+                    scatac_opts.threads,
+                    ncpus
+                );
             }
 
-            let mut args = scatac_opts.as_argv()?;
-            if quiet {
-                args.push(CString::new("--quiet").unwrap());
+            for (flag, name) in [
+                (scatac_opts.sam_format, "--sam-format"),
+                (scatac_opts.bed_format, "--bed-format"),
+                (scatac_opts.use_chr, "--use-chr"),
+                (scatac_opts.check_kmer_orphan, "--check-kmer-orphan"),
+                (scatac_opts.struct_constraints, "--struct-constraints"),
+            ] {
+                if flag {
+                    warn!("{} is not supported by piscem-rs and will be ignored", name);
+                }
             }
 
-            info!("cmd: {:?}", args);
-            let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-            let args_len: c_int = args.len() as c_int;
-
-            let map_ret = unsafe { run_pesc_sc_atac(args_len, arg_ptrs.as_ptr()) };
-            if map_ret != 0 {
-                bail!("mapper returned exit code {}; failure", map_ret);
-            }
+            let barcode = scatac_opts.barcode.unwrap_or_default();
+            let args = MapScatacArgs {
+                index: PathBuf::from(&scatac_opts.index),
+                reads: scatac_opts.reads.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                read1: scatac_opts.read1.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                read2: scatac_opts.read2.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                barcode: barcode.iter().map(PathBuf::from).collect(),
+                output: scatac_opts.output.clone(),
+                threads: scatac_opts.threads,
+                bc_len: scatac_opts.bclen as usize,
+                no_tn5_shift: scatac_opts.no_tn5_shift,
+                no_poison: scatac_opts.no_poison,
+                check_ambig_hits: !scatac_opts.ignore_ambig_hits,
+                max_ec_card: scatac_opts.max_ec_card,
+                max_hit_occ: scatac_opts.max_hit_occ as usize,
+                max_hit_occ_recover: scatac_opts.max_hit_occ_recover as usize,
+                max_read_occ: scatac_opts.max_read_occ as usize,
+                end_cache_capacity: scatac_opts.end_cache_capacity,
+                bin_size: scatac_opts.bin_size as u64,
+                bin_overlap: scatac_opts.bin_overlap as u64,
+                thr: scatac_opts.thr,
+                min_overlap: 30,
+                skipping_strategy: None,
+                quiet,
+            };
+            map_scatac::run(args)?;
         }
 
         Commands::MapBulk(bulk_opts) => {
@@ -476,23 +442,31 @@ fn main() -> Result<(), anyhow::Error> {
                 );
             }
             if bulk_opts.threads > ncpus {
-                bail!("the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
-                    bulk_opts.threads, ncpus);
-            }
-
-            let mut args = bulk_opts.as_argv()?;
-
-            if quiet {
-                args.push(CString::new("--quiet").unwrap());
+                bail!(
+                    "the number of provided threads ({}) should be <= the number of logical CPUs ({}).",
+                    bulk_opts.threads,
+                    ncpus
+                );
             }
 
-            let arg_ptrs: Vec<*const c_char> = args.iter().map(|s| s.as_ptr()).collect();
-            let args_len: c_int = args.len() as c_int;
-
-            let map_ret = unsafe { run_pesc_bulk(args_len, arg_ptrs.as_ptr()) };
-            if map_ret != 0 {
-                bail!("mapper returned exit code {}; failure", map_ret);
-            }
+            let args = MapBulkArgs {
+                index: PathBuf::from(&bulk_opts.index),
+                reads: bulk_opts.reads.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                read1: bulk_opts.read1.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                read2: bulk_opts.read2.unwrap_or_default().iter().map(PathBuf::from).collect(),
+                output: bulk_opts.output.clone(),
+                threads: bulk_opts.threads,
+                skipping_strategy: bulk_opts.skipping_strategy,
+                no_poison: bulk_opts.no_poison,
+                struct_constraints: bulk_opts.struct_constraints,
+                ignore_ambig_hits: bulk_opts.ignore_ambig_hits,
+                max_ec_card: bulk_opts.max_ec_card,
+                max_hit_occ: bulk_opts.max_hit_occ as usize,
+                max_hit_occ_recover: bulk_opts.max_hit_occ_recover as usize,
+                max_read_occ: bulk_opts.max_read_occ as usize,
+                quiet,
+            };
+            map_bulk::run(args)?;
         }
     }
     Ok(())
diff --git a/src/piscem_commands.rs b/src/piscem_commands.rs
index ad7545c..bc7b2a5 100644
--- a/src/piscem_commands.rs
+++ b/src/piscem_commands.rs
@@ -1,8 +1,6 @@
-use anyhow::{anyhow, bail, Result};
+use anyhow::{Result, anyhow, bail};
 use clap::{ArgGroup, Args};
-use std::ffi::CString;
-use std::path::{Path, PathBuf};
-use std::str::FromStr;
+use std::path::PathBuf;
 
 trait DefaultMappingParams {
     const MAX_EC_CARD: u32;
@@ -14,6 +12,7 @@ trait DefaultMappingParams {
     const BIN_SIZE: u32;
     const BIN_OVERLAP: u32;
     const BCLEN: u16;
+    const END_CACHE_CAPACITY: usize;
 }
 
 struct DefaultParams;
@@ -28,14 +27,7 @@ impl DefaultMappingParams for DefaultParams {
     const BIN_SIZE: u32 = 1000;
     const BIN_OVERLAP: u32 = 300;
     const BCLEN: u16 = 16;
-}
-
-/// Trait to produce a proper set of command-line arguments
-/// from a populated struct.  There is a single method,
-/// `as_argv`, which produces a Vec<CString> that can be parsed
-/// and passed to a C function as the `char** argv` parameter.
-pub trait AsArgv {
-    fn as_argv(&self) -> Result<Vec<CString>>;
+    const END_CACHE_CAPACITY: usize = 5_000_000;
 }
 
 fn klen_is_good(s: &str) -> Result<usize> {
@@ -111,6 +103,12 @@ pub(crate) struct BuildOpts {
     #[arg(long, help_heading = "Index Construction Parameters")]
     pub no_ec_table: bool,
 
+    /// If provided (default is not to clip polyA), then reference sequences
+    /// ending with polyA tails of length greater than or equal to this value
+    /// will be clipped.
+    #[arg(long, help_heading = "Index Construction Parameters")]
+    pub polya_clip_length: Option<usize>,
+
     /// path to (optional) ',' sparated list of decoy sequences used to insert poison
     /// k-mer information into the index.
     #[arg(long, value_delimiter = ',')]
@@ -132,10 +130,6 @@ pub(crate) struct MapSCOpts {
     #[arg(short, long, help_heading = "Input")]
     pub index: String,
 
-    /// list available geometries supported by the underlying `pesc-sc` mapper
-    // #[arg(long, help_heading = "Advanced")]
-    // pub list_geometries: bool,
-
     /// geometry of barcode, umi and read
     #[arg(short, long)]
     pub geometry: String,
@@ -188,6 +182,10 @@ pub(crate) struct MapSCOpts {
     #[arg(long)]
     pub ignore_ambig_hits: bool,
 
+    /// includes the positions of each mapped read in the resulting RAD file.
+    #[arg(long)]
+    pub with_position: bool,
+
     /// determines the maximum cardinality equivalence class
     /// (number of (txp, orientation status) pairs) to examine (cannot be used with
     /// --ignore-ambig-hits).
@@ -284,7 +282,6 @@ pub(crate) struct MapBulkOpts {
     #[arg(
         long,
         short,
-        requires = "check_ambig_hits",
         default_value_t = DefaultParams::MAX_EC_CARD,
         conflicts_with = "ignore_ambig_hits",
         help_heading = "Advanced options"
@@ -306,183 +303,6 @@ pub(crate) struct MapBulkOpts {
     pub max_read_occ: u32,
 }
 
-impl AsArgv for MapSCOpts {
-    fn as_argv(&self) -> Result<Vec<CString>> {
-        // first check if the relevant index files exist
-        let mut idx_suffixes: Vec<String> = vec!["sshash".into(), "ctab".into(), "refinfo".into()];
-
-        if !self.ignore_ambig_hits {
-            idx_suffixes.push("ectab".into());
-        }
-
-        {
-            let idx_path = get_index_path(&self.index)?;
-            for s in idx_suffixes {
-                let req_file = idx_path.with_extension(s);
-                if !req_file.exists() {
-                    bail!("To load the index with the specified prefix {}, piscem expects the file {} to exist, but it does not!", &self.index, req_file.display());
-                }
-            }
-        }
-
-        let r1_string = self.read1.join(",");
-        let r2_string = self.read2.join(",");
-
-        let mut args: Vec<CString> = vec![
-            CString::new("sc_ref_mapper").unwrap(),
-            CString::new("-i").unwrap(),
-            CString::new(self.index.clone()).unwrap(),
-            CString::new("-g").unwrap(),
-            CString::new(self.geometry.clone()).unwrap(),
-            CString::new("-1").unwrap(),
-            CString::new(r1_string.as_str()).unwrap(),
-            CString::new("-2").unwrap(),
-            CString::new(r2_string.as_str()).unwrap(),
-            CString::new("-t").unwrap(),
-            CString::new(self.threads.to_string()).unwrap(),
-            CString::new("-o").unwrap(),
-            #[cfg(not(target_os = "windows"))]
-            CString::new(std::os::unix::ffi::OsStrExt::as_bytes(
-                <PathBuf as Clone>::clone(&self.output)
-                    .into_os_string()
-                    .as_os_str(),
-            ))
-            .unwrap(),
-            // NOTE: Windows is completely untested
-            #[cfg(target_os = "windows")]
-            CString::new(self.output.into_os_string().to_str()?).unwrap(),
-        ];
-
-        /*if self.list_geometries {
-            args.push(CString::new("--list-geometries").unwrap());
-        }*/
-
-        if self.ignore_ambig_hits {
-            args.push(CString::new("--ignore-ambig-hits").unwrap());
-        } else {
-            args.push(CString::new("--max-ec-card").unwrap());
-            args.push(CString::new(self.max_ec_card.to_string()).unwrap());
-        }
-
-        if self.no_poison {
-            args.push(CString::new("--no-poison").unwrap());
-        }
-
-        args.push(CString::new("--skipping-strategy").unwrap());
-        args.push(CString::new(self.skipping_strategy.to_string()).unwrap());
-
-        if self.struct_constraints {
-            args.push(CString::new("--struct-constraints").unwrap());
-        }
-
-        args.push(CString::new("--max-hit-occ").unwrap());
-        args.push(CString::new(self.max_hit_occ.to_string()).unwrap());
-
-        args.push(CString::new("--max-hit-occ-recover").unwrap());
-        args.push(CString::new(self.max_hit_occ_recover.to_string()).unwrap());
-
-        args.push(CString::new("--max-read-occ").unwrap());
-        args.push(CString::new(self.max_read_occ.to_string()).unwrap());
-
-        Ok(args)
-    }
-}
-
-fn get_index_path(base: &str) -> Result<PathBuf> {
-    if Path::new(base).exists() {
-        bail!(
-            concat!("The path {} was provided as the base path for the index, but this corresponds ",
-                    "to a specific existing file. The provided path should be the file stem (e.g. without the extension)."),
-            base);
-    }
-
-    if let Some(_ext) = Path::new(base).extension() {
-        Ok(PathBuf::from_str(&format!("{}.dummy", base))?)
-    } else {
-        Ok(PathBuf::from_str(base)?)
-    }
-}
-
-impl AsArgv for MapBulkOpts {
-    fn as_argv(&self) -> Result<Vec<CString>> {
-        let mut idx_suffixes: Vec<String> = vec!["sshash".into(), "ctab".into(), "refinfo".into()];
-
-        if !self.ignore_ambig_hits {
-            idx_suffixes.push("ectab".into());
-        }
-
-        {
-            let idx_path = get_index_path(&self.index)?;
-            for s in idx_suffixes {
-                let req_file = idx_path.with_extension(s);
-                if !req_file.exists() {
-                    bail!("To load the index with the specified prefix {}, piscem expects the file {} to exist, but it does not!", &self.index, req_file.display());
-                }
-            }
-        }
-
-        let mut args: Vec<CString> = vec![
-            CString::new("bulk_ref_mapper").unwrap(),
-            CString::new("-i").unwrap(),
-            CString::new(self.index.clone()).unwrap(),
-            CString::new("-t").unwrap(),
-            CString::new(self.threads.to_string()).unwrap(),
-            CString::new("-o").unwrap(),
-            #[cfg(not(target_os = "windows"))]
-            CString::new(std::os::unix::ffi::OsStrExt::as_bytes(
-                <PathBuf as Clone>::clone(&self.output)
-                    .into_os_string()
-                    .as_os_str(),
-            ))
-            .unwrap(),
-            // NOTE: Windows is completely untested
-            #[cfg(target_os = "windows")]
-            CString::new(self.output.into_os_string().to_str()?).unwrap(),
-        ];
-
-        if let Some(ref unpaired_reads) = &self.reads {
-            let r_string = unpaired_reads.clone().join(",");
-            args.push(CString::new("-r").unwrap());
-            args.push(CString::new(r_string.as_str()).unwrap());
-        } else if let (Some(ref r1), Some(ref r2)) = (&self.read1, &self.read2) {
-            let r1_string = r1.clone().join(",");
-            let r2_string = r2.clone().join(",");
-            args.push(CString::new("-1").unwrap());
-            args.push(CString::new(r1_string.as_str()).unwrap());
-            args.push(CString::new("-2").unwrap());
-            args.push(CString::new(r2_string.as_str()).unwrap());
-        }
-
-        if self.ignore_ambig_hits {
-            args.push(CString::new("--ignore-ambig-hits").unwrap());
-        } else {
-            args.push(CString::new("--max-ec-card").unwrap());
-            args.push(CString::new(self.max_ec_card.to_string()).unwrap());
-        }
-
-        if self.no_poison {
-            args.push(CString::new("--no-poison").unwrap());
-        }
-
-        args.push(CString::new("--skipping-strategy").unwrap());
-        args.push(CString::new(self.skipping_strategy.to_string()).unwrap());
-
-        if self.struct_constraints {
-            args.push(CString::new("--struct-constraints").unwrap());
-        }
-
-        args.push(CString::new("--max-hit-occ").unwrap());
-        args.push(CString::new(self.max_hit_occ.to_string()).unwrap());
-
-        args.push(CString::new("--max-hit-occ-recover").unwrap());
-        args.push(CString::new(self.max_hit_occ_recover.to_string()).unwrap());
-
-        args.push(CString::new("--max-read-occ").unwrap());
-        args.push(CString::new(self.max_read_occ.to_string()).unwrap());
-
-        Ok(args)
-    }
-}
 
 #[derive(Args, Clone, Debug)]
 pub(crate) struct MapSCAtacOpts {
@@ -513,13 +333,12 @@ pub(crate) struct MapSCAtacOpts {
     #[arg(short = 'r', long, help_heading = "Input", value_delimiter = ',', conflicts_with_all = ["read1", "read2"])]
     pub reads: Option<Vec<String>>,
 
-    /// path to a ',' separated list of read 2 files
+    /// path to a ',' separated list of barcode files
     #[arg(
         short = 'b',
         long,
         help_heading = "Input",
-        value_delimiter = ',',
-        requires = "read1"
+        value_delimiter = ','
     )]
     pub barcode: Option<Vec<String>>,
 
@@ -543,24 +362,28 @@ pub(crate) struct MapSCAtacOpts {
     #[arg(long)]
     pub no_poison: bool,
 
-    /// apply structural constraints when performing mapping.
-    #[arg(short = 'c', long)]
+    /// [DEPRECATED] apply structural constraints when performing mapping.
+    /// This option is no longer supported and will be ignored.
+    #[arg(short = 'c', long, hide = true)]
     pub struct_constraints: bool,
 
     /// the skipping strategy to use for k-mer collection
     #[arg(long, default_value = &DefaultParams::SKIPPING_STRATEGY, value_parser = clap::builder::PossibleValuesParser::new(["permissive", "strict"]))]
     pub skipping_strategy: String,
 
-    /// output mappings in sam format
-    #[arg(long)]
+    /// [DEPRECATED] output mappings in sam format.
+    /// This option is no longer supported and will be ignored.
+    #[arg(long, hide = true)]
     pub sam_format: bool,
 
-    /// output mappings in bed format
-    #[arg(long)]
+    /// [DEPRECATED] output mappings in bed format.
+    /// This option is no longer supported and will be ignored.
+    #[arg(long, hide = true)]
     pub bed_format: bool,
 
-    /// use chromosomes as color
-    #[arg(long)]
+    /// [DEPRECATED] use chromosomes as color.
+    /// This option is no longer supported and will be ignored.
+    #[arg(long, hide = true)]
     pub use_chr: bool,
 
     /// threshold to be considered for pseudoalignment, default set to 0.7
@@ -579,10 +402,10 @@ pub(crate) struct MapSCAtacOpts {
     #[arg(long)]
     pub no_tn5_shift: bool,
 
-    /// Check if any mapping kmer exist for a mate which is not mapped,
+    /// [DEPRECATED] Check if any mapping kmer exist for a mate which is not mapped,
     /// but there exists mapping for the other read.
-    /// If set to true and a mapping kmer exists, then the pair would not be mapped (default false)
-    #[arg(long)]
+    /// This option is no longer supported and will be ignored.
+    #[arg(long, hide = true)]
     pub check_kmer_orphan: bool,
 
     /// determines the maximum cardinality equivalence class
@@ -611,140 +434,11 @@ pub(crate) struct MapSCAtacOpts {
     #[arg(long, default_value_t = DefaultParams::MAX_READ_OCC, help_heading = "Advanced options")]
     pub max_read_occ: u32,
 
+    /// the length of the barcode sequence
     #[arg(long, default_value_t = DefaultParams::BCLEN, help_heading = "Advanced options")]
     pub bclen: u16,
-}
 
-impl AsArgv for MapSCAtacOpts {
-    fn as_argv(&self) -> Result<Vec<CString>> {
-        // first check if the relevant index files exist
-        let idx_suffixes: Vec<String> = vec!["sshash".into(), "ctab".into(), "refinfo".into()];
-
-        // if !self.ignore_ambig_hits {
-        //     idx_suffixes.push("ectab".into());
-        // }
-
-        {
-            let idx_path = get_index_path(&self.index)?;
-            for s in idx_suffixes {
-                let req_file = idx_path.with_extension(s);
-                if !req_file.exists() {
-                    bail!("To load the index with the specified prefix {}, piscem expects the file {} to exist, but it does not!", &self.index, req_file.display());
-                }
-            }
-        }
-
-        let mut args: Vec<CString> = vec![
-            CString::new("scatac_ref_mapper").unwrap(),
-            CString::new("-i").unwrap(),
-            CString::new(self.index.clone()).unwrap(),
-            CString::new("-t").unwrap(),
-            CString::new(self.threads.to_string()).unwrap(),
-            CString::new("-o").unwrap(),
-            #[cfg(not(target_os = "windows"))]
-            CString::new(std::os::unix::ffi::OsStrExt::as_bytes(
-                <PathBuf as Clone>::clone(&self.output)
-                    .into_os_string()
-                    .as_os_str(),
-            ))
-            .unwrap(),
-            // NOTE: Windows is completely untested
-            #[cfg(target_os = "windows")]
-            CString::new(self.output.into_os_string().to_str()?).unwrap(),
-        ];
-
-        // if let (Some(ref r1), Some(ref r2), Some(ref b)) = (&self.read1, &self.read2, &self.barcode)
-        // {
-        //     let r1_string = r1.clone().join(",");
-        //     let r2_string = r2.clone().join(",");
-        //
-        //     args.push(CString::new("-1").unwrap());
-        //     args.push(CString::new(r1_string.as_str()).unwrap());
-        //     args.push(CString::new("-2").unwrap());
-        //     args.push(CString::new(r2_string.as_str()).unwrap());
-        //     args.push(CString::new("-b").unwrap());
-        //     args.push(CString::new(b_string.as_str()).unwrap());
-        // }
-        let b_string = self.barcode.as_ref().unwrap().clone().join(",");
-        if let Some(ref unpaired_reads) = &self.reads {
-            let r_string = unpaired_reads.clone().join(",");
-            args.push(CString::new("-r").unwrap());
-            args.push(CString::new(r_string.as_str()).unwrap());
-        } else if let (Some(ref r1), Some(ref r2)) = (&self.read1, &self.read2) {
-            let r1_string = r1.clone().join(",");
-            let r2_string = r2.clone().join(",");
-            args.push(CString::new("-1").unwrap());
-            args.push(CString::new(r1_string.as_str()).unwrap());
-            args.push(CString::new("-2").unwrap());
-            args.push(CString::new(r2_string.as_str()).unwrap());
-        }
-
-        args.push(CString::new("-b").unwrap());
-        args.push(CString::new(b_string.as_str()).unwrap());
-        /*if self.list_geometries {
-            args.push(CString::new("--list-geometries").unwrap());
-        }*/
-
-        // if self.ignore_ambig_hits {
-        //     args.push(CString::new("--ignore-ambig-hits").unwrap());
-        // } else {
-        //     args.push(CString::new("--max-ec-card").unwrap());
-        //     args.push(CString::new(self.max_ec_card.to_string()).unwrap());
-        // }
-
-        if self.no_poison {
-            args.push(CString::new("--no-poison").unwrap());
-        }
-
-        args.push(CString::new("--skipping-strategy").unwrap());
-        args.push(CString::new(self.skipping_strategy.to_string()).unwrap());
-
-        if self.struct_constraints {
-            args.push(CString::new("--struct-constraints").unwrap());
-        }
-
-        if self.bed_format {
-            args.push(CString::new("--bed-format").unwrap());
-        }
-
-        if self.use_chr {
-            args.push(CString::new("--use-chr").unwrap());
-        }
-
-        if self.sam_format {
-            args.push(CString::new("--sam-format").unwrap());
-        }
-
-        if self.check_kmer_orphan {
-            args.push(CString::new("--kmers-orphans").unwrap());
-        }
-
-        args.push(CString::new("--thr").unwrap());
-        args.push(CString::new(self.thr.to_string()).unwrap());
-
-        if self.no_tn5_shift {
-            args.push(CString::new("--tn5-shift").unwrap());
-            args.push(CString::new("false").unwrap());
-        }
-
-        args.push(CString::new("--bin-size").unwrap());
-        args.push(CString::new(self.bin_size.to_string()).unwrap());
-
-        args.push(CString::new("--bin-overlap").unwrap());
-        args.push(CString::new(self.bin_overlap.to_string()).unwrap());
-
-        args.push(CString::new("--bclen").unwrap());
-        args.push(CString::new(self.bclen.to_string()).unwrap());
-
-        // args.push(CString::new("--max-hit-occ").unwrap());
-        // args.push(CString::new(self.max_hit_occ.to_string()).unwrap());
-
-        // args.push(CString::new("--max-hit-occ-recover").unwrap());
-        // args.push(CString::new(self.max_hit_occ_recover.to_string()).unwrap());
-
-        // args.push(CString::new("--max-read-occ").unwrap());
-        // args.push(CString::new(self.max_read_occ.to_string()).unwrap());
-
-        Ok(args)
-    }
+    /// the capacity of the cache used to provide fast lookup for k-mers at the ends of unitigs
+    #[arg(long, default_value_t = DefaultParams::END_CACHE_CAPACITY, help_heading = "Advanced options")]
+    pub end_cache_capacity: usize,
 }