fix(perf): improve performance with rust updates

* Improved test tooling with mise.
* Removed redundant checks.
* Replaced clone() with dereference for Copy types.
* Optimized HashMap access and eliminated redundant operations
* Improved Rust code conventions and idioms
* Improved samfile parsing
* Raised rust errors into python
* Eliminated unnecessary HashMap cloning in hot loops
* Eliminated redundant SAM file I/O by implementing single-pass architecture

Author: igboyes

.gitignore

@@ -6,3 +6,4 @@
 __pycache__
 subtracted_read_ids.txt
 target
+CLAUDE.md

.mise.toml

@@ -0,0 +1,31 @@
+[tools]
+python = "3.12"
+poetry = "latest"
+
+[tasks.test-setup]
+description = "Build base Docker image for testing"
+run = "docker build --target dev -t pathoscope:dev ."
+
+[tasks.test]
+description = "Run tests in Docker"
+depends = ["test-setup"]
+run = "./scripts/test-docker.sh"
+
+[tasks.test-watch]
+description = "Run tests in watch mode"
+depends = ["test-setup"]
+run = "./scripts/test-docker.sh --watch"
+
+[tasks.test-shell]
+description = "Interactive shell in test container"
+depends = ["test-setup"]
+run = "./scripts/test-docker.sh --shell"
+
+[tasks.test-rust]
+description = "Run Rust tests only"
+depends = ["test-setup"]
+run = "docker run --rm -v \"$(pwd):/app\" -w /app pathoscope:dev cargo test"
+
+[tasks.test-clean]
+description = "Clean up test Docker resources"
+run = "docker rmi pathoscope:dev 2>/dev/null || true"

Dockerfile

@@ -51,11 +51,19 @@ COPY --from=poetry /app/.venv /app/.venv
 COPY --from=poetry /app/python /app/python
 COPY fixtures.py workflow.py VERSION* ./
 
-FROM deps AS test
+FROM deps AS dev
 WORKDIR /app
-ENV PATH="/root/.local/bin:/root/.cargo/bin:${PATH}"
+ENV PATH="/root/.local/bin:/root/.cargo/bin:${PATH}" \
+    POETRY_CACHE_DIR='/tmp/poetry_cache' \
+    POETRY_NO_INTERACTION=1 \
+    POETRY_VIRTUALENVS_IN_PROJECT=1 \
+    POETRY_VIRTUALENVS_CREATE=1
 RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
 RUN curl -sSL https://install.python-poetry.org | python -
+# Pre-install common dev tools for faster iterations
+RUN pip install pytest-watch
+
+FROM dev AS test
 COPY Cargo.lock Cargo.toml pyproject.toml poetry.lock ./
 COPY src ./src
 COPY python ./python

scripts/test-docker.sh

@@ -0,0 +1,79 @@
+#!/bin/bash
+set -euo pipefail
+
+# Colors for output
+GREEN='\033[0;32m'
+BLUE='\033[0;34m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+IMAGE_NAME="pathoscope:dev"
+CONTAINER_NAME="pathoscope-test-$$"
+
+# Function to cleanup on exit
+cleanup() {
+    if docker ps -q -f name="$CONTAINER_NAME" | grep -q .; then
+        echo -e "${YELLOW}Cleaning up container...${NC}"
+        docker rm -f "$CONTAINER_NAME" >/dev/null 2>&1 || true
+    fi
+}
+
+# Set trap to cleanup on script exit
+trap cleanup EXIT INT TERM
+
+# Check if image exists, build if not
+if ! docker image inspect "$IMAGE_NAME" >/dev/null 2>&1; then
+    echo -e "${BLUE}Building dev image...${NC}"
+    docker build --target dev -t "$IMAGE_NAME" .
+fi
+
+# Parse command line arguments
+MODE="test"
+PYTEST_ARGS=""
+
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --watch)
+            MODE="watch"
+            shift
+            ;;
+        --shell)
+            MODE="shell"
+            shift
+            ;;
+        *)
+            PYTEST_ARGS="$PYTEST_ARGS $1"
+            shift
+            ;;
+    esac
+done
+
+case $MODE in
+    "shell")
+        echo -e "${GREEN}Starting interactive shell...${NC}"
+        docker run -it --rm \
+            --name "$CONTAINER_NAME" \
+            -v "$(pwd):/app" \
+            -w /app \
+            "$IMAGE_NAME" \
+            bash
+        ;;
+    "watch")
+        echo -e "${GREEN}Starting test watch mode...${NC}"
+        docker run -it --rm \
+            --name "$CONTAINER_NAME" \
+            -v "$(pwd):/app" \
+            -w /app \
+            "$IMAGE_NAME" \
+            bash -c "poetry install --no-root && poetry run maturin develop --release && poetry run pytest-watch$PYTEST_ARGS"
+        ;;
+    "test")
+        echo -e "${GREEN}Running tests...${NC}"
+        docker run --rm \
+            --name "$CONTAINER_NAME" \
+            -v "$(pwd):/app" \
+            -w /app \
+            "$IMAGE_NAME" \
+            bash -c "echo 'Running Rust tests...' && cargo test && echo 'Running Python tests...' && poetry install --no-root && poetry run maturin develop --release && poetry run pytest$PYTEST_ARGS"
+        ;;
+esac