rogtk 0.1.18

Rust-based genomics toolkit - high-performance backend for ogtk

rust ogtk

Installation

Standard installation:

pip install -e src/rogtk/
# or
maturin develop
# HTSLIB support
LIBCLANG_PATH=$CONDA_PREFIX/lib maturin develop --features htslib --release

With HTSlib support (for parallel BAM processing):

# Requires libclang
mamba install libclang
# Build with HTSlib feature
LIBCLANG_PATH=$CONDA_PREFIX/lib maturin develop --features htslib --release

Example

import rogtk.rogtk as rogtk
rogtk.sum_as_string(1, 2)

Useful references

setuptools Here one can control 'release' or 'debug' options

• bio::alignment
• seal alignment

Notes:

compilations not updating

The issue was that even after running maturin develop (or build with or
without --release) there were some .so files for the python package that were
not overwritten. That's why starting from scratch worked (once) since those
original files were gone. After I delete it (together with the __pycache__ dir)
the python side is up to date.