mumu

fast and robust C++ implementation of lulu, a R package for post-clustering curation of metabarcoding data

mumu is not a strict lulu clone. There is a bug in lulu that prevents some merging. Additionaly, mumu can chain merges, not lulu. This results in slightly more merging with mumu (by a few percent).

mumu is fully tested, with 145 carefully crafted individual black-box tests, covering 100% of the application-specific C++ code. Tests are written using common Unix/Linux shell utilities. Some C++ internal tests are also used (assertions), but these are only active at compile-time, or at runtime when compiling with the debug flag.

mumu uses C++20 features to make the code simpler, easier to maintain and to port to other systems. The downside is that using mumu requires a recent compiler and C++ libraries (GCC 10 or more recent, clang 17 or more recent). If your system only provides an older compiler, a recipe for a singularity/Apptainer/docker image is available.

About the name of the project, m is simply the next letter after l, hence mumu. Any similarity to actual words is purely coincidental.

Getting Started

• clone or download a copy the repository:

git clone https://github.com/frederic-mahe/mumu.git
cd ./mumu/
make
make check
make install  # as root or sudo

• dependencies are minimal:

  • a GNU/Linux 64-bit system,
  • make (version 4 or more recent),
  • a recent GCC compiler (GCC 10 or more recent, clang 17 or more recent),
  • GNU Awk and other GNU tools for testing

• run (see mumu --help and man mumu for details):

mumu \
    --otu_table OTU.table \
    --match_list matches.list \
    --log /dev/null \
    --new_otu_table new_OTU.table

• alternatively, build an Apptainer (ex-singularity) image for systems with older compilers:

# build image with singularity 3.8.5
# (Alpine edge with GCC 11.2 [2022-02-25])
singularity \
    build \
    --fakeroot \
    --force mumu-alpine.sif \
    mumu-alpine.recipe

# test (image is appr. 4 MB)
singularity run mumu-alpine.sif --help

Native compilation on Windows machine, as well as BSD systems is a work in progress.

wrapper

• Adrien Taudière (@adrientaudiere) published mumu_pq, a wrapper that allows to use mumu on phyloseq objects (R).

Roadmap

mumu is currently feature-complete (nothing is missing), but refactoring will continue and new versions will be released as soon as more C++ features (C++20 modules, C++23 ranges, etc.) are standardized and supported by compilers.

• replicate lulu's results,
• fix lulu's bug,
• allow chained merges,
• high software quality score (softwipe),
• allow empty input files,
• allow process substitutions (input/output),
• compile without warnings with GCC 10,
• compile without warnings with GCC 11,
• compile without warnings with GCC 12.2,
• compile without warnings with GCC 12.3 and GCC 13,
• compile without warnings with GCC 14 (alpha)
• compile with clang-17, 18 and 19 (std::ranges is not supported in clang-16),
• investigate the five minor failed tests when running on Alpine (as root),
• add a row of column header to the log file? (see issue #4)
• allow named pipes (input/output),
• test performances on ARM64 GNU/Linux (Raspberry),
• faster output with std::format (in 2024),
• native compilation on Windows (issue with getopt.h) ,
• native compilation on BSD (issue with the Makefile),
• native compilation on macOS

mumu releases follow the Semantic Versioning 2.0.0 rules.