v0.5

Changes

• Reworked command-line interface, long options have been added
• GGCAT dependency is directly retrieved from bioconda when installing via conda or singularity image
• muset/muset_pa: input list of file must now be provided via the --file option
• muset: option -i/--in-matrix now allows to also provide either a text matrix or a kmtricks output directory
• muset: default output is a unitig matrix containing only the abundance information
• muset: added --out-frac option to output a companion unitig matrix containing the fraction of unitig's k-mers within a sample
• muset: added -r/--min-utg-frac option to set average abundance only when k-mer fraction is greater or equal than the provided threshold (abundance is set to 0.0 otherwise)
• muset: added -u/--logan option to process input files as unitigs with abundance from Logan.
• muset: unless provided in input, kmtricks matrix is written in its own subdirectory
• muset: added --keep-temp parameter to keep some intermediate files that now are removed by default (the k-mer matrix built in the first step of the pipeline is not considered an intermediate file)
• Less verbose logging (logs of ggcat and sshash are written to a file and not displayed)
• Log file is now written in the output directory
• A reduced and modified version of kmtricks is now fully integrated within the source code
• Full C++ implementation of the tool (kmat_tools was still based on several C-like functions)
• Moved license from MIT to AGPL, as kmtricks is AGPL

Bug fixes

• muset_pa: the -r option did not work as expected for a value of 1.0