CLARC v1.2.0 - Revised tool

As part of manuscript revisions the kind reviewers have given us great suggestions that we have implemented in this new release of CLARC.

New Features

We have introduced support for running CLARC on PPanGGOLiN results using the -ppanggo flag
Users can now specify the maximum number of cores to use with the --max_cores flag. If a value for --max_cores is not specified, then CLARC will use all available cores.
Added the --linkage_cut flag which allows users to adjust the linkage threshold. For example, setting --linkage_cut 0.01 will consider COGs that co-occur in <1% of cases.
Added the --connection_cut flag which allows users to define how connected clusters should be. Setting --connection_cut 0.90 will select clusters that are at least 90% connected instead of requiring full connectivity.

To enhance the user experience, CLARC now automatically generates the “needed_sample_names.txt” file if it is not provided. This file is created by extracting and formatting the names of all samples used in the input pangenome analysis. If the user wishes to focus the analysis on a specific subpopulation, they can still provide a custom “needed_sample_names.txt” file containing only the relevant samples, as in previous CLARC versions.
Now the output directory is created if it is not specified and warns the user if it already exists.
We've optimized the source code so CLARC is now more computationally efficient and runs considerably faster; Now the linkage, BLASTN, and functional annotation steps are properly parallelized. We have also made the final clustering algorithm considerably more efficient by building a lookup table to summarize the clusters instead of using a loop.