v3.1.0 - Fagiolo

vgan 3.1.0 - Fagiolo includes fixes for read mapping errors in all three subcommands. Please update all graph files with the new versions from our FTP server (description for each subcommand in the wiki).

vgan 3.1.0 now includes a standalone gam2prof command. It follows the same functionality as bam2prof for graph alignment files (game files). The manual can be called using vgan gam2prof

HaploCart had no changes but requires a re-download of its graph files for this version.

Additionally, we added a few new functionalities to euka and soibean.
euka:

1. --maxBins allows the user to adjust the number of bins required to have read mappings for the evenness of coverage estimation, making euka more sensitive.
2. -M option allows the use of alternative minimizes for mapping with vg giraffe
   soibean:
3. --alignment-detail will print out a tsv file with all alignments to each node ID
4. --pathThres In addition to the previous command, the user can define which alignments should be printed out, e.g. --pathThres 1 will print out only alignments that map to a signature node (show a unique variance for one of the paths present in the graph).
5. -M option allows the use of alternative minimizes for mapping with vg giraffe

Last, euka and soibean no longer require the data structure of the share/vgan/damageProfils. When ancient damage profiles are provided the likelihoods are adjusted, otherwise the default of ancient damage probability is set to 0.