pangenome/pggb: pggb 0.5.4 - Fatica

The main power-ups in this version are in smoothxg:

• the partial order alignment (POA) is executed on unique sequences by duplicating the POA blocks before their alignment, strongly improving the performance;
• final graphs no longer contain uncovered edges, leading to a bit simpler graph topologies.

Moreover, we update vcfwave in order to correctly manage inversions in the VCF file normalization.

Updating pggb's components, we fixed several bugs and now the log files will be a bit less verbose (in order to avoid gigabyte-scale logs for long runs).

This introduces:

• update smoothxg to perform the POA on unique sequences #280 by @AndreaGuarracino
• fix versioning #282 by @AndreaGuarracino
• support metric parameter suffixes #290 by @ekg
• update singularity syntax in the README.md #293 by @petersudmant
• add tools for gfa2evaluation in Dockerfile #295 by @subwaystation
• update smoothxg to avoid uncovered edges #304 by @AndreaGuarracino
• update pggb's components #281, #283, #285, #286, #296, #303 by @AndreaGuarracino
• Update vcflib to get the fixed vcfwave #311 by @AndreaGuarracino