vg v1.28.0 - Acquafredda

Changes in this release:

• vg surject now supports GAF input with -G.
• vg surject can now take GAMP files from vg mpmap as input with -m
• vg surject is now substantially faster
• vg mpmap can now toggle between output formats (including single path and linear formats) with a single option. Some command line arguments have changed semantic meaning.
• vg mpmap's spliced alignment is now significantly more accurate.
• Divided handles with reversing self-edges no longer drop the edge.
• New path cover GBWT defaults: n = 64 for local haplotypes and 16 otherwise.
• Giraffe now properly sets paired end read cross-references
• vg deconstruct includes new option -a to process every snarl (instead of just top-level snarls)
• vg mpmap -m now correctly removes the full length bonus from reported scores
• -lpthread and -lm can be linked dynamically again
• Base quality-adjusted scoring now adjusts the full length bonus.
• Updated with less-patched Raptor dependency
• vg convert calls with -g as the last option will now convert to the correct format, not always Protobuf
• Now vg outputs raw handle graph files readable by libbdsg without the need for vg view -x/--extract-tag.
• vg msga handles terrible alignments better.
• vg giraffe can now output to SAM/BAM/CRAM directly
• Dependency retrieval no longer upgrades already-installed packages
• vg giraffe, vg map, vg mpmap, and vg surject now take a .dict file to order HTSlib sequence headers via --ref-paths.
• GaplessExtender no longer matches non-ACGT characters.
• SAM header lines in dict files are now tested
• vg add now supports overlapping reference paths, as in Cactus graphs

New and Updated Submodules

• libvgio, raptor, dozeu, and vcflib have been updated.
• htslib has been removed. We now use the HTSlib from vcflib.