halv2g 2024-07-18

hal2vg 1.1.6 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes, halMergeChroms, halUnclip,filter-paf-deletions count-vg-hap-cov
• Source Tarball: hal2vg-v1.1.6.tar.gz
  Install instructions in README.md

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

Release notes

• Update HAL to version with big bottomsegment path (adding support for pangenomes with > 500 genomes)
• Revert change in from v1.1.5 so that reference paths get SAMPLE#0#CONTIG rather than SAMPLE#CONTIG. Even though vg now (again) supports the latter, it is confusing wrt pan-sn standard and not supported in gfa w-lines.