hal2vg 2024-08-12

hal2vg 1.1.8 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-v1.1.8.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

• clip-vg -c option added to not fail when trying to forwardize reference paths with cycles

halv2g 2024-07-23

hal2vg 1.1.7 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-v1.1.7.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

• clip-vg sped up on graphs with high path depth.

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.

hal2vg 1.1.5 2023-08-08

hal2vg 1.1.5 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-v1.1.5.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

• Revert change in from v1.1.4 now that vg once again works with SAMPLE#CONTIG path names via the v1.50.1 patch release.

hal2vg 1.1.4 2023-08-02

hal2vg 1.1.4 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-v1.1.4.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

• Make sure reference paths without haplotype information get HAPLOTYPE=0 instead of HAPLOTYPE=NO_HAPLOTYPE. This fixes compatiblity with vg 1.50.0 which is more strict about these things.

hal2vg 1.1.3 2023-03-14

hal2vg 1.1.3 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-v1.1.3.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

• Fix bug in count-vg-hap-cov where zero-values were not properly handled in some places.

hal2vg 1.1.2 2022-11-21

hal2vg 1.1.2 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-v1.1.2.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

• Add -s option to filter-paf-deletions to prevent small contigs from making big deletions.

hal2vg 1.1.1 2022-11-09

hal2vg 1.1.1 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-v1.1.1.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

This release patches a libhandlegraph bug that caused the path metadata library to abort with errors for no reason.

hal2vg 1.1.0 2022-11-07

hal2vg 1.1.0 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-v1.1.0.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

• count-vg-hap-cov added to make coverage stats table
• hal2vg and clip-vg updated to use vg's new PathMetadata interface where possible.

hal2vg 1.0.17 2022-04-12

hal2vg 1.0.17 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 and filter-paf-deletions
• Source Tarball: hal2vg-v1.0.17.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

• Fix numerous bugs in filter-paf-deletions that prevented it from effectively doing its job
• Add -o option to clip-vg to report clipped regions in a BED file
• Add -a option to clip-vg to consider regions unaligned if they don't align to given prefix