hal2vg 1.0.16 2021-12-20

hal2vg 1.0.16 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-v1.0.16.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 clip-vg -e to properly forwardize self-loops -- a bug previously left out edges in some cases leaving invalid paths
• Add filter-paf-deletions to remove mappings that would induce large deletions in resulting sequence graph

hal2vg 1.0.15 2021-09-03

hal2vg 1.0.15 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 and halUnclip
• Source Tarball: hal2vg-v1.0.15.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

Adds halUnclip to insert centromeres (or any sequence chopped out using cactus-preprocess) back into the hal file from a given set of fasta files. Alignment blocks are unchanged, but sequences with _sub_x_y suffixes get glued back together and renamed.

hal2vg 1.0.14 2021-07-30

hal2vg 1.0.14 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.14.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

Why so many releases? Because Cactus's release and Docker build are pinned to binary hal2vg releases, so every update required for Cactus necessitates a release here. Never thought there would be so many...

• clip-vg reverted back to the state that Cactus remains pinned on (equivalent to v1.0.11)
• nested subpath naming support added to hal2vg

hal2vg 1.0.13 2021-07-21

hal2vg 1.0.13 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.13.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 -s option generalized to accept a minimum fraction of softmasked bases

hal2vg 1.0.12 2021-07-14

hal2vg 1.0.12 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.12.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 -s option added to restrict clipping with -u (unaligned) to softmaksed bases

hal2vg 1.0.11 2021-05-17

hal2vg 1.0.11 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.11.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 -d option added to filter out paths (and nodes unique to them) with given prefix (used in pipeline to filter out minigraph segments)

hal2vg 1.0.10 2021-05-06

hal2vg 1.0.10 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.10.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

• hal2vg will automatically translate _sub_X_Y into [X-Y]. The former is what cactus-graphmap-split uses to mark subpaths in HAL (without using special characters that annoy hubs). The latter is what vg expects.

• clip-vg updated to properly resolve subpath naming when splitting. Note: it is not fully handled in the bed input (so a bed file with chr1 would not be applied to a path with chr1[100-300])... but the bed logic is currently not part of the pipeline...

v1.0.9: Merge pull request #43 from ComparativeGenomicsToolkit/chop

hal2vg 1.0.9 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg, halRemoveDupes and halMergeChroms
• Source Tarball: hal2vg-v1.0.9.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

halMergeChroms binary added. It can be used to merge separate chromosome hal files, such as those produced by the Cactus Pangenome Pipeline, into a single file.

hal2vg 1.0.8 2021-03-08

hal2vg 1.0.8 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg and halRemoveDupes
• Source Tarball: hal2vg-v1.0.8.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 generalized to remove unaligned gaps (-u) without needing a bed file. Also, when a reference prefix is given (-e) it will make sure all steps in reference paths are in forward orientation (to be compatible with rGFA). Also, when a reference prefix is given, connected components that are not anchored to any reference paths are cut by default (keep them with -n)

hal2vg 1.0.7 2021-02-09

hal2vg 1.0.7 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg and halRemoveDupes
• Source Tarball: hal2vg-v1.0.7.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

halRemoveDupes fixed to remove necessary vertical edges