hal2vg 1.0.6 2021-02-08

hal2vg 1.0.6 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-v1.0.6.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

halRemoveDupes added to clean out duplications from a reference genome. There are a tiny number of these, and I still don't know exactly why.

clip-vg gets new option to modify path names to make them easier to import into W-lines.

hal2vg 1.0.5 2021-02-02

hal2vg 1.0.5 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg
• Source Tarball: hal2vg-v1.0.5.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

clip-vg generalized to be able to clip by length (instead of bed) as well as to allow partial clips (ie leave nodes that aren't unique to clipped interval, instead of aborting)

hal2vg 1.0.4 2021-02-01

hal2vg 1.0.4 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg); also clip-vg
• Source Tarball: hal2vg-v1.0.4.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

This release includes the clip-vg binary in addition to hal2vg. It can be used to clip regions from a BED file out of a graph (providing they are not aligned).

v1.0.3: Merge pull request #33 from ComparativeGenomicsToolkit/pinch-snps

hal2vg 1.0.3 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg)
• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x clip-vg)
• Source Tarball: hal2vg-v1.0.3.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

This release includes the clip-vg binary in addition to hal2vg. It can be used to clip regions from a BED file out of a graph (providing they are not aligned).

hal2vg 1.0.2 2020-12-01

hal2vg 1.0.2 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg)
• Source Tarball: hal2vg-v1.0.2.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

This release is roughly 3X faster than previous releases.

hal2vg 1.0.1 2020-09-07

hal2vg 1.0.1 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg)
• Source Tarball: hal2vg-v1.0.1.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 contains a bugfix required to use the subsetting options such as --targetGenomes and --ignoreGenomes without crashing.

hal2vg 1.0.0 2020-08-19

hal2vg 1.0.0 is available in the following forms:

• Static Linux Binary: hal2vg (Don't forget to mark it executable: chmod +x hal2vg)
• Source Tarball: hal2vg-v1.0.0.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

This release uses Hal2vg's Pinch Graph library to create the sequence graph.

Notable Changes:

• Bespoke STL-based structures and algorimths replaced with Pinch Graph library
• SNPS are aligned through using the column iterator instead of tables
• Much more performant than original implementaiton, but still only tested on smallish graphs

hal2vg v0.1: Original hal2sg-based logic

This is a snapshot of the hal2vg logic as it was before being completely re-written to use Cactus's Pinch Graph library.

It works reasonably well on small graphs, and could be useful to sanity check the newer logic. It also provides various subsetting and filtering options that aren't yet available in the new version.

But.. it scales very badly, especially in the degree of the HAL tree nodes, making it unusable for a lot of the whole-genome data we're now interested in.