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...