vg 1.10.0 - Rionero

Docker image: quay.io/vgteam/vg:v1.10.0-0-ga4811915-t226-run

This release includes:

• A new backwards-compatible file format. Most files, including .vg and .gam, are now blocked-gzip compressed to permit random access.
• GAM sorting and indexing (with vg gamsort) for efficient random access to reads in GAM files.
• A new "xdrop" aligner backend.
• Support for repeated read annotations.
• Improvements to the vg mpmap aligner and its MAPQ computation.
• Fixes to vg paths so paths extracted from a GBWT are now valid.
• Thread name listing support in vg paths.
• An improved vg augment interface.
• Faster VCF parsing during graph construction and GBWT indexing.
• Correct semantics for vg snarls --max_nodes.
• Ability to get edge counts via the xg::XG public interface.

Breaking Changes

• vg find no longer has a -i/--alns-in option. You should use --alns-on instead; it's much simpler to think about.
• vg msga behavior has changed.

New System Dependencies

None

New and Updated Submodules

The vcflib and htslib submodules have been updated.

The dozeu and libdeflate submodules are new.

The htslib submodule has moved to https://github.com/vgteam/htslib. Developers will need to do a git submodule sync.

All Changes