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@adamnovak adamnovak released this 16 Jul 19:14
· 10667 commits to master since this release
v1.9.0
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Docker image: quay.io/vgteam/vg:v1.9.0-0-g3286e131-t206-run

This release includes:

  • No more CLI tests for vg deconstruct (as the command is still under development)
  • GFA output streaming, and a new GFA importer
  • A new, as-yet-unused distance estimator intended for paired-end mapping
  • mpmap tuning improvements and new options
  • Functional support for building graphs from structural-variants in VCFs (vg construct -S)
  • An increased Protobuf message size limit, and improved constructed graph chunking, which should solve most message-too-big-related errors
  • Mitigations for strand and position bias when choosing between equivalent alignments
  • Faster and more accurate haplotype thread generation for GBWT construction
  • Random, samtools-compatible downsampling of alignments with vg filter -d
  • Support for circular paths in the xg format and tools
  • Better error detection for invalid option arguments
  • More version and build metadata in vg version
  • Bugfixes and improvements to the build process:
    • More correct net graph traversals
    • Addition of missing return statements to alleviate many potential crashes
    • Correct pairing of reads dumped from the buffer in mpmap

Breaking Changes

  • This release generates XG version 10. It can read previous versions, but new indexes cannot be read by previous versions.
  • The behavior of the new GFA importer differs form previous versions. Also, it validates GFA input more aggressively, and overlaps that are longer than sequences are no longer permitted.
  • Previously, all whitespace was accepted as a GFF file separator. Now only tabs (which the spec requires) are accepted.
  • vg is more conservative about its argument parsing. Numbers with trailing garbage after them, or decimals on integer parameters, will now generally be rejected with an error message, instead of being silently accepted.
  • The vg version output looks different. Anyone who may be parsing it will need to adapt their code.

New Dependencies

None

New and Updated Submodules

The fastahack, gbwt, gcsa2, gfakluge, and vcflib submodules have all been updated.

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

All Changes

Assets 3
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