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vg 1.12.0 - Parolise
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@adamnovak adamnovak released this 19 Nov 23:21
· 9793 commits to master since this release
v1.12.0
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Learn about vigilant mode.

Docker image: quay.io/vgteam/vg:v1.12.0

This release includes:

  • Ability to delay population scoring until after rescue in vg mpmap
  • Improvements to Doxygen documentation generation
  • Correct parsing of SVLEN and END fields for structural variants in VCF files
  • Snarl-based distance indexing for clustering MEMs
  • An initial Target Value Search implementation for distance computation in DAGs, with an A* implementation
  • Improved mpmap stability
  • Support for lower-case characters in the reference given to vg construct
  • Ability for vg filter to defray away entire reads
  • Ability to index an XG to GCSA without going through a VG file
  • Much faster path insertion in VG::edit
  • Checks for cyclic VCF reference paths in variant calling
  • Ability to simplify out rare variants with vg simplify
  • More efficient Clang build process for repeat builds
  • Ability to suppress missing variant warnings when building a GCSA index
  • Bugfix for calling long indels with multi-node alleles
  • Fix for a bug that corrupted alt paths split across chunks when building the xg
  • Improved Basic Operations tutorial
  • Support for calling inversions and some other well-behaved non-ultrabubbles
  • Ability to run vg call without passing the base graph
  • SV recall improvements in vg call
  • A watchdog to find slow reads in vg mpmap
  • Simplifications to the Mac Travis build process
  • Suppression of empty calls
  • Refactored indexing code that can work on GAM and VG files.

New System Dependencies

None

New and Updated Submodules

The following submodules have been updated: vcflib,

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