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TRGT v1.0.0
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@tmokveld tmokveld released this 02 May 14:09
· 6 commits to main since this release
v1.0.0
e231f95

Summary of changes:

Breaking changes:

  • TRGT and TRVZ are now merged into a single binary. Users need to run subcommands trgt genotype and trgt plot for genotyping and visualization, respectively.
  • A padding base is now automatically added to all genotyped allele sequences in the VCF file, ensuring better compliance with VCF standards and handling of zero-length alleles.

Other changes:

  • Added a new subcommand trgt validate. This command allows for validation of a repeat catalog against a given reference genome and reports statistics for any malformed entries.
  • Lower memory footprint: Better memory management significantly reduces memory usage with large repeat catalogs.
  • Updated error handling: Malformed entries are now logged as errors without terminating the program.
  • Added shorthand CLI options to simplify command usage.

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

Note: TRGT is still in active development. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binaries are available below.

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