RTG Core 3.13 / RTG Tools 3.13

[RTG Announcements]

Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core, and our utility package, RTG Tools.  This release includes new features and commands, along with the usual assortment of minor features and bug fixes. Several of these result in command line arguments or changes to program outputs, so check existing scripts for compatibility before upgrading. Larger changes of note:

* RTG Core is now released under the BSD license, there are no longer separate non-commercial and commercial releases.

* A new command cnveval assists when evaluating CNV calling algorithms. This tool uses many of the same conventions as vcfeval and is supported by vcf2rocplot/rocplot.

* Improved ROC curve slicing and dicing.

* The minimum Java version required is now Java 11. We explicitly include the Nashorn JavaScript interpreter which was removed from Java 17 onwards, in order to retain vcffilter JavaScript capability in these newer Java releases.

RTG Core 3.13 may be downloaded from https://github.com/RealTimeGenomics/rtg-core/releases/latest or build from the updated source code at https://github.com/RealTimeGenomics/rtg-core.

RTG Tools 3.13 may be downloaded from https://github.com/RealTimeGenomics/rtg-tools/releases/latest or build from the updated source code at https://github.com/RealTimeGenomics/rtg-tools.

There have been many other minor improvements and feature additions. Detailed changes are listed below by area.  For more information on new features, see the RTG Operations Manual.


### Variant Calling Evaluation and Analysis

* cnveval: A new tool to evaluate CNV calls with respect to a truth set. See
  the user manual for more information on how to use and options.

* vcf2rocplot: Add support for cnveval annotated VCF files as input.

* vcfeval/cnveval/vcf2rocplot: New flag --roc-cross-join to allow easily
  outputting ROC curves corresponding to the intersection of selected criteria
  (e.g: snps within BED file x).  See the user manual for more
  information. Contributed by Ricky Magner.

* vcfeval/cnveval/vcf2rocplot: New flag --at-score for selecting summary
  metrics with respect to a user specified VCF score field value.

* vcfeval/cnveval/vcf2rocplot: --vcf-score-field can now take a JavaScript
  expression for custom dynamic score criteria.

* vcfeval: Gracefully handle malformed VCF that have an ALT allele the same as
  REF.

* vcfeval: Correct VCF field definition for CALL_ALTERNATE and BASE_ALTERNATE.

* bndeval: Fix behaviour when sequence names contain ":".

* bndeval: Add the various --at-* and --roc flags for consistency with other
  evaluation tools.

* rocplot: Add the ability to show points (via UI and --points flag).

* rocplot Improve error messages when running in a headless environment or
  without fonts installed.

* vcffilter: Gracefully handle malformed QUAL values.

* vcffilter: Improve --javascript differentiation between inline and
  file-based JavaScript.

### Formatting, Mapping and Aligning

* map / coverage: When running in an environment without fonts, skip report
  generation.

* coverage: Support coverage regions larger than 2^31.

* sammerge: Fix a problem where taking a subsample of a previously subsampled
  file had very poor statistical behavior (typically 0% or 100% of reads would
  be retained irrespective of the subsample fraction or seed). Note: this
  change means that a different subsample will be produced compared to
  previous releases (even when the same seed is specified).

### Other

* rtg: The launcher script supports newer macbooks with Apple silicon.

* index: Support indexing .gvcf.gz files.