RTG Core 3.12 / RTG Tools 3.12

[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 features of note:

* Several improvements to vcfeval, which now includes the ability to match variant calls of non-diploid genomes and to output additional ROC stratifications, including user-defined custom JavaScript stratifications.

* A new command vcf2rocplot for aggregating and regenerating ROC information from one or more vcfeval annotated evaluation outputs. This is particularly useful for aggregating results from multiple samples or re-evaluating with respect to different score criteria or stratifications.

Commercial users of RTG Core may download the update from our website at http://realtimegenomics.com/products/rtg-core-downloads. Non-commercial users can download the update from our website at http://realtimegenomics.com/products/rtg-core-non-commercial or build from the source on github at https://github.com/RealTimeGenomics/rtg-core.

Users of RTG Tools, which is made freely available for non-commercial or commercial use alike, can download the new version from our website at http://realtimegenomics.com/products/rtg-tools or build from the source code on github at https://github.com/RealTimeGenomics/rtg-tools.


Detailed changes are listed below by area.  For more information on new features, see the RTG Operations Manual which is included within the distribution as HTML and PDF.

### Variant Calling and Evaluation

* calling: Fixed a rare exception during variant calling arising from
  attempted output of an empty region when calling a single base region
  with --all mode.

* vcfeval: Support for the comparison of sample calls with ploidy greater
  than 2. This is enabled via the new flag --sample-ploidy N (the GT of
  any calls without the specified ploidy will be ignored). Note that as
  the ploidy increases the search space of possible phasings can expand
  significantly, which may cause long run times and/or regions where
  vcfeval cannot fully evaluate the alternatives.

* vcfeval: New flag --roc-subset to allow stratifications by common
  variant types. While the default is to produce SNP and non-SNP
  breakdowns, this flag allows a couple more presets.

* vcfeval: New flag --roc-regions to allow stratification by overlap with
  regions loaded from BED file, for example the stratification regions
  provided by the Genome in a Bottle project.

* vcfeval: New flag --roc-expr to allow custom stratifications defined by
  a user-supplied JavaScript expression, for example to stratify by depth
  of coverage during calling, variant allelic fraction or other
  annotations present in the input VCFs. For more information see the
  user manual.

* vcf2rocplot: New beta command to produce a rocplot-compatible data file
  from one or more vcfeval output directories. See the user manual
  for more information on usage.

* rocplot: User-selectable preset palettes are available via
  --palette. In particular, several of the palettes are more color-blind
  friendly than the default palette.

* rocplot: Fix graph bounds maintenance when switching between ROC/PR.

* rocplot: Unified the GUI vs non-GUI plot styles. Both default to the
  "pretty" version with background gradient etc (previously the GUI
  default), and a new flag --plain switches to the plain style (which was
  previously the non-GUI default).

* rocplot: (GUI) Supports loading ROC data files by drag and drop into
  the graph or curve configuration widget areas.

* rocplot: PNG images now include rocplot command line as image metadata
  for future reference. A new flag --cmd when run on a previously saved
  rocplot PNG image containing this metadata will display the rocplot
  command line.

### Variant Processing and Analysis

* vcffilter: Javascript filters can now easily test for genomic range
  overlaps with ranges loaded from BED or VCF. See the user manual for
  more information.

* vcfdecompose: Graceful error handling of the case where the supplied
  SDF does not contain a reference sequence named in the VCF.

* vcfmerge: Ensure that when merging files with and without GT that the
  GT is maintained as the first FORMAT field, as per VCF specification.

### Other

* docker: Include fontconfig in docker images so that image writing
  during rocplot and other command reports doesn't crash.

* childsim: Better detection of inconsistent sex declarations in VCF
  header / pedigree.

* samplesim: With appropriate reference.txt configuration specifying
  expected ploidy, now allows the simulation of higher ploidies.

* many: Improved the handling of SAM records containing invalid CIGAR
  fields.

* misc: Updated htsjdk to 2.23.0.

* misc: Updated the JRE used in bundled builds to Zulu Community OpenJDK
  8u282.

* misc: Compatibility testing with JDK 15. Note that JDK15 removes the
  nashorn JavaScript engine, which disables the JavaScript functionality
  of vcffilter, vcfeval, vcf2rocplot unless your JVM has been augmented
  with the GraalVM JavaScript engine.