RTG Core 3.11 / RTG Tools 3.11

[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 several 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:

* A new command, mapp, for mapping protein query sequences against a protein database. This command is complementary to the existing translated protein search of the mapx command, and usage is very similar.

* A new command for variant calling tumor samples when no matched normal is available. This command, tumoronly, uses a similar bayesian model as the existing somatic command (and several of the improvements made during development of the tumor-only calling scenario have also been applied to the somatic caller). See the user manual for more information.

* Several improvements to simulation tools, particularly oriented toward the simulation of variants within members of a pedigree. Quite substantial improvements to speed and memory use have been made, as well as adding the ability to utilize genetic map files to choose recombination sites when simulating children.

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.

### Basic Formatting and Mapping

* mapp: This new command is like mapx but for protein query sequences.

* map/mapf: Supports --format fastq-interleaved to allow mapping
  directly from paired end interleaved FASTQ files.

* mapx: The flag --min-dna-read-length has been renamed to
  --min-read-length (the old flag name will still work).

### Variant Calling and Evaluation

* tumoronly: New command for detection of somatic variants without a
  matched normal sample.

* all callers: The --Xformat-annotation flag can be used to enable
  output of additional FORMAT annotations ADF, ADR, ADF1, ADF2, ADR1,
  ADR2 containing allelic counts per arm and orientation that can be
  used for strand and arm-specific filtering.

* vcfeval: Fixed a rare race-condition crash that could occur when using
  --decompose.

* vcfeval: Added support for the summary metrics to report at
  user-selectable threshold criteria as an alternative to maximized
  F-measure, via the new flags --at-precision and --at-sensitivity.

* vcfeval/bndeval/cnveval: New flag --no-roc option to skip the creation
  of ROC data output files.

### Variant Processing and Analysis

* vcfsplit: This new command allows efficient splitting of a large
  multi-sample VCF into individual sample VCFs, as the input VCF is only
  read a single time. See the user manual for more information including
  supported command line options.

* vcfsubset: The values provided to --keep-sample and --remove-sample
  argument can now be a file, listing one sample name per line.

* vcfsubset: Significantly faster when subsetting samples from a VCF
  containing many input samples.

* vcfdecompose/vcfmerge: Smarter handling of Number=R INFO and FORMAT
  attributes during variant alteration.

* vcfsubset/vcfannotate/vcfmerge: These commands now accept the
  --bed-regions and --region flags to restrict processing to the regions
  of interest.

* vcfmerge: Fixed missed cases of allele set changes when warning about
  Number=R/A/G incompatibility.

* vcfmerge: Now has new flags for controlling the merging of multiple
  records at the same position. --no-merge-records disables all merging
  of multiple records at the same position, and --no-merge-alts disables
  merging of multiple records at the same position when the set of ALTs
  changes.

* vcfmerge: Now supports --no-header to suppress output of the VCF
  header.

* vcffilter: When filtering structural variant records, now takes the
  end position into account (if present) when applying region-based
  filtering via --include-bed, --include-vcf, --exclude-bed, and
  --exclude-vcf. (Note that --region and --bed-regions should not be
  used, as tabix indices are not aware of SV variant spans)

* vcffilter: Fixed JavaScript incorrectly interpreting the setting an
  ID, FILTER, or INFO field to the value '0' as clearing the field.

* vcffilter: JavaScript extensions can now write to stderr via the new
  error() function.

* vcffilter: JavaScript extensions can set new values for CHROM and POS.

* vcfdecompose: Improved the handling of AD and related fields when the
  set of ALT alleles changes.

### Other

* pedsamplesim: Simulation for many samples is now significantly faster
  and much more memory efficient.

* samplesim/denovosim/childsim: Reduced memory use.

* childsim: Initial support for employing genetic maps for LD-aware
  crossover point selection. This is enabled by the --genetic-map-dir
  flag, which specifies a directory containing genetic maps. See the
  user manual for more information on the genetic maps feature.

* simulators: Fixed a bug where a reference sequence name that looked
  like a region specification (e.g. "name:start-end") was inadvertently
  being interpreted as a genomic region, giving unexpected results.

* many: Updated the version of htsjdk that we use for SAM/BAM/CRAM
  processing, for improved support with newer Java versions.  Note that
  this new htsjdk is more restrictive in the names that can be used for
  reference sequences, so there is a chance that this will produce
  errors when processing old data that does not comply with the new
  naming constraints.

* sdfsubseq: When outputting a sub-sequence in FASTA/FASTQ format, the
  output sequence name has been changed from "source[start,end]" to
  "source:start-end", to comply with the new htsjdk sequence naming
  restrictions.

* many: Updated the JRE used in bundled builds to Zulu Community OpenJDK
  8u242.

* many: VCF header parsing is more lenient in the case where fields are
  declared multiple times.

* many: Fixed off-by-one error during single region based tabix VCF
  record retrieval where sometimes extra records abutting the requested
  region would be returned.

* many: VCF output is now VCFv4.2, and along with this several
  commands now use the new Number=R type.