RTG Core 3.8.2 / RTG Tools 3.8.2

[RTG Announcements]

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.8.2. The changes in this version are listed below.  Commercial users 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 updated source code on github at https://github.com/RealTimeGenomics/rtg-core.

We have also produced updated builds of our utilities package, RTG Tools 3.8.2, which is made freely available for non-commercial or commercial use alike. More information and download links are available from our website at http://realtimegenomics.com/products/rtg-tools or build from the updated source on github at https://github.com/RealTimeGenomics/rtg-tools.

RTG Core 3.8.2 (2017-06-20)

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This release primarily includes bugfixes and minor improvements:

* vcfeval: Records where the REF/ALT contain bases not permitted by the

  VCF specification are now skipped (and reported in the log) rather

  than terminating execution.

* vcfeval: (`combine` and `ga4gh` output modes only) These modes were

  inserting a redundant VCF header entry containing the command line,

  which has been removed.

* vcfeval: GA4GH output mode now supports loose positional matching of

  variants (within +/-30bp by default, and adjustable via

  --Xloose-match-distance).

* many: Prevent number formatting issues in non-English locales. The

  locale is now forced to US.

* many: Some commands were not appending gzip termination blocks to VCF

  outputs, which could result in subsequent warning messages being

  produced by some third party tools.

* many: Improve the consistency of exception handling in cases where the

  exception is thrown in a worker thread.

* many: Attempting to supply file lists via shell process redirection

  would fail in non-obvious ways. File lists from process redirection

  are not currently supported and are now checked for up-front.

* minor: When setting up rtg bash tab completion, issue a warning if an

  incompatible completion function has already been installed. (This can

  happen on some linux distros if you have the system `bash-completion`

  package installed and attempt to tab-complete rtg before installing

  rtg bash completion.)

* minor: Fix a typo in the example configuration settings in rtg.cfg

  (specifically, RTG_JAVA_OPTS was incorrectly listed as

  RTG_JAVA_OPTIONS).