RTG Core 3.4.1 / RTG Tools 3.4.1

[RTG Announcements]

We have two new releases available today!

The first of these is RTG Core 3.4.1, which includes bug fixes as well as improvements to documentation and error handling, so users should update to the new release.  The changes compared to RTG Core 3.4 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 on github.

The second release is our utilities package, RTG Tools 3.4.1, which is made freely available for non-commercial or commercial use alike. This version has many improvements since the previous 1.0 version. More information and download links are available from our website at http://realtimegenomics.com/products/rtg-tools

Release Notes for RTG Core 3.4.1

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This is primarily a bugfix release:

* snp/family/population: Fixed a crash that could occur when calling

  across blocks of Ns when the only hypothesis presented by the reads

  was a deletion of sufficient length.

* snp/family/population: When calling across blocks of Ns, under some

  circumstances no variant call would be made.

* snp/family/population: Extremely large GQ and DNP FORMAT values are

  now capped at the maximum permitted by BCF (2147483647). Previously,

  values above this could occasionally trigger a crash.

* wrapper: Changes to streamline the first run configuration and to

  bring Unix and Windows wrappers closer to equivalence, including

  clearer instructions of how to customize initial

  configuration. Crash reporting is now opt-out rather than opt-in.

* unix wrapper: When the operating system fails to allocate memory to

  the JVM (typically due to other memory-intensive processes running

  on the same machine) this is now presented as a user message, rather

  than triggering a crash report talkback.

* many: input list files are now validated during loading rather than

  after loading the list. This gives much better error handling in the

  case where a user accidentally gives the name of an alignment file

  as an input list file.

* Other improvements and cleanups to documentation.