RTG Core 3.4.2 / RTG Tools 3.4.2

[RTG Announcements]

Today we have made new stable releases which include bug fixes as well as improvements to documentation and error handling, so users should update to the new release.  

The first of these is RTG Core 3.4.2, the changes compared to RTG Core 3.4.1 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. 

We have also produced updated builds of our utilities package, RTG Tools 3.4.2, 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

Release notes for RTG Core 3.4.2

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This is primarily a bugfix release:

* somatic: Fix a crash that could occur when calling across Ns in the

  reference.

* snp/family/population/somatic: Under some circumstances, I/O

  exceptions could trigger a crash talkback rather than being

  presented as a regular user-level error message for the user to act

  on.

* chrstats: Fixed inconsistent output destinations between

  single-sample vs multiple sample case, and do not create a log file

  for this command in the current directory.

* chrstats: Detect when the user has not set up a reference SDF with

  chromosome specification information and provide an appropriate

  error message indicating how to correct the situation.

* many: Improved error handling when requesting indexed region

  retrieval of BED/VCF/SAM files for coordinates outside the range

  that can be addressed by tabix/bam indexes.

* many: Improved error handling when errors are encountered during VCF

  header parsing, providing more information on where the problem was.

* many: Improved error handling when errors are encountered during

  tabix indexing.