RTG Core 3.5.1 / RTG Tools 3.5.1

[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 3.5.1. 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 3.5.1, 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 3.5.1 (2015-09-07)

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This release primarily includes bugfixes and minor improvements:

* coverage: Fix an exception that could occur if running with a

  reference SDF supplied that had chromosomes in a different order

  compared to the BAM sequence dictionary (typically this could occur

  when running coverage on third-party BAMs)

* extract: When extracting multiple regions these regions are now

  sorted.

* vcfeval: When an entire chromosome contained only baseline or only

  called variants, the summary statistics for FP/FN were not being

  incremented correctly.

* vcfeval: Fixed a case where path-finding could get confused and drop

  variants.

* vcfeval: Speed improvement in post-processing.

* many: Improved error reporting for commands that involve processing

  multiple BAM files, so that the name of the particular file causing

  the problem is included.

* wrapper: Fixed the java version number check so that it works

  correctly with openjdk 1.8