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Old 03-01-2015, 07:05 PM   #2
Len Trigg
Registered Vendor
Location: New Zealand

Join Date: Jun 2011
Posts: 29
Default RTG Core 3.4.2 / RTG Tools 3.4.2

(Adding here rather than making a new thread for this point release)

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 Non-commercial users can download the update from our website at 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

Release notes for RTG Core 3.4.2

This is primarily a bugfix release:

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

* 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

* 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.
Len Trigg, Ph.D.
Real Time Genomics
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