RTG Core 3.4.1 / RTG Tools 3.4.1

[Len Trigg]

We have two new releases available today!

The first of these is for our full mapping / variant detection / metagenomic analysis suite, 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...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
--------------------------------

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.

[Len Trigg]

(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 http://realtimegenomics.com/products/rtg-core-downloads. Non-commercial users can download the update from our website at http://realtimegenomics.com/products...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
--------------------------------

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.

[Len Trigg]

New stable releases are now available 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 3.4.3, the changes compared to RTG Core 3.4.2 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...non-commercial or build from the updated source on github.

We have also produced updated builds of our utilities package, RTG Tools 3.4.3, 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

RTG Core 3.4.3 (2015-03-19)
---------------------------

This is primarily a bugfix release:

* map: Fixed a crash that could occur when mapping without any sample
sex specified but when using a reference genome containing
chromosome sex information.

* somatic: Fixed a rare crash that could occur when calling across
blocks of Ns when the only hypothesis presented by the reads was a
deletion of sufficient length.

* vcfeval: Improved handling in situations where variants are so dense
within a region that there are too many possible haplotypes to
feasibly resolve. Previously operation would abort, now a warning is
issued and both baseline and called variants within that region are
ignored.

[Len Trigg]

New stable releases are now available which include minor improvements and bug fixes. In particular, heavy users of vcfeval or rocplot will benefit from updating to the new release.

The first of these is our full analysis suite, RTG Core 3.4.4. 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...non-commercial or build from the updated source on github.

We have also produced updated builds of our utilities package, RTG Tools 3.4.4, 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


RTG Core 3.4.4 (2015-03-20)
---------------------------

This release primarily includes bugfixes and minor improvements:

* vcffilter: The --keep-filter and --remove-filter options now
recognize '.' as a value that can be filtered on. For example, to
keep only variants that have a FILTER column that corresponds to
non-filtered, use -k . -k PASS.

* vcfeval: Enabled skipping over more extremely complex edge cases
that could otherwise cause exceedingly long computation times.

* rocplot: Add the ability to click on a point within the graph to
show in the status bar the true positives / false positives /
precision / sensitivity scores equivalent to that point.

* rocplot: The individual curve sliders that can be used to simulate
the effects of various threshold cut-offs did not work very well for
curves corresponding to scores with very wide ranges and non-uniform
distribution (such as GQ and QUAL often are). These sliders are
improved so they work better with these curves, and adjusting the
sliders also displays accuracy metrics in the status bar, to aid in
threshold selection.

* rocplot: It was sometimes possible to zoom in to negative
coordinates.

* aview: Fix display of BED regions that do not have a region name
contained within the BED file.

[Len Trigg]

New stable releases are now available which include minor improvements and bug fixes. In particular, those using the somatic caller or vcfeval/rocplot will benefit from updating to the new release.

The first of these is our full analysis suite, RTG Core 3.4.5. 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...non-commercial or build from the updated source on github.

We have also produced updated builds of our utilities package, RTG Tools 3.4.5, 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


RTG Core 3.4.5 (2015-05-22)
---------------------------

This release primarily includes bugfixes and minor improvements:

* somatic: If the input mappings contained unmapped records with
assigned coordinates, these were erroneously being included as
evidence, resulting in spurious calls when calling with non-zero
contamination specified.

* vcfeval: Implemented an algorithm optimization that permits the
evaluation of situations that previous versions would skip over as
being too-complex (primarily where there were long runs of abutting
variants), as well as yielding a general speed improvement.

* avrbuild: Add checks that the user has specified at least one VCF
annotation for use as a predictor attribute.

* vcffilter: Fix bug when filtering on the FILTER declared last in the
header for files that contained inadvertent duplicate FILTER header
declarations or containing an explicit declaration for the PASS
filter.

* rocplot: Minor improvements to file chooser handling, and also
include F-measure as an additional accuracy statistic in the status
bar.