VarSeq 1.3.5 Release Notes

New Features

Bugs Fixed

  • Fixed an issue that prevented the sample selector from being displayed when no affected samples exist.
  • Fixed export options to allow for non-visible fields to be included in the exported files.
  • Guard against crashing VSPipeline when passing invalid arguments.
  • Fixed field merge behavior and field upgrade behavior when importing more variants into an existing project.
  • Prevent merging variants across samples with sample type of “cancer” when the alternate alleles do not match.
  • Do not move DP and FILTER fields to sample level fields when there is more than one sample in a single source.
  • Add guard in dialog creation when computing Targeted Region Coverage to prevent crashes when using X-terminals or MacOSX.
  • Updated import default options to not make fields into lists unless it is required.
  • Fixed missing value reporting for sample Coverage Statistics.
  • Fixed issue with appending samples from multiple files when not all sample have data in each file.
  • Fixed merge behavior for read depth field when sample has multiple values at a site and advanced options for allelic primitives and multi-allelic split are selected.
  • Removed Chr M/MT aliasing to prevent merging these these two chromosomes from hg19 and 1kg assemblies when merging samples with different M/MT assemblies.
  • Fixed bug with allelic primitives and multi-allelic split not sorting variants after splitting. Ensures consistent results when reimporting the generated TSF file into a new project or merging new samples in.

Polishes

  • VSPipeline polishes:
    • Disabled instantiation of Titan Grid for table views to prevent crashes when importing millions of variants when visualization in a table is not required.
    • Include all fields when using a sample_fields_file on import, only require explicitly setting expected fields if the name is different than an one of the auto-detected names.
    • Dampened progress messages to only show non-redundant messages.
  • Removed status of import and algorithms from table view and moved to the toolbar on the main window.
  • Added “Delete Algorithm” option to download prompt for annotation sources.
  • When algorithms are added that require a download, show the download pending in the algorithm status list. If the download is canceled from the download manager, have the status dialog indicate a download is required.
  • Upgraded progress bar at the bottom of each window to be click-able and once expanded will show progress for each individual running task as well as the number of tasks waiting.
  • Added support for choices (combo) in report template params.
  • On import, when associating BAM files, the option for clearing the detected BAM files has been added. Click on the trash can to clear the list of BAM files. The auto-detection of sample name matching to BAM files has also been fixed to select BAM files that exactly match the sample name.
  • Changed field type for imported Identifier field to string array to help improve merging of data from multiple files.
  • When importing sample information from a text file any additional fields are imported in their original sort order instead of alphabetically.
  • Added VarSeq version to project log and reformatted log columns to improve legibility.
  • When merging samples ensure the “Samples” column is the first column in the sample table.
  • Updated Cancer Gene Panel report template
  • Updated ACMG Hereditary Gene Panel report template
  • Computing Alt Allele Freq (AF) separately for each sample so that different fields can be used in the formula for each sample.


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