VarSeq 1.3.5 Release Notes
- 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.
- 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.