SVS 8.4.2 Release Notes

New Features

Bugs Fixed

  • Import VCFs and Variant Filesbug fixes:
    • Fixed import of additional spreadsheets for the Mac version of SVS.
    • Fixed issue with specifying affection status from a sample entity text file.
  • Prevent progress dialog from popping up when a Python script prompt dialog is open if a progress loop was running before the dialog was created.
  • Prevent crash when opening the Data Source Library if the source tree contains a local source that was watching a folder that was deleted while the program was closed.
  • Fixed issue merging marker maps fields with a case mismatch in the name when outputting results for Variant Classification.
  • Make sure that all executables have the correct permissions for Linux x64 and RHEL builds (aria2c, assistant, etc.)
  • In GenomeBrowse for BAM alignment plots, remember the edited value for Filter Multi-Mapped Alignments when the option is checked and unchecked.
  • Fixed Import Illumina Final Report python api to not crash when creating the spreadsheets. This will fix the crash with the add on script Illumina Text File Wrapper Script.
  • Fixed issue with Annotate and Filter Variants tool when selecting full dbNSFP tracks for version 2.9 and 3.0.

Polishes

  • Added option to output bin Betas and Standard Errors for CMC with Regression.
  • When visualizing annotation sources in GenomeBrowse set labels in the following preferred order: “Identifier” > “Ref/Alt” > “Gene Name” > “Name”
  • Allow indexing of string array fields for annotation sources. This supports querying against these fields in GenomeBrowse.
  • Added HTML format flags into annotation Source Editor so visualization of these fields can be improved though HTML formatting.
  • Allow for coverage computation for VCF files in GenomeBrowse that do not contain a Genotype (GT) field but does have other sample level FORMAT files.
  • Provide option to ignore data extents warning when converting a data file to an annotation source.
  • Renamed Annotation Download Window buttons to make it clear that downloaded tracks will not be deleted through this dialog.

 



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