ReadCounts-2.3.4

• Add optional whitelist file for cell barcodes, update STARsolo read grouping strategy to use barcodes.tsv whitelist

SCReadCounts-1.1.4

• Fix bug in command-ling logging for non-default read-grouping strategy.

SCReadCounts-1.1.3

• Provide STARsolo tag-based read-grouping strategy for cell barcodes.
• Improve handling of missing values in read-grouping logic.
• Fix bug resulting in incorrect output when text-format output files are chosen.
• Ensure text-format output files do not print None for missing values.

ReadCounts-2.3.3

• Provide STARsolo tag-based read-grouping strategy for cell barcodes.
• Improve handling of missing values in read-grouping logic.
• Ensure text-format output files do not print None for missing values.

SCReadCounts-1.1.2

• Make an additional count matrix output option Var;Ref the default to avoid Excel misinterpretation
• Reinstate the graphical user-interface for the Linux packaged release
• Move example output files to subdirectory
• Make the inability to start the GUI (due to missing Python modules or other issues) explicit.
• Fix MacOS menu-bar label

ReadCounts-2.3.2

• Reinstate the graphical user-interface for the Linux packaged release
• Move example output files to subdirectory
• Make the inability to start the GUI explicit.
• Fix MacOS menu-bar label

SCReadCounts-1.1.1

• Bug fix: reading Excel formatted counts by readCountsMatrix
• Darwin labeled release for MacOS now labelled as macOS.
• Linux packaged version now supports Excel-based output options

ReadCounts-2.3.1

• Darwin labeled release for MacOS now labelled as macOS.
• Linux packaged version now supports Excel-based output options

SCReadCounts-1.1.0

• Bug fix: hanlding of non-numeric chromosomes in readCountMatrix.
• New argument for managing extended output options for readCounts: genotype likelihood, and read filtering statistics.
  • Replaces -F option for "Full" output, and
  • Outputs genotype likelihood statistics to readCounts output file only if requested.
• Rename the "R" column in the readCounts output table as "VAF"
• Removal of the -U/Unique option - this is now implemented using the ReadFiltering system.
• Removal of the -d/Debug option.

ReadCounts-2.3.0

• New argument for managing extended output options: genotype likelihood, and read filtering statistics.
  • Replaces -F option for "Full" output, and
  • Outputs genotype likelihood statistics only if requested.
• Rename the "R" column in the output table as "VAF"
• Removal of the -U/Unique option - this is now implemented using the ReadFiltering system.
• Removal of the -d/Debug option.