SCReadCounts-1.4.0

• New experimental tools for fast single-cell SNV discovery and read counting

SCReadCounts-1.3.2

• Fix bug where .gz and .bz2 files with the same name as output files were overwritten

SCExecute-1.3.3

• Fix bug where .gz and .bz2 files with the same name as output files were overwritten

ReadCounts-2.5.2

• Fix bug where .gz and .bz2 files with the same name as output files were overwritten

SCReadCounts-1.3.1

• New tool scVarLoci, work in progress (alpha)
• Fix logging for SCReadCounts options
• Remove batching of SNVs for readCounts
• Tweaks of pysam.pileup API call

ReadCounts-2.5.1

• Bug fix for varLoci
• Bug fix for extended output - read filtering statistics
• Update command-line argument order for varLoci
• Tweaks of pysam.pileup API call

SCReadCounts-1.3.0

• Addition of experimental tool, varLoci, for extraction of putative variant loci directly from BAM file
• Re-ordering of options in GUI to make things more understandable
• Documentation updates for consistency and correctness

SCExecute-1.3.2

• Better instrumentation for SCExecute - elapsed time, memory logging
• update scBAMStats to handle edge cases better

ReadCounts-2.5.0

• Addition of experimental tool, varLoci, for extraction of putative variant loci directly from BAM file
• Re-ordering of options in GUI to make things more understandable
• Documentation updates for consistency and correctness

SCReadCounts-1.2.0

• Better memory management, batch SNVs if necessary
• Can now count UMIs in a read-group (cell-barcode) not just number of reads
• Explicit options for Cell- and UMI-Barcode label logic for extracting tags
• Predefined cell-barcode and UMI-barcode logic for CellRanger in addition to UMI-tools and STARsolo.
• Directional counts, VAF values (forward, reverse) if desired