v1.2.1

• bug fix in handleDups() when no overlapping variants are present
• allow for multiple targets per variant in output file
• making -W (--nowarn) the default, retained for back-compatibility
• added -w (--warn) to override -W

v1.2.0

Added RNA scoring to scoreVariants with -R

• added new makeRNAPipeline script to set up processing for FASTQ files of cDNA
• added new generateRNACounts file to extract RNA counts from BAMs

Modified target column in score file for double-covered variants to now be a semicolon-separated list of both targets

v1.1.1

• Adding logic to variant scoring with scoreVariants to filter out variants based on altered codon context using -W

v1.1.0

• updated scoring model for SNVs and deletions, now using a straightforward continuous-time linear model
• joint scoring of SNVs and deletions with bin/scoreVariants to produce a single score output file
• Gaussian mixture model-based functional class assignment replaces the previous Z-score method
• model parameters -- e.g., estimated GMM component means and variances, and class threshold values -- are now output to TSV when scoring variants
• improved recognition of and labeling of programmed variants falling within codons containing "required edits" (positive control for editing, but that change the nucleic acid context of the codon)

v1.0.2

minor update to add support for outputting HGVS p. notation in score files

v1.0.1

Minor changes from v1.0.0

• updated column names in score file
• introduced new logic to require 1000 variants before applying functional class labels
• added new Ensembl consequence for upstream_gene_variant

v1.0.0

Initial release of SGE data analysis code. Supports computing per-variant scores and confidence intervals, along with functional class assignments, for SNVs.