1.2.2

Fixed all build compilation warnings.

v1.2.1

• Bugfix for #6, backtracking with new alignment algorithm is now correct.

v1.2.0

Stratified Variant Comparison

vcfdist now supports stratified variant comparison by outputting summary.vcf in GA4GH compatible intermediate VCF format. This format is described in the Supplementary Material of "Best practices for benchmarking germline small-variant calls in human genomes" by Krusche et al. Instructions for using hap.py's helper script qfy.py to perform a stratified variant evaluation are now included in the README. This fixes #4.

v1.1.0

Update to new alignment algorithm. When calculating precision and recall, the definition of sync points (which separate complex variants from one another) has been modified to now occur on transitions. Matching bases on the reference, truth, and query are no longer required. As a result, adjacent variants can be separately classified. For example, if only one of two adjacent SNPs is correct, they can now be classified as a FP and FP, rather than two PP.

The settings for printing verbosity have now been modified for a cleaner default.

v1.0.2

Fixed compilation bug from renaming GRP -> CPX, and output alignment.

v1.0.1

• Improved documentation (#5) regarding build process and outputs.
• Single bugfix (#1) to build process.
• Minor changes to output TSV column headers.

v1.0.0

Initial bioRxiv release of paper.