v2.15.5

2.15.5 (2024-11-13)

Bug Fixes

• update pharmcat_regions.bed on data update (8911fa1)
• data: update data (f429762)
• preprocessor: add a check and test on the GVCFBlock comment in the gVCF header lines (76b31dd)
• preprocessor: add a function to fill up homozygous reference genotypes (f302af6)
• preprocessor: add back --missing-to-ref (fad76c9)
• preprocessor: check whether the index file exists before indexing the uniallelic position VCF (d2078f0)
• preprocessor: improve the check on the gVCF END block (6854ec3), closes #199
• preprocessor: make search path precedence count (1b5754d)
• preprocessor: matching pattern for GVCFBlock in the header (6509882)
• preprocessor: only retrieve regions to extract once (3964b13)
• preprocessor: remove -refRegion argument from preprocessor (5331c2b)
• preprocessor: replace the "--missing-to-ref" functionality with two separate functions, --absent-to-ref and --unspecified-to-ref. (98f7559)
• preprocessor: simplifies the check on sex chromosome haploidy (90a0306)