Changes in version 1.8.7                        

Bug fixes

  - get_component_variants() no longer errors on valid strings that
    combine a phased heterozygous locus with a homozygous locus (e.g.
    pfcrt:72_73:C|S_V). The homozygous allele is now correctly carried
    across all phased components.
  - check_position_string() now validates every distinct input.
    Previously, when the input contained duplicates, an invalid string
    positioned after the duplicates could be skipped and wrongly pass
    validation.
  - check_variant_string() and check_position_string() now report the
    reason for failure in the error condition itself (via
    conditionMessage()), instead of printing it to the console and
    raising an empty error. This makes the reason available to calling
    code that catches the error.

Behaviour changes

  - drop_read_counts() and position_from_variant_string() now preserve
    the format of the input rather than re-normalising it. In
    particular, position ranges (e.g. 72-74) are kept compact rather
    than expanded to 72_73_74, and the concise amino-acid notation (e.g.
    CV) is preserved rather than rewritten as C_V. Genes are still
    returned in alphabetical order.

Internal

  - Substantial refactor of the internals for speed and to remove
    duplicated code, with no change to the documented behaviour of the
    affected functions. The largest gains are in drop_read_counts() and
    position_from_variant_string() (now pure string operations), with
    smaller gains across most other functions.
  - Removed the unused tidyr dependency.