Changes in version 0.99.9                        

DOCUMENTATION

  - Vignettes suppress long startup messages

  - Updated run-times and plots in tabix vs Rsamtools vignette

                       Changes in version 0.99.8                        

BUG FIXES

  - For tabix(), converting GRanges inputs of width 1 now returns them
    as chr:start-start instead of chr:start which was invalid for the
    htslib API and caused a block of records to be returned instead of
    just the locus.

                       Changes in version 0.99.7                        

BREAKING CHANGES

  - Functions that return GenomicRanges or SummarizedExperiment will
    fail if those packages are not loaded so that users don't receive
    objects they can't interact with

DOCUMENTATION

  - bsseq creation now runs for the make_mat_bsseq example

                       Changes in version 0.99.6                        

BREAKING CHANGES

  - make_bsseq_mat changed to make_mat_bsseq for consistency with other
    matrix creating functions

BUG FIXES

  - Fixed MacOS and clang issues (version checking, using the correct
    linkage tools) in configuration script

  - Explicitly coerce path to string for bedfile prefix extraction in
    Cpp_summarize_regions

ENHANCEMENTS

  - Added windows as supported platform but without multithreading
    support

  - pbapply progress bar added to tabix() functions

INTERNAL

  - Explicitly return result from tabix.single helper function.

  - Removed unused C++ variables

  - file.path used instead of pasting paths

DOCUMENTATION

  - bsseq added to Suggests to run in examples and vignettes

  - Changed all \dontrun to \donttest

  - All vignettes set to BiocStyle

  - BiocFileCache now used for all vignette file downloads

  - Reading the genes file in the "performance" vignette fixed to read
    only three columns

  - Added more information on bitpacking limits for make_mat_bsseq

  - Allowed creation of BSseq objects in data structures vignette

  - Package description updated to add information about methylation
    support

  - Replaced all references to CpG with more general methylation

  - Added CpH as supported in documentation

                       Changes in version 0.99.5                        

INTERNAL

  - tabix executable-dependent tests are skipped if tabix is not
    installed

                       Changes in version 0.99.4                        

  - tabix executable added to SystemRequirements

                       Changes in version 0.99.1                        

  - Updated LICENSE files for R CMD check

                       Changes in version 0.99.0                        

  - Pre-release for manuscript and Bioconductor review