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Changelog

Source: NEWS.md

iscream 0.99.9

DOCUMENTATION

  • Vignettes suppress long startup messages

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

iscream 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.

iscream 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

iscream 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

iscream 0.99.5

INTERNAL

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

iscream 0.99.4

  • tabix executable added to SystemRequirements

iscream 0.99.1

  • Updated LICENSE files for R CMD check

iscream 0.99.0

  • Pre-release for manuscript and Bioconductor review