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BEDMatrix 2.0.4

  • Use prefixed Calloc and Free to comply with CRAN.

BEDMatrix 2.0.3

  • Replace testthat with tinytest.
  • Do not mix up minor/major and first/second alleles in documentation.

BEDMatrix 2.0.2

  • Fix that BED files larger than 2GB cannot be loaded in Windows.
  • Do not produce -Wunused-function warnings in exported BEDMatrix.h header.

BEDMatrix 2.0.1

  • Fix extra ; outside of compute_num_bytes_per_variant function in exported BEDMatrix.h header (found by CRAN incoming checks).

BEDMatrix 2.0.0

  • Extractions can be canceled with Control-c.
  • Reimplement package in C, drop Rcpp.
  • Genotypes can be extracted on the C level in other packages by adding BEDMatrix to the LinkingTo field of the DESCRIPTION file and including the BEDMatrix.h in your C code. The header file contains the BEDMatrix struct and the following functions: compute_num_bytes_per_variant(), extract_genotype_linear(), extract_genotype_cartesian(), and recode_genotype().

BEDMatrix 1.6.1

  • Re-add C++11 requirement to avoid warnings from Boost headers on Windows.

BEDMatrix 1.6.0

  • Follow Bioconductor S4 practices. If you have used new() to create BEDMatrix instances, please use the constructor BEDMatrix() instead.
  • Fix non-character rownames or colnames when data.table package is installed.
  • Drop C++11 requirement.
  • Update citation instructions.

BEDMatrix 1.5.0

  • Add simple_names option to BEDMatrix initialization function (contributed by Alex Ochoa).
  • Fix single indexing for index values greater than .Machine$integer.max (previously generated NAs).
  • Minor performance improvements.

BEDMatrix 1.4.1

  • Specify fileset name in messages during instantiation.

BEDMatrix 1.4.0

  • Support subsetting by NA.
  • Use crochet package for subsetting
  • Fix minor subsetting bugs
  • Update example
  • Remove intermediate S3 BEDMatrix type

BEDMatrix 1.3.0

  • Speed up character subsetting.
  • Speed up detection of n, p, rownames, and colnames during initialization if data.table package is installed.
  • Support str function.

BEDMatrix 1.2.0

  • Support path without extension (like PLINK).
  • Add path attribute (to reattach instance after saving it to RData).
  • Add length method.
  • Add as.matrix method.
  • Add is.matrix method.
  • Store dimensions in S3 wrapper as dims attribute to allow for faster recreation when saved.
  • Fix bug that modified i and j when subsetting.

BEDMatrix 1.1.0

  • Restore cross-platform compatibility by dropping the system dependency on Boost.IOStreams in favor of Boost.Interprocess which provides header-only memory-mapping and is therefore supported by the BH package.

BEDMatrix 1.0.1

  • Ensure that the same C compiler and compiler flags are used in the configure tests as when compiling R.
  • Improve messages in configure script to distinguish between Boost headers and Boost libraries.

BEDMatrix 1.0.0

Initial release.