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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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