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ChangeLog
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ChangeLog
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2024-09-30 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Update SQLite C codes
2024-09-30 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Revise URL used in README
2024-09-24 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Add R_NO_REMAP to better support calling R API for C codes
2024-01-30 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix Rprintf() related issues on ARM64 (Mac M1)
2023-11-28 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix Rprintf() related issues
2023-09-01 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Change Date field
2023-08-31 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix roxygen2 related issue
* Fix realloc(size = 0) issue
* Fix function prototype warning
2023-04-1 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Remove travis (substituted by GitHub actions)
* Fix license issues
2023-04-1 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix uninitialize return values
2023-01-28 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Change CXX11 to CXX17 in configure.ac
2023-01-24 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix warnings related to "Compiled code should not call entry points"
2022-11-14 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Fix warnings when this compiler option is on: [-Wstrict-prototypes]
2021-11-07 Xiaowei Zhan <zhanxw@bunny.swmed.edu>
* Change configure.ac to comply to CRAN policy
* Fix broken links
2019-08-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug related to column names when using single chrom indices
2019-08-21 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve column names when using single chrom indices
2019-03-21 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support single chromosome index for bcf
2019-02-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug related to query BGenIndex file (use int64)
2019-01-09 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support single chromosome index for vcf
2019-01-05 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Revise R/CPP interface codes
2019-01-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add partial supports for binary PLINK file formats
2018-11-29 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add supports for BGEN file formats
* Fix CRAN reported warnings (e.g. compiler flags)
2017-05-03 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix crashes when reading meta-analysis score and cov files together
2017-04-05 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add option multiAllelic (default: FALSE) to support bi-/multi- allelic
* Register native routines per CRAN policy
2017-03-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add back-compatiability (group by both chr:pos_ref/alt and chr:pos)
2017-02-07 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug of corner case when paring regions
2016-12-29 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug dealing with multi-allelic when loading multiple files
2016-12-21 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve alignment for multi-allelic meta results in rvmeta.readData
2016-12-19 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add support for multi-allelic sites
2016-09-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add namespace std
* Fix some compilers warnings
2016-05-04 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Revise DESCRIPTION
2016-05-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix header macro (use _DEFAULT_SOURCE)
* Fix off-by-one bug when reporting codon number
* Fix memory leak
2015-10-20 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve code stability
2015-09-29 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Update CITATION
2015-09-16 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Relax covariance file format restriction to accomodate rmw
* Add feature to generate Makefiles
2015-08-13 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix bug when tabix file does not have headers
2015-07-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add function to faciliate parallel computation
2015-07-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Expand tilde in the file names before passing them to C
2015-06-25 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix UBSAN reported error: when NA_INTEGER + NA_INTEGER causes int overflow
2015-06-18 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Remove stringr dependency
2015-06-17 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Remove C++11 support. Not all R platforms has C++11 compiler
2015-06-07 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Not suport Solaris 10 due to difficulties in setting up build env.
2015-06-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support load summary statistics for binary trait
2015-05-19 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add timeout = 3 seconds when checking new version
2015-05-16 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support travis
2015-05-12 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a corner case to avoid crash
2015-04-27 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Update codes
2014-12-21 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve error messages
2014-05-04 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add sanity check codes and demo codes
2014-05-01 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add more checks for VCF/BCF index files
2014-04-20 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix conditional macros (WIN32) for comply R extentsion requirement
2014-04-18 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix address sanitizer warnings
2014-04-17 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add function to extract covariance by paris
2014-04-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Enclose citation information
2014-04-14 zhanxw <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve stability when read tabix file
2014-04-13 zhanxw <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix an initialization problem to pass UBSAN check
* Support compilation in Windows
2014-04-13 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add support for Solaris system (x86 Sun Studio 12.3)
2014-04-12 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support more annotation types
2014-04-09 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support basic annotation
2014-03-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change by default not creating tabix index
2014-01-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Rename tabix() to tabix.read()
* Add tabix.createIndex()
2014-01-25 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add function to export summary statistics
2013-11-29 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Update using "static inline" qualier in ksort.h
2013-11-19 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add configure.win and src/config.h to formally suport Windows build.
2013-11-15 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support clang compilation on various platforms (since version 1.9.1)
2013-11-08 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve (Important!!) readVCFToListByGene function. Variants belonging to a certain gene can be distinguished.
2013-11-07 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change (Important!!) to avoid extracting duplicated variants
2013-11-05 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support read MetaSkew file (outputs from 'rvtests --model skew')
2013-11-04 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add tabix.read.header() to read header lines of tabix files
2013-11-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add tabix.read.table() to directly read tabix file as data frame
2013-09-27 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add more unit-test codes
* Fix BCF reading bug
* Revise to give friendly error messages
2013-09-25 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support BCF file
2013-09-16 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support load parameters estimated from null model
2013-09-15 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support loading case/control frequencies from meta-analysis results
2013-08-29 Xiaowei Zhan <zhanxw@amd.csgstat.sph.umich.edu>
* Add automatic test cases
2013-08-28 Xiaowei Zhan <zhanxw@amd.csgstat.sph.umich.edu>
* Fix crashing when loding meta analysis files
2013-08-01 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support loading HWE from all samples / cases only / controls only.
2013-07-28 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Allow loading score statistics only (skipping covariance files)
2013-07-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support site only VCF files
2013-05-25 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add support for binary trait
2013-05-24 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug when merging regions
2013-04-12 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add examples and documentations
2013-03-24 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Keep gene/region order consistent
* Remove excessive prompt message
2013-03-19 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* New version