ChangeLog

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