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