20160504

2016-05-04 Xiaowei Zhan [email protected]

* Reduce memory consumption for logistic regression
* Clean codes

2016-04-22 Xiaowei Zhan [email protected]

    * Fix crash when analyzing large samples (>80,000)
    * Add experimental multiple trait analysis
    * Add richer outputs for --meta score model e.g. SE(beta)
    * Add estimates for residual model (pheno~covar) in --meta score model
    * Clean codes (refactoring codes in the large-scale)
    * Update third-party libraries

2015-12-01 Xiaowei Zhan [email protected]

    * Fix a bug in meta covariance file (happens only when: unrelated individuals, has covariates, residual variance not one)
    * Improve single variant score test (--single score)
    * Add (optionally) SE for score test in meta-analysis models (e.g. --meta score[se])
    * Clean codes

2015-11-18 Xiaowei Zhan [email protected]

    * Add analytic SKAT-O model
    * Clean codes

2015-11-10 Xiaowei Zhan [email protected]

    * Improve kinship calculation (--kinshipEigen)
    * Improve dosage supports for both autosomes and X chromosomes
    * Improve logistic regression speed in meta analysis
    * Add allelic Fisher's exact test
    * Add NumPolyVar in gene/set based tests
    * Add pre-regression checkings
    * Avoid SegFault when the data files are inaccessible
    * Clean codes

20151007

2015-10-07 Xiaowei Zhan [email protected]

    * Fix a bug when generating covariance matrix

Version 20150902

2015-09-02 Xiaowei Zhan [email protected]

    * Improve stability of logistic regression model
    * Clean codes
    * Revise documentation
    * Support multi-allelic sites better
    * Fix allele frequency calculations for dosages in meta models
    * Fix reset function so that results are reset each time

2015-08-27 Xiaowei Zhan [email protected]

    * Revise Price's VT implementation
    * Clean up codes
    * Include zlib

Version 20150812

2015-08-14 Xiaowei Zhan [email protected]

    * Add version checker for Linux version
    * Improve user interface by print effective commandline options

2015-08-14 Xiaowei Zhan [email protected]

    * Improve SKAT accuracy to match SKAT R package
    * Add option maxMAF for vcf2plink

2015-07-20 Xiaowei Zhan [email protected]

    * Fix covariance bugs for binary traits of unrelated individuals

2015-07-01 Xiaowei Zhan [email protected]

    * Improve stability for Price's VT test
    * Improve error handling when files are missing
    * Fix calculation of minor allele frequency when extracting genotypes

Version 20150629

OBSOLETE VERSION

Please download the newer version

2015-06-30 Xiaowei Zhan [email protected]

    * Improve SKAT speed
    * Improve error handling when files are missing
    * Provide more warning messages

2015-06-02 Xiaowei Zhan [email protected]

    * Output more statistics for binary meta-analysis
    * Remove 'auto' keyword to support more g++ compiler

2015-05-11 Xiaowei Zhan [email protected]

    * Change '--meta score' for binary related individuals
    * Improve documentation

Version 20150509

2015-05-09 Xiaowei Zhan [email protected]

* Fix and verified '--meta cov' outputs
* Improve SKAT permutation
* Improve documentation

2015-04-30 Xiaowei Zhan [email protected]

* Support generating meta analysis summary statistics for binary traits related individuals
* Fix '--meta cov' calculation in the hemizygous region

Version 20150424

2015-04-23 Xiaowei Zhan [email protected]

* Update PAR region definition (now support hg38/GRCh38)
* Fix duplicated variants in gene/set based tests

Version 20150402

2015-04-02 Xiaowei Zhan [email protected]

* Fix output formats for Firth regression

Version 20150401

2015-04-01 Xiaowei Zhan [email protected]

    * Fix bug when dealing binary phenotypes
    * Imporve stability in Firth regression
    * Revise banner

Version 20150208

2015-02-08 Xiaowei Zhan [email protected]

* Improve numeric stability for linear mixed models