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ChangeLog
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2019-02-05 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix crash (#59)
2019-01-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix crash (#77)
* Fix hide-covar option for firth test (#75)
2017-10-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Minor text changes
2017-10-09 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support BGEN format (see example/experimental/cmd.sh)
* Add bgen2vcf, bgenFileInfo utilities
* Add timeout when checking new version
* Improve speed of covariance calculation
* Update combineKinship.py
* Support KGGSeq inputs
2017-08-18 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve speed of covariance calculations
* Clean codes
2017-07-13 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix beta estimation in binary score tests for unrelated individuals
2017-06-13 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug related Wald test outputs (fix #30)
* Fix zero af in famscore (fix #34)
2017-06-09 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add "--outputID" to output VCF ID to association results (fix #14, #24)
* Improve error messages when loading decomposed kinship file (fix #29)
* Add "RVTESTS successfully exit" to stdout (fix #31)
* Add FASTLMM_DEBUG environment variable to ease debugging (refer to #32)
* Fix strtol related warning (possibly) (refer to #33)
* Clean codes
2017-04-27 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add boltCov model
2017-04-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a critical bug related to AF calculation (issue 15)
* Fix siteFile flag and provide prompt when it's used
2017-04-12 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support comma as a separator in parameter options
2017-03-07 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix SE calculation in '--single score' (continuous/binary traits)
* Add --numThreads option (may increase speed)
* Improve BoltLMM model
* Add more test cases
* Fix .dim file outputs from vcf2kinship
2017-02-28 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug when loading a group of variants
* Fix SE calculation in '--single score' for quantitative traits
* Fix BoltLMM implementation
* Improve SkatO robustness
* Revise documentation
2017-02-10 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix bugs (issue #13)
* Improve supports for multi-allelic variants
* Improve codes (more functions), revise documentation
2017-01-10 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add more test cases
* Add support for loading multiple phenotypes (--multiplePheno)
* Add a score model for multiple phenotypes (--single mtscore)
* Add an approx model for multiple phenotypes (--single fastmtscore)
* Change bolt model options (--meta score[bolt] --boltPlink)
* Fix a bug that crashed SKAT-O
* Clean codes
2016-09-28 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add a new fast meta-analysis models (--meta bolt[genotypeFile=XXX])
* Update third libraries
2016-06-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add support for MKL library (USE_MKL=[dynamic|static])
2016-06-24 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug related to flipping to minor alleles
2016-05-16 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Optimize code (faster speed, smaller memory consumption)
2016-05-04 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Reduce memory consumption for logistic regression
* Clean codes
2016-04-22 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* 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 <zhanxw@fantasia.csgstat.sph.umich.edu>
* 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 <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add analytic SKAT-O model
* Clean codes
2015-11-10 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* 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
2015-10-07 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix a bug when generating covariance matrix
2015-09-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* 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 <zhanxw@fantasia.csgstat.sph.umich.edu>
* Revise Price's VT implementation
* Clean up codes
* Include zlib
2015-08-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add version checker for Linux version
* Improve user interface by print effective command line options
2015-08-14 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve SKAT accuracy to match SKAT R package
* Add option maxMAF for vcf2plink
2015-07-20 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix covariance bugs for binary traits of unrelated individuals
2015-07-01 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve stability for Price's VT test
* Improve error handling when files are missing
* Fix calculation of minor allele frequency when extracting genotypes
2015-06-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve SKAT speed
* Improve error handling when files are missing
* Provide more warning messages
2015-06-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Output more statistics for binary meta-analysis
* Remove 'auto' keyword to support more g++ compiler
2015-05-11 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change '--meta score' for binary related individuals
* Improve documentation
2015-05-09 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix and verified '--meta cov' outputs
* Improve SKAT permutation
* Improve documentation
2015-04-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support generating meta analysis summary statistics for binary traits related individuals
* Fix '--meta cov' calculation in the hemizygous region
2015-04-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Update PAR region definition (now support hg38/GRCh38)
* Fix duplicated variants in gene/set based tests
2015-04-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix output formats for Firth regression
2015-04-01 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix bug when dealing binary phenotypes
* Improve stability in Firth regression
* Revise banner
2015-03-24 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Revise documentation
* Fix conservative p-values in analyticVT models
* Fix statistics in many rare variant tests
2015-03-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve FamSkat speed
* Fix outputs for FpTest
* Add auto-indexing function for "--meta score" model
* Fix bug when outputting zero frequency
2015-03-18 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support dosage (vcf2kinship)
* Fix memory leaks (rvtests)
* Improve prompt messages
2015-03-02 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Clean code
* Support log for vcf2kinship
2015-02-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Restructure classes and reduce duplicated codes
2015-02-08 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve numeric stability for linear mixed models
2015-01-04 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve speed and outputs of family-based models
* Fix bug when generating covariance matrix
* Support compiling on OSX Yosemite
* Plan to handle multi-allelic variants better
2014-12-11 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Report heritability estimation in family-based models
* Add variable threshold test using analytical approach
* Add family-based tests: famCMC, famZeggini and famSKAT
* Add Firth regression
* Fix bugs in famLRT
2014-10-11 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Clean codes
* Upgrade PCRE to version 8.36
2014-10-06 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix allele frequency calculation in related samples
2014-07-29 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change AF = 0 to NA when the sites are all missing
2014-07-23 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Update U, V statistics for unrelated individual such that SE(effect_size) = 1/sqrt(V)
* Improve vcf2kinship error messages
2014-06-20 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix effect estimation in linear score test when covariates exists
2014-06-13 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix trait summary in the MetaScore file header
* Improve model stability in MetaCov model
2014-04-17 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix "--meta score" model outputs again... This time the results have been verified by Merlin
2014-04-16 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix "--meta score" model outputs on X chromosome hemizygous region
* Add header in "--meta score" model outputs
2014-04-01 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* New parallel computation option (--thread) in vcf2kinship
2014-03-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve: allele frequency calculation is faster
* Improve: faster calculation of covariance in "--meta" models
2014-03-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve: for "--meta recessive" model, output PVALUE = NA instead of 1 at monomorphic sites
* Improve: frequency filtering for dosage and genotype
* Change: Pvalue header for burden tests are now "Pvalue"
2014-03-25 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Improve: greatly improve the speed for cov,dominant and recessive models
* Fix: MetaCov model now have the correct suffix
2014-02-28 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change: for dominant/recessive model, automatically generate covariance
2014-02-27 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change: for X chrom, also use male to get AF
* Support generating covariance matrix for dominant/recessive model
* Change now, by default, rvtests drops samples with missing covariates (to resume previous behavior, imputing to the mean, use --imputeCov).
2014-02-20 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Revise --useResidualAsPhenotype, now regress out intercept by default
2014-02-11 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Fix bug in MetaCov outputs
2013-11-26 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Support X chromosome analysis
2013-05-03 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Change frequency cutoff to minor allele frequency cutoffs when using --freqLower / --freqUpper
2013-04-30 Xiaowei Zhan <zhanxw@fantasia.csgstat.sph.umich.edu>
* Add conditional analysis
* Add family burden tests