From 60f86db94ee2b4f826300cb0e73cb658ac7bdfd8 Mon Sep 17 00:00:00 2001 From: xiangzhou Date: Sun, 24 Jul 2016 15:58:31 -0400 Subject: version 0.95alpha --- src/mvlmm.cpp | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) (limited to 'src/mvlmm.cpp') diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp index 7655b50..5deda06 100644 --- a/src/mvlmm.cpp +++ b/src/mvlmm.cpp @@ -3185,12 +3185,17 @@ void MVLMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_ //start reading genotypes and analyze - size_t csnp=0; + size_t csnp=0, t_last=0; + for (size_t t=0; t1) {break;} if (t%d_pace==0 || t==(ns_total-1)) {ProgressBar ("Reading SNPs ", t, ns_total-1);} + if (indicator_snp[t]==0) {continue;} // read SNP header id.clear(); rs.clear(); @@ -3293,7 +3298,7 @@ void MVLMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_ for (size_t i=0; i1) { //gsl_vector_set(x, i, 2-geno); //} @@ -3310,7 +3315,7 @@ void MVLMM::Analyzebgen (const gsl_matrix *U, const gsl_vector *eval, const gsl_ gsl_vector_memcpy (&Xlarge_col.vector, x); csnp++; - if (csnp%msize==0 || t==indicator_snp.size()-1 ) { + if (csnp%msize==0 || c==t_last ) { size_t l=0; if (csnp%msize==0) {l=msize;} else {l=csnp%msize;} @@ -3656,7 +3661,11 @@ void MVLMM::AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gs gsl_matrix_memcpy (B_null, B); //start reading genotypes and analyze - size_t csnp=0; + size_t csnp=0, t_last=0; + for (size_t t=0; t=1) {break;} !safeGetline(infile, line).eof(); @@ -3705,7 +3714,7 @@ void MVLMM::AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gs gsl_vector_memcpy (&Xlarge_col.vector, x); csnp++; - if (csnp%msize==0 || t==indicator_snp.size()-1 ) { + if (csnp%msize==0 || c==t_last ) { size_t l=0; if (csnp%msize==0) {l=msize;} else {l=csnp%msize;} @@ -4068,7 +4077,11 @@ void MVLMM::AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl b=ch[0]; } - size_t csnp=0; + size_t csnp=0, t_last=0; + for (size_t t=0; t::size_type t=0; t