diff options
| -rw-r--r-- | .gitignore | 4 | ||||
| -rw-r--r-- | Makefile | 11 | ||||
| -rwxr-xr-x | bin/gemma | bin | 4823751 -> 0 bytes | |||
| -rw-r--r-- | src/io.cpp | 10 |
4 files changed, 20 insertions, 5 deletions
@@ -0,0 +1,4 @@ +.gitignore +*.o +*.tar.gz +bin/ @@ -18,6 +18,7 @@ WITH_LAPACK = 1 FORCE_32BIT = FORCE_DYNAMIC = FORCE_FLOAT = +DIST_NAME = gemma-0.95alpha # -------------------------------------------------------------------- # Edit below this line with caution @@ -110,6 +111,14 @@ $(OBJS) : $(HDR) clean: rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ ${SRC_DIR}/*_float.* + +DIST_COMMON = COPYING.txt README.txt Makefile +DIST_SUBDIRS = src doc example bin + tar: - tar cvzf gemma-0.93.tar.gz COPYING.txt README.txt Makefile src doc example bin + mkdir -p ./$(DIST_NAME) + cp $(DIST_COMMON) ./$(DIST_NAME)/ + cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/ + tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/ + rm -r ./$(DIST_NAME) diff --git a/bin/gemma b/bin/gemma Binary files differdeleted file mode 100755 index 6734240..0000000 --- a/bin/gemma +++ /dev/null @@ -563,11 +563,12 @@ bool ReadFile_geno (const string &file_geno, const set<string> &setSnps, const g if (flag_poly!=1) {indicator_snp.push_back(0); continue;} - if (hwe_level!=0) { + if (hwe_level!=0 && maf_level!=-1) { if (CalcHWE(n_0, n_2, n_1)<hwe_level) {indicator_snp.push_back(0); continue;} } //filter SNP if it is correlated with W + //unless W has only one column, of 1s for (size_t i=0; i<genotype->size; ++i) { if (gsl_vector_get (genotype_miss, i)==1) {geno=maf*2.0; gsl_vector_set (genotype, i, geno);} } @@ -577,7 +578,7 @@ bool ReadFile_geno (const string &file_geno, const set<string> &setSnps, const g gsl_blas_ddot (genotype, genotype, &v_x); gsl_blas_ddot (Wtx, WtWiWtx, &v_w); - if (v_w/v_x >= r2_level) {indicator_snp.push_back(0); continue;} + if (W->size2!=1 && v_w/v_x >= r2_level) {indicator_snp.push_back(0); continue;} indicator_snp.push_back(1); ns_test++; @@ -698,12 +699,13 @@ bool ReadFile_bed (const string &file_bed, const set<string> &setSnps, const gsl if ( (n_0+n_1)==0 || (n_1+n_2)==0 || (n_2+n_0)==0) {indicator_snp.push_back(0); continue;} - if (hwe_level!=1) { + if (hwe_level!=1 && maf_level!=-1) { if (CalcHWE(n_0, n_2, n_1)<hwe_level) {indicator_snp.push_back(0); continue;} } //filter SNP if it is correlated with W + //unless W has only one column, of 1s for (size_t i=0; i<genotype->size; ++i) { if (gsl_vector_get (genotype_miss, i)==1) {geno=maf*2.0; gsl_vector_set (genotype, i, geno);} } @@ -713,7 +715,7 @@ bool ReadFile_bed (const string &file_bed, const set<string> &setSnps, const gsl gsl_blas_ddot (genotype, genotype, &v_x); gsl_blas_ddot (Wtx, WtWiWtx, &v_w); - if (v_w/v_x > r2_level) {indicator_snp.push_back(0); continue;} + if (W->size2!=1 && v_w/v_x > r2_level) {indicator_snp.push_back(0); continue;} indicator_snp.push_back(1); ns_test++; |