diff options
Diffstat (limited to 'src/param.cpp')
| -rw-r--r-- | src/param.cpp | 9 |
1 files changed, 4 insertions, 5 deletions
diff --git a/src/param.cpp b/src/param.cpp index 034b25c..017d588 100644 --- a/src/param.cpp +++ b/src/param.cpp @@ -323,7 +323,7 @@ void PARAM::ReadFiles(void) { trim_individuals(indicator_idv, ni_max); trim_individuals(indicator_cvt, ni_max); // The following reads the geno file to get the SNPs - only for BIMBAM - if (is_bimbam && ReadFile_bimbam_geno(file_geno, setSnps, W2, indicator_idv, indicator_snp, + if (ReadFile_bimbam_geno(file_geno, setSnps, W2, indicator_idv, indicator_snp, maf_level, miss_level, hwe_level, r2_level, mapRS2chr, mapRS2bp, mapRS2cM, snpInfo, ns_test) == false) { error = true; @@ -1285,8 +1285,7 @@ void PARAM::ReadBIMBAMGenotypes(gsl_matrix *UtX, gsl_matrix *K, const bool calc_ error = true; } } else { - // Read BIMBAM - if (is_bimbam && ReadFile_geno(file_geno, indicator_idv, indicator_snp, UtX, K, calc_K) == false) { + if (ReadFile_geno(file_geno, indicator_idv, indicator_snp, UtX, K, calc_K) == false) { error = true; } } @@ -1311,10 +1310,10 @@ void PARAM::CalcKin(gsl_matrix *matrix_kin) { file_str = file_geno; if (is_mdb) error = !BimbamKin(file_str, setKSnps, indicator_snp, a_mode - 20, d_pace, - matrix_kin, ni_max == 0) == false); + matrix_kin, ni_max == 0); else error = !BimbamKin(file_str, setKSnps, indicator_snp, a_mode - 20, d_pace, - matrix_kin, ni_max == 0) == false); + matrix_kin, ni_max == 0); } |