Simplify a bit and make guix.scm work without running out of RAM

3 files changed, 9 insertions, 11 deletions

diff --git a/guix.scm b/guix/guix.scm
index 1efe946..90ef001 100644
--- a/guix.scm
+++ b/guix/guix.scm
@@ -1,14 +1,16 @@
 ;; To use this file to build HEAD of gemma:
 ;;
-;;   guix build -f guix.scm       # default builds pangemma-git
+;;   guix build -f guix/guix.scm       # default builds pangemma-git
 ;;
 ;; To get a development container (e.g., run in emacs shell).
 ;;
-;;   guix shell -C -D -F -v 3 -f guix.scm # pangemma-shell-git
+;;   guix shell -C -D -F -f guix/guix.scm # pangemma-shell-git
+;;
+;; see premake5.lua for build/test instructions
 ;;
 ;; optimized for arch:
 ;;
-;;   guix shell --tune=native -C -D -F -v 3 # pangemma-shell-git
+;;   guix shell --tune=native -C -D -F # pangemma-shell-git
 ;;
 ;; see premake5.lua header for examples.
 ;;
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);
 
   }
 
diff --git a/src/param.h b/src/param.h
index 978196c..38b9430 100644
--- a/src/param.h
+++ b/src/param.h
@@ -372,7 +372,4 @@ public:
 
 size_t GetabIndex(const size_t a, const size_t b, const size_t n_cvt);
 
-#define is_bimbam (!is_mdb)
-#define compute_kinship (a_mode == M_KIN || a_mode == M_KIN2)
-
 #endif