[Fix] Permutation number was not initialized

choishingwan · Oct 9, 2019 · f900601 · f900601
1 parent 10ff53c
commit f900601
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Showing 5 changed files with 82 additions and 49 deletions.
diff --git a/inc/commander.hpp b/inc/commander.hpp
@@ -42,8 +42,8 @@
 #include <windows.h>
 #endif
 
-const std::string version = "2.2.10";
-const std::string date = "2019-10-08";
+const std::string version = "2.2.10.b";
+const std::string date = "2019-10-09";
 class Commander
 {
 public:

diff --git a/inc/genotype.hpp b/inc/genotype.hpp
@@ -200,6 +200,14 @@ class Genotype
     {
         std::fill(m_in_regression.begin(), m_in_regression.end(), 0);
     }
+    void reset_std_flag()
+    {
+        std::fill(m_exclude_from_std.begin(), m_exclude_from_std.end(), 0);
+    }
+    void exclude_from_std(const size_t idx)
+    {
+        SET_BIT(idx, m_exclude_from_std.data());
+    }
     /*!
      * \brief Function to prepare the object for PRSice. Will sort the
      * m_existed_snp vector according to their p-value.
@@ -481,6 +489,7 @@ class Genotype
     std::vector<uintptr_t> m_founder_include2;
     std::vector<uintptr_t> m_sample_include;
     std::vector<uintptr_t> m_sample_include2;
+    std::vector<uintptr_t> m_exclude_from_std;
     std::vector<uintptr_t> m_in_regression;
     std::vector<uintptr_t> m_haploid_mask;
     std::vector<size_t> m_sort_by_p_index;

diff --git a/inc/prsice.hpp b/inc/prsice.hpp
@@ -316,8 +316,6 @@ class PRSice
     long long m_max_fid_length = 3;
     long long m_max_iid_length = 3;
     int m_best_index = -1;
-    size_t m_num_perm = 0;
-    bool m_perform_prset = false;
     bool m_quick_best = true;
     bool m_printed_warning = false;
     const std::string m_prefix;
@@ -342,7 +340,8 @@ class PRSice
      * regression flag for each sample
      * \param target is the target genotype object
      */
-    void update_sample_included(const std::string& delim, Genotype& target);
+    void update_sample_included(const std::string& delim, const bool binary,
+                                Genotype& target);
     /*!
      * \brief gen_pheno_vec is the function responsible for generating the
      * phenotype vector
@@ -450,7 +449,7 @@ class PRSice
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>& PQR,
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>::PermutationType&
             Pmat,
-        const Eigen::MatrixXd& Rinv, const Eigen::Index& rank,
+        const Eigen::MatrixXd& Rinv,
         std::map<size_t, std::vector<size_t>>& set_index,
         std::vector<double>& obs_t_value,
         std::vector<std::atomic<size_t>>& set_perm_res, const bool is_binary);
@@ -463,8 +462,7 @@ class PRSice
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>& PQR,
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>::PermutationType&
             Pmat,
-        const Eigen::MatrixXd& Rinv, const Eigen::Index& rank,
-        std::vector<double>& obs_t_value,
+        const Eigen::MatrixXd& Rinv, std::vector<double>& obs_t_value,
         std::vector<std::atomic<size_t>>& set_perm_res, const bool is_binary);
     /*!
      * \brief The "producer" for generating the permuted phenotypes
@@ -487,7 +485,7 @@ class PRSice
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>& PQR,
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>::PermutationType&
             Pmat,
-        const Eigen::MatrixXd& R, const Eigen::Index& rank, bool run_glm);
+        const Eigen::MatrixXd& R, bool run_glm);
     /*!
      * \brief Funtion to perform single threaded permutation
      * \param decomposed is the pre-decomposed independent matrix. If run glm is
@@ -502,7 +500,7 @@ class PRSice
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>& PQR,
         const Eigen::ColPivHouseholderQR<Eigen::MatrixXd>::PermutationType&
             Pmat,
-        const Eigen::MatrixXd& R, const Eigen::Index& rank, const bool run_glm);
+        const Eigen::MatrixXd& R, const bool run_glm);
 
     void parse_pheno(const bool binary, const std::string& pheno,
                      std::vector<double>& pheno_store, double& first_pheno,

diff --git a/src/genotype.cpp b/src/genotype.cpp
@@ -792,6 +792,10 @@ void Genotype::load_samples(bool verbose)
                           + misc::to_string(m_num_female)
                           + " female(s)) observed\n";
     message.append(misc::to_string(m_founder_ct) + " founder(s) included");
+
+    const uintptr_t unfiltered_sample_ctl =
+        BITCT_TO_WORDCT(m_unfiltered_sample_ct);
+    m_exclude_from_std.resize(unfiltered_sample_ctl, 0);
     if (verbose) m_reporter->report(message);
     m_sample_selection_list.clear();
 }
@@ -1474,9 +1478,7 @@ void Genotype::standardize_prs()
     size_t num_prs = m_prs_info.size();
     for (size_t i = 0; i < num_prs; ++i)
     {
-        if (!IS_SET(m_sample_include, i)
-            || (m_prs_calculation.scoring_method == SCORING::CONTROL_STD
-                && m_sample_id[i].pheno != "0"))
+        if (!IS_SET(m_sample_include, i) || IS_SET(m_exclude_from_std, i))
             continue;
         if (m_prs_info[i].num_snp == 0) { rs.push(0.0); }
         else