From 33092acee232fc30c38d92877864cb37d5b412f7 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Fri, 27 Sep 2024 14:10:48 +0200
Subject: [PATCH] debug ld clump

---
 src/LD.cpp    | 27 ++++++++++++++-------------
 src/Utils.hpp |  4 ++--
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/LD.cpp b/src/LD.cpp
index f1dcb38..4a6c326 100644
--- a/src/LD.cpp
+++ b/src/LD.cpp
@@ -69,19 +69,20 @@ std::tuple<Int2D, Int2D> get_target_snp_idx(const SNPld& snp_t,
   Int1D idx, bp;
   UMapIntInt mpos;
   int c, s, e, p, i;
-  Int1D ord;
-  for (c = 0; c < (int)snp.chr.size(); c++) {
-    i = 0;
-    while (snp_t.chr[i] != snp.chr[c]) {
-      i++;
-    }
-    ord.push_back(i);
-  }
-  if (!std::is_sorted(ord.begin(), ord.end()))
-    cao.error(
-        "the association file may be not sorted or not matching the order of "
-        ".kept.bim file!");
-
+  // Int1D ord;
+  // for (c = 0; c < (int)snp.chr.size(); c++) {
+  //   i = 0;
+  //   while (snp_t.chr[i] != snp.chr[c]) {
+  //     i++;
+  //   }
+  //   ord.push_back(i);
+  // }
+  // if (!std::is_sorted(ord.begin(), ord.end()))
+  //   cao.error(
+  //       "the association file may be not sorted or not matching the order of "
+  //       ".kept.bim file!");
+
+  cao.print("hellooooooooooooooooooooooooooo");
   Int2D idx_per_chr(snp_t.chr.size());
   Int2D bp_per_chr(snp_t.chr.size());
   for (int tc = 0; tc < (int)snp_t.chr.size(); tc++) {
diff --git a/src/Utils.hpp b/src/Utils.hpp
index 73ef46a..bce09da 100644
--- a/src/Utils.hpp
+++ b/src/Utils.hpp
@@ -51,8 +51,8 @@ struct SNPld {
   std::vector<int> pos;          // pos of each SNP
   std::vector<int> end_pos;      // 0-based index for last snp pos
   std::vector<std::string> chr;  // chr sequences
-  std::vector<int> ws;           //  the snp index, i.e the index for lead SNP
-  std::vector<int> we;  // the number of SNPs (including lead SNP) in a window
+  std::vector<int> ws, we;           //  the snp index, i.e the index for lead SNP
+  // std::vector<int> we;  // the number of SNPs (including lead SNP) in a window
   Double1D af;          // allele frequency
 };