From 28588ac3c083a35a94b6b8eeb4bc2a140455ea94 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Sat, 2 Jul 2022 17:20:19 +0100
Subject: [PATCH] fix bug for pcangsd

---
 CHANGELOG.org      |  3 +++
 Makefile           |  2 +-
 src/FileBeagle.cpp | 10 +++++-----
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.org b/CHANGELOG.org
index b25911e..e29a04e 100644
--- a/CHANGELOG.org
+++ b/CHANGELOG.org
@@ -1,3 +1,6 @@
+- v0.2.1
+  - bug fix for PCAngsd
+
 - v0.2.0
   - add =--maf= option for SNPs filtering
   - faster parser for beagle file
diff --git a/Makefile b/Makefile
index 15ce418..46861d8 100755
--- a/Makefile
+++ b/Makefile
@@ -19,7 +19,7 @@ IOMP5         = 0
 
 ########################### end ###########################
 
-VERSION=0.2.0
+VERSION=0.2.1
 # detect OS architecture and add flags
 Platform     := $(shell uname -s)
 
diff --git a/src/FileBeagle.cpp b/src/FileBeagle.cpp
index 3d5165d..355f2be 100644
--- a/src/FileBeagle.cpp
+++ b/src/FileBeagle.cpp
@@ -34,17 +34,17 @@ void FileBeagle::read_all()
     while (tgets(fp, &buffer, &bufsize))
     {
         if (buffer != original)
-        {
             original = buffer;
-        }
         tok = strtok_r(buffer, delims, &buffer);
         tok = strtok_r(NULL, delims, &buffer);
         tok = strtok_r(NULL, delims, &buffer);
-        for (i = 0; i < nsamples * 3; i++)
+        for (i = 0; i < nsamples; i++)
         {
             tok = strtok_r(NULL, delims, &buffer);
-            assert(tok != NULL);
-            P(i, j) = strtod(tok, NULL);
+            P(2 * i + 0, j) = strtod(tok, NULL);
+            tok = strtok_r(NULL, delims, &buffer);
+            P(2 * i + 1, j) = strtod(tok, NULL);
+            tok = strtok_r(NULL, delims, &buffer);
         }
         buffer = original;
         j++;