Help message clarification

apparently no one read it in detail (that's why the error can still be here after almost a year...)
choishingwan · Oct 13, 2017 · 4ed41c2 · 4ed41c2
1 parent cc3b6e5
commit 4ed41c2
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/PRSice.R b/PRSice.R
@@ -43,9 +43,9 @@ help_message <-
     --beta                  Whether the test statistic is in the form of \n
                             BETA or OR. If set, test statistic is assume\n
                             to be in the form of BETA.\n
-    --A1                    Column header containing the reference allele\n
+    --A1                    Column header containing allele 1 (effect allele)\n
                             Default: A1\n
-    --A2                    Column header containing the alternative allele\n
+    --A2                    Column header containing allele 2 (reference allele)\n
                             Default: A2\n
     --bp                    Column header containing the SNP coordinate\n
                             Default: BP\n

diff --git a/inc/prsice.hpp b/inc/prsice.hpp
@@ -64,11 +64,11 @@ class PRSice
         std::ofstream log_file_stream;
         log_file_stream.open(m_log_file.c_str(), std::ofstream::app);
         if (!log_file_stream.is_open()) {
-        	std::string error_message =
-        			"ERROR: Cannot open log file: " + m_log_file;
-        	throw std::runtime_error(error_message);
+            std::string error_message =
+                "ERROR: Cannot open log file: " + m_log_file;
+            throw std::runtime_error(error_message);
         }
-        log_file_stream << "Seed: "<< m_seed << std::endl;
+        log_file_stream << "Seed: " << m_seed << std::endl;
         log_file_stream.close();
         bool has_binary = false;
         for (auto&& b : m_target_binary) {

diff --git a/src/commander.cpp b/src/commander.cpp
@@ -533,11 +533,11 @@ void Commander::info()
         "                            BETA or OR. If set, test statistic is "
         "assume\n"
         "                            to be in the form of BETA.\n"
-        "    --A1                    Column header containing the reference "
-        "allele\n"
+        "    --A1                    Column header containing allele 1 (effect "
+        "allele)\n"
         "                            Default: A1\n"
-        "    --A2                    Column header containing the alternative "
-        "allele\n"
+        "    --A2                    Column header containing allele 2 "
+        "(reference allele)\n"
         "                            Default: A2\n"
         "    --bp                    Column header containing the SNP "
         "coordinate\n"