Updates to release info

#792

Makefile

@@ -37,8 +37,8 @@ GSL_LIBRARY_DIR ?= "\"Enter_your_GSL_library_path_here\""
 GSL_INCLUDE_DIR ?= "\"Enter_your_GSL_include_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
 MOTHUR_TOOLS="\"Enter_your_mothur_tools_path_here\""
-VERSION = "\"1.46.0\""
-RELEASE_DATE = "\"8/25/21\""
+VERSION = "\"1.47.0\""
+RELEASE_DATE = "\"1/21/22\""
 
 
 # Set a static logfile name

Makefile_cluster

@@ -1,7 +1,7 @@
 USEREADLINE ?= yes
 USEBOOST ?= yes
-VERSION = "\"1.45.2\""
-RELEASE_DATE = "\"4/9/21\""
+VERSION = "\"1.47.0\""
+RELEASE_DATE = "\"1/21/22\""
 MOTHUR_TOOLS="\"/nfs/turbo/schloss-lab/bin/mothur_src/tools/\"" 
 
 # Optimize to level 3:

Mothur.xcodeproj/project.pbxproj

@@ -4086,7 +4086,7 @@
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"/Users/swestcott/Desktop/release\\\"\"",
-					"VERSION=\"\\\"1.44.3\\\"\"",
+					"VERSION=\"\\\"1.47.0\\\"\"",
 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
 					"MOTHUR_TOOLS=\"\\\"/Users/swestcott/desktop/mothur/tools/\\\"\"",
 				);
@@ -4176,7 +4176,7 @@
 				GCC_NO_COMMON_BLOCKS = YES;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.44.3\\\"\"",
+					"VERSION=\"\\\"1.47.0\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/swestcott/Desktop/release\\\"\"",
 					"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
 					"MOTHUR_TOOLS=\"\\\"/Users/swestcott/desktop/mothur/tools/\\\"\"",

makefile-internal

@@ -4,8 +4,8 @@ USEBOOST ?= yes
 USEHDF5 ?= yes
 USEGSL ?= yes
 LOGFILE_NAME ?= yes
-VERSION = "\"1.44.3\""
-RELEASE_DATE = "\"1/21/21\""
+VERSION = "\"1.47.0\""
+RELEASE_DATE = "\"1/21/22\""
 
 # Optimize to level 3:
     CXXFLAGS += -O3 -std=c++11

source/commands/seqerrorcommand.cpp

@@ -261,8 +261,49 @@ int SeqErrorCommand::execute(){
 			megAlignmentFile << megaAlignVector[i] << endl;
 		}
         megAlignmentFile.close();
+
+        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.\n");
+
+
+        bool extraOutput = false;
+        if (extraOutput) {
+            //read error.chimera
+            ifstream in; util.openInputFile(errorChimeraFileName, in);
+            int chimeraCount = 0;
+            while (!in.eof()) {
+                if (m->getControl_pressed()) { break; }
+
+                string line = util.getline(in); util.gobble(in);
+                vector<string> pieces = util.splitWhiteSpace(line);
+
+                if (pieces.size() != 0) {
+                    if (pieces[pieces.size()-1] == "2") {
+                        chimeraCount++;
+                    }
+                }
+            }
+            in.close();
+            m->mothurOut("\nTrue chimeras found: " + toString(chimeraCount) + "\n");
+            m->mothurOut("\nReference names for chimeras:\n\n");
+
+            //read error.summary to extract names of parents
+            ifstream in2; util.openInputFile(errorSummaryFileName, in2);
+            while (!in2.eof()) {
+                if (m->getControl_pressed()) { break; }
+
+                string line = util.getline(in2); util.gobble(in2);
+                vector<string> pieces = util.splitWhiteSpace(line);
+
+                if (pieces.size() != 0) {
+                    if (pieces[pieces.size()-1] == "2") {
+                        cout << pieces[1] << endl;
+                    }
+                }
+            }
+            in2.close();
+
+        }
 
-		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.\n");
 
 		m->mothurOut("\nOutput File Names: \n");
 		for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]+"\n");  }