X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=e7b2c6acedf523f8249c8159ed186a6b8d5b8892;hp=033fbcad422abb62cd2470866bd4666db9e907bd;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=b0997605981902442138b9309e9c43d95c3ba10a

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 033fbca..e7b2c6a 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -294,7 +294,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
             
             summaryfile = validParameter.validFile(parameters, "summary", true);
 			if (summaryfile == "not open") { summaryfile = ""; abort = true; }
-			else if (summaryfile == "not found") { summaryfile = "";  }	
+			else if (summaryfile == "not found") { summaryfile = "";  }
+            else { m->setSummaryFile(summaryfile); }
             
             if ((namefile != "") && (countfile != "")) {
                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
@@ -682,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -713,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -816,7 +817,7 @@ int ScreenSeqsCommand::screenAlignReport(map<string, string>& badSeqNames){
             m->mothurRemove(outSummary+".temp");
         }
         
-        if (numFastaSeqs != count) {  m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; }
+        if (numFastaSeqs != count) {  m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your align report file, quitting.\n"); m->control_pressed = true; }
         
         
         return count;
@@ -1018,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
 			if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
                 nameMap = ct.getNameMap();
             }
 			getSummary(positions); 
@@ -1819,7 +1820,6 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 		vector<int> longHomoPolymer;
         vector<int> numNs;
 		
-        vector<unsigned long long> positions;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		positions = m->divideFile(fastafile, processors);
 		for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }	
@@ -1844,8 +1844,9 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 		int pid;
 		MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 		
-		if (pid == 0) { 
-			driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]);
+		if (pid == 0) {
+            linePair tempLine(0, positions[positions.size()-1]);
+			driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, tempLine);
 #else
 		int numSeqs = 0;
 		//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -2205,7 +2206,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }
 		
@@ -2408,10 +2409,10 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 		}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 	}
 		
 			
 		goodFile.close();
@@ -2503,7 +2504,7 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
 			}
 			
 			//report progress
-			if((i) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();		}
+			if((i) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n"); 		}
 		}
 				
 		return 1;