X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=bf702e13534f507576bee7c24bcf6462aacb7ca3;hp=051aa99434f6bb21a8d3b3b54cb2cc671eab98d2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 051aa99..bf702e1 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -14,7 +14,7 @@
 vector<string> ScreenSeqsCommand::setParameters(){	
 	try {
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
-        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,true,true); parameters.push_back(pcontigsreport);
+        CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,false,true); parameters.push_back(pcontigsreport);
         CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport);
         CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary);
         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
@@ -683,7 +683,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummary(positions); 
@@ -714,7 +714,7 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
             if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
             getSummaryReport();
@@ -817,7 +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;
@@ -1019,7 +1019,7 @@ int ScreenSeqsCommand::screenFasta(map<string, string>& badSeqNames){
 			if (namefile != "") { nameMap = m->readNames(namefile); }
             else if (countfile != "") {
                 CountTable ct;
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 nameMap = ct.getNameMap();
             }
 			getSummary(positions); 
@@ -1820,7 +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)])); }	
@@ -1845,8 +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)
@@ -2119,7 +2119,7 @@ int ScreenSeqsCommand::screenGroupFile(map<string, string> badSeqNames){
 		while(!inputGroups.eof()){
 			if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 
-			inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
+			inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group; m->gobble(inputGroups);
 			it = badSeqNames.find(seqName);
 			
 			if(it != badSeqNames.end()){
@@ -2128,7 +2128,6 @@ int ScreenSeqsCommand::screenGroupFile(map<string, string> badSeqNames){
 			else{
 				goodGroupOut << seqName << '\t' << group << endl;
 			}
-			m->gobble(inputGroups);
 		}
 		
 		if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
@@ -2177,19 +2176,18 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
 			if (m->control_pressed) { goodCountOut.close(); in.close(); m->mothurRemove(goodCountFile); return 0; }
             
 			in >> name; m->gobble(in); 
-            in >> thisTotal; m->gobble(in);
+            in >> thisTotal; 
             rest = m->getline(in); m->gobble(in);
             
 			it = badSeqNames.find(name);
 			
 			if(it != badSeqNames.end()){
-				badSeqNames.erase(it);
+				badSeqNames.erase(it); 
 			}
 			else{
 				goodCountOut << name << '\t' << thisTotal << '\t' << rest << endl;
 			}
 		}
-		
 		if (m->control_pressed) { goodCountOut.close();  in.close(); m->mothurRemove(goodCountFile);  return 0; }
         
 		//we were unable to remove some of the bad sequences
@@ -2206,7 +2204,7 @@ int ScreenSeqsCommand::screenCountFile(map<string, string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile, true);
+            ct.readTable(goodCountFile, true, false);
             ct.printTable(goodCountFile);
         }