changed random forest output filename

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 3718c9a9c0cf843d9f91311b8b7b3cdee814f455..e7b2c6acedf523f8249c8159ed186a6b8d5b8892 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -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);
+                ct.readTable(countfile, true);
                 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);
+                ct.readTable(countfile, true);
                 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);
+                ct.readTable(countfile, true);
                 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)
@@ -2206,7 +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);
         }
                
@@ -2409,10 +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();
@@ -2504,7 +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;