working on pam

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index e9002bd7c12781eb6fd2fdb284da2ea06e65c4fa..70aa55d38502237388c520aeae892daf4891e73c 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -203,7 +203,7 @@ int SeqSummaryCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
                
@@ -364,7 +364,7 @@ int SeqSummaryCommand::execute(){
                int size = startPosition.size();
                
                //find means
-               double meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
+               unsigned long long meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
                meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
                for (int i = 0; i < size; i++) {
                        meanStartPosition += startPosition[i];
@@ -374,8 +374,9 @@ int SeqSummaryCommand::execute(){
                        meanLongHomoPolymer += longHomoPolymer[i];
                }
                 
-               //this is an int divide so the remainder is lost
-               meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
+        double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer;
+                
+               meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size;
                                
                int ptile0_25   = int(size * 0.025);
                int ptile25             = int(size * 0.250);
@@ -399,7 +400,7 @@ int SeqSummaryCommand::execute(){
                m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
                m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
                m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
-               m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
+               m->mothurOut("Mean:\t" + toString(meanstartPosition) + "\t" + toString(meanendPosition) + "\t" + toString(meanseqLength) + "\t" + toString(meanambigBases) + "\t" + toString(meanlongHomoPolymer)); m->mothurOutEndLine();
 
                if ((namefile == "") && (countfile == "")) {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
                else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
@@ -448,15 +449,20 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 
                bool done = false;
                int count = 0;
-       
+        
+        
                while (!done) {
                                
                        if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
-                                       
+            
+            if (m->debug) { m->mothurOut("[DEBUG]: count = " + toString(count) + "\n");  }
+            
                        Sequence current(in); m->gobble(in);
            
                        if (current.getName() != "") {
                                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n");  }
+                
                                int num = 1;
                                if ((namefile != "") || (countfile != "")) {
                                        //make sure this sequence is in the namefile, else error 
@@ -474,12 +480,13 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                        ambigBases.push_back(current.getAmbigBases());
                                        longHomoPolymer.push_back(current.getLongHomoPolymer());
                                }
-                               
                                count++;
                                outSummary << current.getName() << '\t';
                                outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
                                outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
                                outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + current.getName() + '\t' + toString(current.getNumBases()) + "\n");  }
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -488,13 +495,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        #else
                                if (in.eof()) { break; }
                        #endif
-                       
-                       //report progress
-                       //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
                }
-               //report progress
-               //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
-               
+                               
                in.close();
                
                return count;
@@ -542,7 +544,7 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPo
                                }
                                
                                //for each sequence this sequence represents
-                               for (int i = 0; i < num; i++) {
+                               for (int j = 0; j < num; j++) {
                                        startPosition.push_back(current.getStartPos());
                                        endPosition.push_back(current.getEndPos());
                                        seqLength.push_back(current.getNumBases());