X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.cpp;h=70aa55d38502237388c520aeae892daf4891e73c;hp=fdf95ee6fc5f87ed7629de936f4b0543dc89906a;hb=a2cde58c1e72199498a2142983ef040dce36da10;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index fdf95ee..70aa55d 100644
--- 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(); }
@@ -415,6 +416,13 @@ int SeqSummaryCommand::execute(){
 			}
 		#endif
 
+        //set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("summary");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
+		}
+        
 		return 0;
 	}
 	catch(exception& e) {
@@ -441,15 +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 
@@ -467,12 +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)
@@ -481,13 +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;
@@ -535,7 +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());