X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.cpp;h=70aa55d38502237388c520aeae892daf4891e73c;hp=90a66f8f633212cf69a2930914a1911c5bca1cb1;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=2cfb747aa8f63bde9c1114001e6d2e81ccd26178

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 90a66f8..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(); }
@@ -448,7 +449,8 @@ 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; }
@@ -478,7 +480,6 @@ 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';
@@ -494,13 +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;
@@ -548,7 +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());