working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index ee8835386e1937bd8bc6d51ab2b0779f05f6a679..be75e4fac4ab60697b0dd84de6eeb275d231a5b3 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -170,7 +170,7 @@ int SeqSummaryCommand::execute(){
                                int tag = 2001;
                                int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
-                               vector<unsigned long int> MPIPos;
+                               vector<unsigned long long> MPIPos;
                                
                                MPI_Status status; 
                                MPI_Status statusOut;
@@ -281,7 +281,7 @@ int SeqSummaryCommand::execute(){
                                
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
-                       vector<unsigned long int> positions; 
+                       vector<unsigned long long> positions; 
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                positions = m->divideFile(fastafile, processors);
                                for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
@@ -332,14 +332,14 @@ int SeqSummaryCommand::execute(){
                if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
                
                m->mothurOutEndLine();
-               m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
-               m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
-               m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
-               m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
-               m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
-               m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); 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])); 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])); m->mothurOutEndLine();
+               m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
+               m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine();
+               m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine();
+               m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine();
+               m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine();
+               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();
                if (namefile == "") {  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(); }
                
@@ -415,7 +415,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        }
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = in.tellg();
+                               unsigned long long pos = in.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (in.eof()) { break; }
@@ -438,7 +438,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {       
+int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {      
        try {
                
                int pid;