modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 4eafaf8ed15e7fde8c60f9c3d80a376f1d796f3d..9ab27f9cbd439fe55ed1856c6940f0e42e6ee7e0 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -91,18 +91,20 @@ int SeqSummaryCommand::execute(){
 
                while(!inFASTA.eof()){
                        Sequence current(inFASTA);
-                       startPosition.push_back(current.getStartPos());
-                       endPosition.push_back(current.getEndPos());
-                       seqLength.push_back(current.getNumBases());
-                       ambigBases.push_back(current.getAmbigBases());
-                       longHomoPolymer.push_back(current.getLongHomoPolymer());
-
-                       outSummary << current.getName() << '\t';
-                       outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
-                       outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
-                       outSummary << current.getLongHomoPolymer() << endl;
-                       
-                       numSeqs++;
+                       if (current.getName() != "") {
+                               startPosition.push_back(current.getStartPos());
+                               endPosition.push_back(current.getEndPos());
+                               seqLength.push_back(current.getNumBases());
+                               ambigBases.push_back(current.getAmbigBases());
+                               longHomoPolymer.push_back(current.getLongHomoPolymer());
+                               
+                               outSummary << current.getName() << '\t';
+                               outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+                               outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+                               outSummary << current.getLongHomoPolymer() << endl;
+                               
+                               numSeqs++;
+                       }
                        gobble(inFASTA);
                }
                inFASTA.close();