added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 3bf0d572f88d0ad7ffd76989d71f10807e8cc659..7726b3e00cca9de19971b70656f9581e43e97c8a 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -249,7 +249,8 @@ int Classify::readTaxonomy(string file) {
                
                m->mothurOutEndLine();
                m->mothurOut("Reading in the " + file + " taxonomy...\t");      cout.flush();
-
+        if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
+        
 #ifdef USE_MPI 
                int pid, num, processors;
                vector<unsigned long long> positions;
@@ -296,7 +297,9 @@ int Classify::readTaxonomy(string file) {
                        delete buf4;
 
                        istringstream iss (tempBuf,istringstream::in);
-                       iss >> name >> taxInfo;
+                       iss >> name; m->gobble(iss);
+            iss >> taxInfo;
+            if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
                        taxonomy[name] = taxInfo;
                        phyloTree->addSeqToTree(name, taxInfo);
                }
@@ -309,8 +312,11 @@ int Classify::readTaxonomy(string file) {
        
                //read template seqs and save
                while (!inTax.eof()) {
-                       inTax >> name >> taxInfo;
-                       
+                       inTax >> name; m->gobble(inTax);
+            inTax >> taxInfo;
+            
+            if (m->debug) {  m->mothurOut("[DEBUG]: name = '" + name + "' tax = '" + taxInfo + "'\n");  }
+
                        taxonomy[name] = taxInfo;
                        
                        phyloTree->addSeqToTree(name, taxInfo);
@@ -319,6 +325,8 @@ int Classify::readTaxonomy(string file) {
                }
                inTax.close();
 #endif 
+        
+        
        
                phyloTree->assignHeirarchyIDs(0);