added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 5b81210e89365a9d98048d10c92e9c518fe01938..7ce90733b72b02d6f05175d14b61f73599b58d2c 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,6 +44,7 @@ int GroupMap::readMap() {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -67,6 +68,8 @@ int GroupMap::readMap() {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -110,6 +113,8 @@ int GroupMap::readDesignMap() {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -133,6 +138,8 @@ int GroupMap::readDesignMap() {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -180,6 +187,8 @@ int GroupMap::readDesignMap(string filename) {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -203,6 +212,8 @@ int GroupMap::readDesignMap(string filename) {
                 if (pairDone) { 
                     setNamesOfGroups(seqGroup);
                     
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    
                     it = groupmap.find(seqName);
                     
                     if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }