fixed some bugs found while testing 1.8

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index d638bd2240a46ab20a7b5253e15be5a056a41aa4..1697ff7a0d57534b81e9b1f135cf494ae55c2d34 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -215,7 +215,7 @@ int PreClusterCommand::readFASTA(){
        }
 }
 /**************************************************************************************************/
-
+//this seems to require the names and fasta file to be in the same order???
 int PreClusterCommand::readNamesFASTA(){
        try {
                ifstream inNames;
@@ -238,7 +238,8 @@ int PreClusterCommand::readNamesFASTA(){
                                size++;
                                secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
                        }
-                       Sequence seq(inFasta);
+                       
+                       Sequence seq(inFasta);  gobble(inFasta);
                        if (seq.getName() != firstCol) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
                        else{
                                seqPNode tempNode(size, seq, nameString);