added binary file operations to mothurout class. added comment to sequence class...

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 87027f4df5e0166f25852fec44cd6cfa120c90a7..bf27d264ec5f06f15a3d25b7ac8c5952cd03e17a 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -1298,9 +1298,11 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
         
         if (uniques.size() != 0) {
             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
+                if (m->control_pressed) { break; }
                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
             }
             for (map<string, pairFastqRead>:: iterator it = pairUniques.begin(); it != pairUniques.end(); it++) {
+                if (m->control_pressed) { break; }
                 m->mothurOut("[WARNING]: did not find paired read for " + (it->first).substr(1) + ", ignoring.\n");
             }
             m->mothurOutEndLine();
@@ -1660,6 +1662,7 @@ fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
         
         vector<int> qualScores = convertQual(quality);
         
+        m->checkName(name);
         read.name = name;
         read.sequence = sequence;
         read.scores = qualScores;