added count.groups command and paralellized align.seqs for windows

diff --git a/aligncommand.cpp b/aligncommand.cpp
index b7c684311a5e186576d6f70c91dade75c76b31f4..87ceb2c41a2f22e8a3b55a672641a06095f7f0f2 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -934,7 +934,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                inFASTA.seekg(lines[processors-1]->start-1);
                char c = inFASTA.peek();
                
-               if (c == '>') { //we need to move back
+               if (c != '>') { //we need to move back
                        lines[processors-1]->start--; 
                }