X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=641a3abce04bde1b8002e11af636fcd5e58bc6e2;hb=2a29fceeeb8754c3fd97ba830d2fbed5c4349ee8;hp=1fe60e8954acd14dc1a1e02d37c0d8bd987cc1c0;hpb=367747fb506bf228d3b2d645868d275ba0714e90;p=mothur.git

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 1fe60e8..641a3ab 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -298,7 +298,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
 			}
             else{
                 if(reportFileName != ""){
-                    m->mothurOut("we are ignoring the report file if your sequences are not aligned.  we will check that the sequences in your fasta and and qual fileare the same length.");
+                    m->mothurOut("we are ignoring the report file if your sequences are not aligned.  we will check that the sequences in your fasta and and qual file are the same length.");
                     m->mothurOutEndLine();
                 }
             }
@@ -407,6 +407,13 @@ int SeqErrorCommand::execute(){
 		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
 		m->mothurOutEndLine();
 		
+        //set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("errorseq");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
+        
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -759,7 +766,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
             int numParentSeqs = -1;
             int closestRefIndex = -1;
                         
-            numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned(), outChimeraReport);
+            string querySeq = query.getAligned();
+            if (!aligned) {  querySeq = query.getUnaligned();  }
+            
+            numParentSeqs = chimeraTest.analyzeQuery(query.getName(), querySeq, outChimeraReport);
             
             closestRefIndex = chimeraTest.getClosestRefIndex();
             
@@ -1378,6 +1388,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
 					
 					string sname = "";  nameStream >> sname;
 					sname = sname.substr(1);
+                    
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
 					
 					map<string, int>::iterator it = firstSeqNames.find(sname);
 					
@@ -1438,6 +1452,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
+                    
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                 
                     if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk