From: westcott <westcott>
Date: Tue, 17 May 2011 19:06:36 +0000 (+0000)
Subject: added parameter to chimera.uchime
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=1e8d08e96f4fe99604a6b3502568de464bf60891

added parameter to chimera.uchime
---

diff --git a/addtargets2.cpp b/addtargets2.cpp
index 4e0dbd1..57a4ef5 100644
--- a/addtargets2.cpp
+++ b/addtargets2.cpp
@@ -1,5 +1,5 @@
 //#if	UCHIMES
-
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
 #include "myutils.h"
 #include "chime.h"
 #include "ultra.h"
diff --git a/alignchime.cpp b/alignchime.cpp
index d7b05a8..c97c333 100644
--- a/alignchime.cpp
+++ b/alignchime.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "seq.h"
 #include "chime.h"
diff --git a/alignchimel.cpp b/alignchimel.cpp
index ae152af..8f4cbd5 100644
--- a/alignchimel.cpp
+++ b/alignchimel.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "seq.h"
 #include "chime.h"
diff --git a/alnheuristics.h b/alnheuristics.h
index 9a8d283..cd346cf 100644
--- a/alnheuristics.h
+++ b/alnheuristics.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef alnheuristics_h
 #define alnheuristics_h
 
diff --git a/alnparams.cpp b/alnparams.cpp
index d1b9036..41ee738 100644
--- a/alnparams.cpp
+++ b/alnparams.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include <float.h>	// for FLT_MAX
 #include "mx.h"
@@ -6,12 +8,12 @@
 
 #define TEST	0
 
-void SetBLOSUM62();
+void SetBLOSUM62();
 void SetNucSubstMx(double Match, double Mismatch);
 void ReadSubstMx(const string &FileName, Mx<float> &Mxf);
-
-extern Mx<float> g_SubstMxf;
-extern float **g_SubstMx;
+
+extern Mx<float> g_SubstMxf;
+extern float **g_SubstMx;
 
 void AlnParams::Clear()
 	{
@@ -313,14 +315,14 @@ void AlnParams::SetPenalties(const string &OpenStr, const string &ExtStr)
 void AlnParams::SetMxFromCmdLine(bool IsNucleo)
 	{
 	if (IsNucleo)
-		SetNucSubstMx(opt_match, opt_mismatch);
+		SetNucSubstMx(opt_match, opt_mismatch);
 	else
 		{
 		if (opt_matrix == "")
 			{
 			SubstMxName = "BLOSUM62";
-			SetBLOSUM62();
-			}
+			SetBLOSUM62();
+			}
 		else
 			{
 			ReadSubstMx(opt_matrix, g_SubstMxf);
@@ -361,9 +363,9 @@ void AlnParams::InitFromCmdLine(bool IsNucleo)
 
 // Global
 	if (IsNucleo)
-		Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
+		Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
 	else
-		Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
+		Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
 	SetPenalties(opt_gapopen, opt_gapext);
 	}
 
diff --git a/alnparams.h b/alnparams.h
index 4037912..b159179 100644
--- a/alnparams.h
+++ b/alnparams.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef alnparams_h
 #define alnparams_h
 
diff --git a/alpha.cpp b/alpha.cpp
index 0efca3b..9d82f35 100644
--- a/alpha.cpp
+++ b/alpha.cpp
@@ -1,4 +1,5 @@
 // Generated by /p/py/alphac.py
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
 #include "alpha.h"
 
 unsigned g_CharToLetterAminoStop[256] =
diff --git a/alpha.h b/alpha.h
index e021b7f..e491c9c 100644
--- a/alpha.h
+++ b/alpha.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef alpha_h
 #define alpha_h
 
diff --git a/alpha2.cpp b/alpha2.cpp
index 26bc1c6..08f6e21 100644
--- a/alpha2.cpp
+++ b/alpha2.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "alpha.h"
 #include "timing.h"
diff --git a/blastdb.cpp b/blastdb.cpp
index 70349e5..b1a7b48 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -83,8 +83,10 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 			blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
 			blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
 		#else
-			blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
+			blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
 			blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
 		#endif
 		system(blastCommand.c_str());
 		
@@ -140,8 +142,11 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 			blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 			blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
 		#else
-			blastCommand =  "\"" + path + "blast\\bin\\megablast\" -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+			blastCommand =  "\"" + path + "blast\\bin\\megablast\" -e 1e-10 -d " + "\"" + dbFileName + "\"" + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 			blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
+
 		#endif
 		
 		system(blastCommand.c_str());
@@ -213,7 +218,9 @@ void BlastDB::generateDB() {
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;	//	format the database, -o option gives us the ability
 		#else
-			formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + dbFileName;
+			formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" +  dbFileName + "\"";
+			//wrap entire string in ""
+			formatdbCommand = "\"" + formatdbCommand + "\"";
 		#endif
 		system(formatdbCommand.c_str());								//	to get the right sequence names, i think. -p F
 																	//	option tells formatdb that seqs are DNA, not prot
diff --git a/chainer.h b/chainer.h
index a954dc0..7f54131 100644
--- a/chainer.h
+++ b/chainer.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef chainer_h
 #define chainer_h
 
diff --git a/chime.h b/chime.h
index 1b0662a..f143ea1 100644
--- a/chime.h
+++ b/chime.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef chime_h
 #define chime_h
 
diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 891b77b..a47aed0 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -22,6 +22,24 @@ vector<string> ChimeraUchimeCommand::setParameters(){
 		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pabskew("abskew", "Number", "", "1.9", "", "", "",false,false); parameters.push_back(pabskew);
+		CommandParameter pchimealns("chimealns", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pchimealns);
+		CommandParameter pminh("minh", "Number", "", "0.3", "", "", "",false,false); parameters.push_back(pminh);
+		CommandParameter pmindiv("mindiv", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pmindiv);
+		CommandParameter pxn("xn", "Number", "", "8.0", "", "", "",false,false); parameters.push_back(pxn);
+		CommandParameter pdn("dn", "Number", "", "1.4", "", "", "",false,false); parameters.push_back(pdn);
+		CommandParameter pxa("xa", "Number", "", "1", "", "", "",false,false); parameters.push_back(pxa);
+		CommandParameter pchunks("chunks", "Number", "", "4", "", "", "",false,false); parameters.push_back(pchunks);
+		CommandParameter pminchunk("minchunk", "Number", "", "64", "", "", "",false,false); parameters.push_back(pminchunk);
+		CommandParameter pidsmoothwindow("idsmoothwindow", "Number", "", "32", "", "", "",false,false); parameters.push_back(pidsmoothwindow);
+		CommandParameter pminsmoothid("minsmoothid", "Number", "", "0.95", "", "", "",false,false); parameters.push_back(pminsmoothid);
+		CommandParameter pmaxp("maxp", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxp);
+		CommandParameter pskipgaps("skipgaps", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps);
+		CommandParameter pskipgaps2("skipgaps2", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pskipgaps2);
+		CommandParameter pminlen("minlen", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminlen);
+		CommandParameter pmaxlen("maxlen", "Number", "", "10000", "", "", "",false,false); parameters.push_back(pmaxlen);
+		CommandParameter pucl("ucl", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pucl);
+		CommandParameter pqueryfract("queryfract", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pqueryfract);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -38,12 +56,30 @@ string ChimeraUchimeCommand::getHelpString(){
 		string helpString = "";
 		helpString += "The chimera.uchime command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
 		helpString += "This command is a wrapper for uchime written by Robert C. Edgar.\n";
-		helpString += "The chimera.uchime command parameters are fasta, name, reference and processors.\n";
+		helpString += "The chimera.uchime command parameters are fasta, name, reference, processors, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl and queryfact.\n";
 		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
 		helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
 		helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
 		helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
 		helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
+		helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n";
+		helpString += "The chimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n";
+		helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
+		helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease --min h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
+		helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n";
+		helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n";
+		helpString += "The xa parameter - weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2.\n";
+		helpString += "The chunks parameter is the number of chunks to extract from the query sequence when searching for parents. Default 4.\n";
+		helpString += "The minchunk parameter is the minimum length of a chunk. Default 64.\n";
+		helpString += "The idsmoothwindow parameter is the length of id smoothing window. Default 32.\n";
+		helpString += "The minsmoothid parameter - minimum factional identity over smoothed window of candidate parent. Default 0.95.\n";
+		helpString += "The maxp parameter - maximum number of candidate parents to consider. Default 2. In tests so far, increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit.\n";
+		helpString += "The skipgaps parameter controls how gapped columns affect counting of diffs. If skipgaps is set to T, columns containing gaps do not found as diffs. Default = T.\n";
+		helpString += "The skipgaps2 parameter controls how gapped columns affect counting of diffs. If skipgaps2 is set to T, if column is immediately adjacent to a column containing a gap, it is not counted as a diff. Default = T.\n";
+		helpString += "The minlen parameter is the minimum unaligned sequence length. Defaults 10. Applies to both query and reference sequences.\n";
+		helpString += "The maxlen parameter is the maximum unaligned sequence length. Defaults 10000. Applies to both query and reference sequences.\n";
+		helpString += "The ucl parameter - use local-X alignments. Default is global-X or false. On tests so far, global-X is always better; this option is retained because it just might work well on some future type of data.\n";
+		helpString += "The queryfract parameter - minimum fraction of the query sequence that must be covered by a local-X alignment. Default 0.5. Applies only when ucl is true.\n";
 #ifdef USE_MPI
 		helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
 #endif
@@ -66,6 +102,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(){
 		vector<string> tempOutNames;
 		outputTypes["chimera"] = tempOutNames;
 		outputTypes["accnos"] = tempOutNames;
+		outputTypes["alns"] = tempOutNames;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraUchimeCommand", "ChimeraUchimeCommand");
@@ -98,6 +135,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			vector<string> tempOutNames;
 			outputTypes["chimera"] = tempOutNames;
 			outputTypes["accnos"] = tempOutNames;
+			outputTypes["alns"] = tempOutNames;
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
@@ -278,6 +316,38 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
 			convert(temp, processors);
+			
+			abskew = validParameter.validFile(parameters, "abskew", false);	if (abskew == "not found"){	useAbskew = false;  abskew = "1.9";	}else{  useAbskew = true;  }
+			if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
+			
+			temp = validParameter.validFile(parameters, "chimealns", false);			if (temp == "not found") { temp = "f"; }
+			chimealns = m->isTrue(temp); 
+			
+			minh = validParameter.validFile(parameters, "minh", false);						if (minh == "not found")			{ useMinH = false; minh = "0.3";					}	else{ useMinH = true;			}
+			mindiv = validParameter.validFile(parameters, "mindiv", false);					if (mindiv == "not found")			{ useMindiv = false; mindiv = "0.5";				}	else{ useMindiv = true;			}
+			xn = validParameter.validFile(parameters, "xn", false);							if (xn == "not found")				{ useXn = false; xn = "8.0";						}	else{ useXn = true;				}
+			dn = validParameter.validFile(parameters, "dn", false);							if (dn == "not found")				{ useDn = false; dn = "1.4";						}	else{ useDn = true;				}
+			xa = validParameter.validFile(parameters, "xa", false);							if (xa == "not found")				{ useXa = false; xa = "1";							}	else{ useXa = true;				}
+			chunks = validParameter.validFile(parameters, "chunks", false);					if (chunks == "not found")			{ useChunks = false; chunks = "4";					}	else{ useChunks = true;			}
+			minchunk = validParameter.validFile(parameters, "minchunk", false);				if (minchunk == "not found")		{ useMinchunk = false; minchunk = "64";				}	else{ useMinchunk = true;		}
+			idsmoothwindow = validParameter.validFile(parameters, "idsmoothwindow", false);	if (idsmoothwindow == "not found")	{ useIdsmoothwindow = false; idsmoothwindow = "32";	}	else{ useIdsmoothwindow = true;	}
+			minsmoothid = validParameter.validFile(parameters, "minsmoothid", false);		if (minsmoothid == "not found")		{ useMinsmoothid = false; minsmoothid = "0.95";		}	else{ useMinsmoothid = true;	}
+			maxp = validParameter.validFile(parameters, "maxp", false);						if (maxp == "not found")			{ useMaxp = false; maxp = "2";						}	else{ useMaxp = true;			}
+			minlen = validParameter.validFile(parameters, "minlen", false);					if (minlen == "not found")			{ useMinlen = false; minlen = "10";					}	else{ useMinlen = true;			}
+			maxlen = validParameter.validFile(parameters, "maxlen", false);					if (maxlen == "not found")			{ useMaxlen = false; maxlen = "10000";				}	else{ useMaxlen = true;			}
+			
+			temp = validParameter.validFile(parameters, "ucl", false);						if (temp == "not found") { temp = "f"; }
+			ucl = m->isTrue(temp);
+			
+			queryfract = validParameter.validFile(parameters, "queryfract", false);			if (queryfract == "not found")		{ useQueryfract = false; queryfract = "0.5";		}	else{ useQueryfract = true;		}
+			if (!ucl && useQueryfract) { m->mothurOut("queryfact may only be used when ucl=t, ignoring."); m->mothurOutEndLine(); useQueryfract = false; }
+			
+			temp = validParameter.validFile(parameters, "skipgaps", false);					if (temp == "not found") { temp = "t"; }
+			skipgaps = m->isTrue(temp); 
+
+			temp = validParameter.validFile(parameters, "skipgaps2", false);				if (temp == "not found") { temp = "t"; }
+			skipgaps2 = m->isTrue(temp); 
+
 		}
 	}
 	catch(exception& e) {
@@ -291,6 +361,8 @@ int ChimeraUchimeCommand::execute(){
 	try{
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
+		m->mothurOut("\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n");
+		
 		for (int s = 0; s < fastaFileNames.size(); s++) {
 			
 			m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
@@ -375,23 +447,27 @@ int ChimeraUchimeCommand::execute(){
 			}
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it				
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
-			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.chimera";
+			string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.accnos";
+			string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "uchime.alns";
 			
 			if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	}  return 0;	}
 			
 			int numSeqs = 0;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName); }
-			else{	numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); }
+			if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName); }
+			else{	numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName); }
 #else
-			numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName);
+			numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName);
 #endif
 			if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str());	} return 0; }
-
+			
+			//remove file made for uchime
+			if (templatefile == "self") {  remove(fastaFileNames[s].c_str()); }
 			
 			outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 			outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
+			if (chimealns) { outputNames.push_back(alnsFileName); outputTypes["alns"].push_back(alnsFileName); }
 			
 			m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");	m->mothurOutEndLine();
 		}
@@ -418,7 +494,7 @@ int ChimeraUchimeCommand::execute(){
 }
 //**********************************************************************************************************************
 
-int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos){
+int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns){
 	try {
 		
 		vector<char*> cPara;
@@ -453,6 +529,160 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 		strcpy(tempout, outputFName.c_str());
 		cPara.push_back(tempout);
 		
+		if (chimealns) {
+			char* tempA = new char[12]; 
+			strcpy(tempA, "--uchimealns"); 
+			cPara.push_back(tempA);
+			char* tempa = new char[alns.length()];
+			strcpy(tempa, alns.c_str());
+			cPara.push_back(tempa);
+		}
+		
+		if (useAbskew) {
+			char* tempskew = new char[8]; 
+			strcpy(tempskew, "--abskew"); 
+			cPara.push_back(tempskew);
+			char* tempSkew = new char[abskew.length()];
+			strcpy(tempSkew, abskew.c_str());
+			cPara.push_back(tempSkew);
+		}
+		
+		if (useMinH) {
+			char* tempminh = new char[6]; 
+			strcpy(tempminh, "--minh"); 
+			cPara.push_back(tempminh);
+			char* tempMinH = new char[minh.length()];
+			strcpy(tempMinH, minh.c_str());
+			cPara.push_back(tempMinH);
+		}
+		
+		if (useMindiv) {
+			char* tempmindiv = new char[8]; 
+			strcpy(tempmindiv, "--mindiv"); 
+			cPara.push_back(tempmindiv);
+			char* tempMindiv = new char[mindiv.length()];
+			strcpy(tempMindiv, mindiv.c_str());
+			cPara.push_back(tempMindiv);
+		}
+		
+		if (useXn) {
+			char* tempxn = new char[4]; 
+			strcpy(tempxn, "--xn"); 
+			cPara.push_back(tempxn);
+			char* tempXn = new char[xn.length()];
+			strcpy(tempXn, xn.c_str());
+			cPara.push_back(tempXn);
+		}
+		
+		if (useDn) {
+			char* tempdn = new char[4]; 
+			strcpy(tempdn, "--dn"); 
+			cPara.push_back(tempdn);
+			char* tempDn = new char[dn.length()];
+			strcpy(tempDn, dn.c_str());
+			cPara.push_back(tempDn);
+		}
+		
+		if (useXa) {
+			char* tempxa = new char[4]; 
+			strcpy(tempxa, "--xa"); 
+			cPara.push_back(tempxa);
+			char* tempXa = new char[xa.length()];
+			strcpy(tempXa, xa.c_str());
+			cPara.push_back(tempXa);
+		}
+		
+		if (useChunks) {
+			char* tempchunks = new char[8]; 
+			strcpy(tempchunks, "--chunks"); 
+			cPara.push_back(tempchunks);
+			char* tempChunks = new char[chunks.length()];
+			strcpy(tempChunks, chunks.c_str());
+			cPara.push_back(tempChunks);
+		}
+		
+		if (useMinchunk) {
+			char* tempminchunk = new char[10]; 
+			strcpy(tempminchunk, "--minchunk"); 
+			cPara.push_back(tempminchunk);
+			char* tempMinchunk = new char[minchunk.length()];
+			strcpy(tempMinchunk, minchunk.c_str());
+			cPara.push_back(tempMinchunk);
+		}
+		
+		if (useIdsmoothwindow) {
+			char* tempidsmoothwindow = new char[16]; 
+			strcpy(tempidsmoothwindow, "--idsmoothwindow"); 
+			cPara.push_back(tempidsmoothwindow);
+			char* tempIdsmoothwindow = new char[idsmoothwindow.length()];
+			strcpy(tempIdsmoothwindow, idsmoothwindow.c_str());
+			cPara.push_back(tempIdsmoothwindow);
+		}
+		
+		if (useMinsmoothid) {
+			char* tempminsmoothid = new char[13]; 
+			strcpy(tempminsmoothid, "--minsmoothid"); 
+			cPara.push_back(tempminsmoothid);
+			char* tempMinsmoothid = new char[minsmoothid.length()];
+			strcpy(tempMinsmoothid, minsmoothid.c_str());
+			cPara.push_back(tempMinsmoothid);
+		}
+		
+		if (useMaxp) {
+			char* tempmaxp = new char[6]; 
+			strcpy(tempmaxp, "--maxp"); 
+			cPara.push_back(tempmaxp);
+			char* tempMaxp = new char[maxp.length()];
+			strcpy(tempMaxp, maxp.c_str());
+			cPara.push_back(tempMaxp);
+		}
+		
+		if (!skipgaps) {
+			char* tempskipgaps = new char[14]; 
+			strcpy(tempskipgaps, "--[no]skipgaps"); 
+			cPara.push_back(tempskipgaps);
+		}
+		
+		if (!skipgaps2) {
+			char* tempskipgaps2 = new char[15]; 
+			strcpy(tempskipgaps2, "--[no]skipgaps2"); 
+			cPara.push_back(tempskipgaps2);
+		}
+		
+		if (useMinlen) {
+			char* tempminlen = new char[8]; 
+			strcpy(tempminlen, "--minlen"); 
+			cPara.push_back(tempminlen);
+			char* tempMinlen = new char[minlen.length()];
+			strcpy(tempMinlen, minlen.c_str());
+			cPara.push_back(tempMinlen);
+		}
+		
+		if (useMaxlen) {
+			char* tempmaxlen = new char[8]; 
+			strcpy(tempmaxlen, "--maxlen"); 
+			cPara.push_back(tempmaxlen);
+			char* tempMaxlen = new char[maxlen.length()];
+			strcpy(tempMaxlen, maxlen.c_str());
+			cPara.push_back(tempMaxlen);
+		}
+		
+		if (ucl) {
+			char* tempucl = new char[5]; 
+			strcpy(tempucl, "--ucl"); 
+			cPara.push_back(tempucl);
+		}
+		
+		if (useQueryfract) {
+			char* tempqueryfract = new char[12]; 
+			strcpy(tempqueryfract, "--queryfract"); 
+			cPara.push_back(tempqueryfract);
+			char* tempQueryfract = new char[queryfract.length()];
+			strcpy(tempQueryfract, queryfract.c_str());
+			cPara.push_back(tempQueryfract);
+		}
+		
+		
 		char** uchimeParameters;
 		uchimeParameters = new char*[cPara.size()];
 		for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  } 
@@ -504,7 +734,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 }
 /**************************************************************************************************/
 
-int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename, string accnos) {
+int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename, string accnos, string alns) {
 	try {
 		
 		processIDS.clear();
@@ -526,7 +756,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 		MPI_Comm_size(MPI_COMM_WORLD, &processors); 
 				
 		if (pid == 0) { //you are the root process 
-			num = driver(outputFileName, files[0], accnos);
+			num = driver(outputFileName, files[0], accnos, alns);
 			
 			if (templatefile != "self") {
 				//wait on chidren
@@ -540,11 +770,16 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 					
 					m->appendFiles((accnos + toString(j) + ".temp"), accnos);
 					remove((accnos + toString(j) + ".temp").c_str());
+					
+					if (chimealns) {
+						m->appendFiles((alns + toString(j) + ".temp"), alns);
+						remove((alns + toString(j) + ".temp").c_str());
+					}
 				}
 			}
 		}else{ //you are a child process
 			if (templatefile != "self") { //if template=self we can only use 1 processor
-				num = driver(outputFileName+toString(pid) + ".temp", files[pid], accnos+toString(pid) + ".temp");	
+				num = driver(outputFileName+toString(pid) + ".temp", files[pid], accnos+toString(pid) + ".temp", alns+toString(pid) + ".temp");	
 				
 				//send numSeqs to parent
 				MPI_Send(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
@@ -562,7 +797,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				num = driver(outputFileName + toString(getpid()) + ".temp", files[process], accnos + toString(getpid()) + ".temp");
+				num = driver(outputFileName + toString(getpid()) + ".temp", files[process], accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp");
 				
 				//pass numSeqs to parent
 				ofstream out;
@@ -580,7 +815,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 		}
 		
 		//do my part
-		num = driver(outputFileName, files[0], accnos);
+		num = driver(outputFileName, files[0], accnos, alns);
 		
 		//force parent to wait until all the processes are done
 		for (int i=0;i<processIDS.size();i++) { 
@@ -604,6 +839,11 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 			
 			m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
 			remove((accnos + toString(processIDS[i]) + ".temp").c_str());
+			
+			if (chimealns) {
+				m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
+				remove((alns + toString(processIDS[i]) + ".temp").c_str());
+			}
 		}
 #endif		
 		//get rid of the file pieces.
diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 36e4a39..a7d5ad6 100644
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -26,7 +26,7 @@ public:
 	string getCommandName()			{ return "chimera.uchime";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
 	string getHelpString();	
-	string getCitation() { return "http://drive5.com/uchime/ \nhttp://www.mothur.org/wiki/Chimera.uchime"; }
+	string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime"; }
 	
 	
 	int execute(); 
@@ -34,15 +34,11 @@ public:
 	
 private:
 	vector<int> processIDS;   //processid
-	int driver(string, string, string);
-	int createProcesses(string, string, string);
-	
-#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
-#endif
-	
-	bool abort;
-	string fastafile, templatefile, outputDir, namefile;
+	int driver(string, string, string, string);
+	int createProcesses(string, string, string, string);
+		
+	bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
+	string fastafile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
 	int processors;
 	
 	vector<string> outputNames;
diff --git a/diagbox.h b/diagbox.h
index 0c5846c..2491a58 100644
--- a/diagbox.h
+++ b/diagbox.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef diagbox_h
 #define diagbox_h
 
@@ -184,10 +186,10 @@ Don't have proof..
 		}
 	};
 
-typedef const char *(*NWDIAG)(const byte *A, unsigned LA, const byte *B, unsigned LB,
-  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
-
-const char *NWBandWrap(NWDIAG NW, const byte *A, unsigned LA, const byte *B, unsigned LB,
-  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
+typedef const char *(*NWDIAG)(const byte *A, unsigned LA, const byte *B, unsigned LB,
+  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
+
+const char *NWBandWrap(NWDIAG NW, const byte *A, unsigned LA, const byte *B, unsigned LB,
+  unsigned DiagLo, unsigned DiagHi, bool LeftTerm, bool RightTerm);
 
 #endif // diagbox_h
diff --git a/dp.h b/dp.h
index c771538..d8581fb 100644
--- a/dp.h
+++ b/dp.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef dp_h
 #define dp_h
 
diff --git a/evalue.h b/evalue.h
index c9308db..fe324f8 100644
--- a/evalue.h
+++ b/evalue.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef evalue_h
 #define evalue_h
 
diff --git a/fractid.cpp b/fractid.cpp
index f298877..ad4c157 100644
--- a/fractid.cpp
+++ b/fractid.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "alpha.h"
 
diff --git a/getparents.cpp b/getparents.cpp
index d82f902..26a2cd1 100644
--- a/getparents.cpp
+++ b/getparents.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "chime.h"
 #include "ultra.h"
diff --git a/globalalign2.cpp b/globalalign2.cpp
index 6bb35a9..10f8032 100644
--- a/globalalign2.cpp
+++ b/globalalign2.cpp
@@ -1,5 +1,5 @@
 //#if	UCHIMES
-
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
 #include "dp.h"
 #include "seq.h"
 
diff --git a/help.h b/help.h
index 9d7a89f..1534cd1 100644
--- a/help.h
+++ b/help.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 "\n"
 "Usage\n"
 "-----\n"
diff --git a/hsp.h b/hsp.h
index 339256f..7f003bf 100644
--- a/hsp.h
+++ b/hsp.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef hsp_h
 #define hsp_h	1
 
diff --git a/hspfinder.h b/hspfinder.h
index 2b8e9d8..dc287e9 100644
--- a/hspfinder.h
+++ b/hspfinder.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef hspfinder_h
 #define hspfinder_h
 
diff --git a/make3way.cpp b/make3way.cpp
index ce88f86..dbadd1a 100644
--- a/make3way.cpp
+++ b/make3way.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "sfasta.h"
 #include "path.h"
diff --git a/mx.cpp b/mx.cpp
index 48c347e..9e61d1b 100644
--- a/mx.cpp
+++ b/mx.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "mx.h"
 #include "seqdb.h"
diff --git a/mx.h b/mx.h
index 1438900..2462937 100644
--- a/mx.h
+++ b/mx.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef mx_h
 #define mx_h
 
diff --git a/myopts.h b/myopts.h
index ba901ea..812dd8b 100644
--- a/myopts.h
+++ b/myopts.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef MY_VERSION
 #define MY_VERSION	"4.2"
 #endif
diff --git a/myutils.cpp b/myutils.cpp
index ea983eb..e9d52c2 100755
--- a/myutils.cpp
+++ b/myutils.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include <time.h>
 #include <stdarg.h>
 #include <sys/stat.h>
diff --git a/myutils.h b/myutils.h
index b63ad3c..6122054 100644
--- a/myutils.h
+++ b/myutils.h
@@ -1,8 +1,10 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef myutils_h
 #define myutils_h
 
 #define RCE_MALLOC	0
-
+
 #include <stdio.h>
 #include <sys/types.h>
 #include <string>
@@ -267,8 +269,8 @@ void GetCmdLine(string &s);
 
 extern const char *SVN_VERSION;
 extern const char *SVN_MODS;
-extern bool opt_quiet;
-extern bool opt_version;
-extern FILE *g_fLog;
+extern bool opt_quiet;
+extern bool opt_version;
+extern FILE *g_fLog;
 
 #endif	// myutils_h
diff --git a/orf.h b/orf.h
index 90b29d1..06f73a1 100644
--- a/orf.h
+++ b/orf.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef orf_h
 #define orf_h
 
diff --git a/out.h b/out.h
index 4ca50c7..595e08c 100644
--- a/out.h
+++ b/out.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef out_h
 #define out_h
 
diff --git a/path.cpp b/path.cpp
index 9340344..555830a 100644
--- a/path.cpp
+++ b/path.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "path.h"
 #include "timing.h"
diff --git a/path.h b/path.h
index f63be7e..b04ab74 100644
--- a/path.h
+++ b/path.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef path_h
 #define path_h
 
diff --git a/searchchime.cpp b/searchchime.cpp
index c00a9c4..a1c981a 100644
--- a/searchchime.cpp
+++ b/searchchime.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "ultra.h"
 #include "chime.h"
diff --git a/seq.h b/seq.h
index 9014641..83ba30f 100644
--- a/seq.h
+++ b/seq.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef seq_h
 #define seq_h
 
diff --git a/seqdb.cpp b/seqdb.cpp
index 03de189..be3373a 100644
--- a/seqdb.cpp
+++ b/seqdb.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "seqdb.h"
 #include "alpha.h"
diff --git a/seqdb.h b/seqdb.h
index fafbdd9..6907015 100644
--- a/seqdb.h
+++ b/seqdb.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef seqdb_h
 #define seqdb_h
 
diff --git a/setnucmx.cpp b/setnucmx.cpp
index 030ff5a..123791d 100644
--- a/setnucmx.cpp
+++ b/setnucmx.cpp
@@ -1,11 +1,13 @@
-#include "myutils.h"
-#include "mx.h"
-
-Mx<float> g_SubstMxf;
-float **g_SubstMx;
-
-static const char Alphabet[] = "ACGTU";
-
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
+#include "myutils.h"
+#include "mx.h"
+
+Mx<float> g_SubstMxf;
+float **g_SubstMx;
+
+static const char Alphabet[] = "ACGTU";
+
 void SetNucSubstMx(double Match, double Mismatch)
 	{
 	static bool Done = false;
diff --git a/sfasta.cpp b/sfasta.cpp
index 5e794c6..9559040 100644
--- a/sfasta.cpp
+++ b/sfasta.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "sfasta.h"
 #include "orf.h"
 #include "alpha.h"
@@ -225,8 +227,9 @@ const byte *SFasta::GetNextSeqLo()
 			if (!WarningDone)
 				{
 				if (isgap(c))
-					Warning("Ignoring gaps in FASTA file '%s'",
-						m_FileName.c_str());
+					//Warning("Ignoring gaps in FASTA file '%s'",
+						//m_FileName.c_str());
+					;
 				else if (isprint(c))
 					Warning("Invalid FASTA file '%s', non-letter '%c' in sequence >%s",
 					  m_FileName.c_str(), c, Label);
diff --git a/sfasta.h b/sfasta.h
index ed2f2ff..79ab961 100644
--- a/sfasta.h
+++ b/sfasta.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef sfasta_h
 #define sfasta_h
 
diff --git a/timing.h b/timing.h
index b566e1b..10bd1f7 100644
--- a/timing.h
+++ b/timing.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #define TIMING 0
 #ifndef timing_h
 #define timing_h
diff --git a/tracebackbit.cpp b/tracebackbit.cpp
index 94159cd..d58b900 100644
--- a/tracebackbit.cpp
+++ b/tracebackbit.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "dp.h"
 
 #define TRACE	0
diff --git a/uc.h b/uc.h
index 631ea36..8edef83 100644
--- a/uc.h
+++ b/uc.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef uc_h
 #define uc_h
 
diff --git a/uchime_main.cpp b/uchime_main.cpp
index 40e7f44..0465c72 100644
--- a/uchime_main.cpp
+++ b/uchime_main.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "chime.h"
 #include "seqdb.h"
@@ -107,11 +109,7 @@ int uchime_main(int argc, char *argv[])
 		return 0;
 		}
 
-	//printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
-	//printf("by Robert C. Edgar\n");
-	//printf("http://drive5.com/uchime\n");
-	//printf("This code is donated to the public domain.\n");
-	//printf("\n");
+		
 	if (!optset_w)
 		opt_w = 8;
 	
@@ -203,10 +201,16 @@ int uchime_main(int argc, char *argv[])
 
 		WriteChimeHit(g_fUChime, Hit);
 
-		ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
-		
+		//ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
+			//report progress
+			if((i+1) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(i+1) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();		}
+		}
+		if (!m->control_pressed) { 
+			//report progress
+			if((QuerySeqCount) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(QuerySeqCount) + ", " + toString(HitCount) + " chimeras found."); m->mothurOutEndLine();		}
 		}
 
+
 	Log("\n");
 	Log("%s: %u/%u chimeras found (%.1f%%)\n",
 	  opt_input.c_str(), HitCount, QuerySeqCount, Pct(HitCount, QuerySeqCount));
diff --git a/usort.cpp b/usort.cpp
index 7afbf42..33f102e 100644
--- a/usort.cpp
+++ b/usort.cpp
@@ -1,5 +1,5 @@
 //#if	UCHIMES
-
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
 #include "myutils.h"
 #include "seqdb.h"
 #include "seq.h"
diff --git a/viterbifast.cpp b/viterbifast.cpp
index 2b20174..3f3fc97 100644
--- a/viterbifast.cpp
+++ b/viterbifast.cpp
@@ -1,9 +1,11 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "dp.h"
 #include "out.h"
 #include "evalue.h"
 
 #define CMP_SIMPLE	0
-
+
 #if	SAVE_FAST
 static Mx<float> g_MxDPM;
 static Mx<float> g_MxDPD;
@@ -66,21 +68,21 @@ static void AllocSave(unsigned LA, unsigned LB)
 	g_DPDSimple = g_DPDSimpleMx->GetData();
 	g_DPISimple = g_DPISimpleMx->GetData();
 #endif
-	g_MxDPM.Alloc("FastM", LA+1, LB+1);
-	g_MxDPD.Alloc("FastD", LA+1, LB+1);
-	g_MxDPI.Alloc("FastI", LA+1, LB+1);
-
-	g_MxTBM.Alloc("FastTBM", LA+1, LB+1);
-	g_MxTBD.Alloc("FastTBD", LA+1, LB+1);
-	g_MxTBI.Alloc("FastTBI", LA+1, LB+1);
-
-	g_DPM = g_MxDPM.GetData();
-	g_DPD = g_MxDPD.GetData();
-	g_DPI = g_MxDPI.GetData();
-
-	g_TBM = g_MxTBM.GetData();
-	g_TBD = g_MxTBD.GetData();
-	g_TBI = g_MxTBI.GetData();
+	g_MxDPM.Alloc("FastM", LA+1, LB+1);
+	g_MxDPD.Alloc("FastD", LA+1, LB+1);
+	g_MxDPI.Alloc("FastI", LA+1, LB+1);
+
+	g_MxTBM.Alloc("FastTBM", LA+1, LB+1);
+	g_MxTBD.Alloc("FastTBD", LA+1, LB+1);
+	g_MxTBI.Alloc("FastTBI", LA+1, LB+1);
+
+	g_DPM = g_MxDPM.GetData();
+	g_DPD = g_MxDPD.GetData();
+	g_DPI = g_MxDPI.GetData();
+
+	g_TBM = g_MxTBM.GetData();
+	g_TBD = g_MxTBD.GetData();
+	g_TBI = g_MxTBI.GetData();
 	}
 
 static void SAVE_DPM(unsigned i, unsigned j, float x)
diff --git a/windex.h b/windex.h
index 0b324ca..b1e002d 100644
--- a/windex.h
+++ b/windex.h
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #ifndef windex_h
 #define windex_h
 
diff --git a/writechhit.cpp b/writechhit.cpp
index ea67061..85ec26d 100644
--- a/writechhit.cpp
+++ b/writechhit.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include "chime.h"