From 4160a27002f4a3ca436fcd62eca0366b09f8e901 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 9 May 2011 15:52:45 +0000
Subject: [PATCH] 1.19.0

---
 Mothur.xcodeproj/project.pbxproj |  8 ++++----
 listseqscommand.cpp              | 24 ++++++++++++------------
 mothurout.cpp                    |  4 ++--
 qualityscores.cpp                |  5 ++++-
 splitmatrix.cpp                  |  1 +
 trimseqscommand.cpp              |  4 ++--
 6 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 321c130..4d37747 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1982,8 +1982,8 @@
 				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"../release\\\"\"",
-					"VERSION=\"\\\"1.18.1\\\"\"",
-					"RELEASE_DATE=\"\\\"4/15/2011\\\"\"",
+					"VERSION=\"\\\"1.19.0\\\"\"",
+					"RELEASE_DATE=\"\\\"5/9/2011\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
@@ -2015,8 +2015,8 @@
 				GCC_MODEL_TUNING = "";
 				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.18.1\\\"\"",
-					"RELEASE_DATE=\"\\\"4/15/2011\\\"\"",
+					"VERSION=\"\\\"1.19.0\\\"\"",
+					"RELEASE_DATE=\"\\\"5/9/2011\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 21cb4c7..d60470c 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -257,11 +257,11 @@ int ListSeqsCommand::readFasta(){
 		m->openInputFile(fastafile, in);
 		string name;
 		
-		ofstream out;
-		string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
-		m->openOutputFile(newFastaName, out);
-		int count = 1;
-		string lastName = "";
+		//ofstream out;
+		//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+		//m->openOutputFile(newFastaName, out);
+		//int count = 1;
+		//string lastName = "";
 		
 		while(!in.eof()){
 			
@@ -269,20 +269,20 @@ int ListSeqsCommand::readFasta(){
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
-			if (lastName == "") { lastName = name; }
-			if (name != lastName) { count = 1; }
-			lastName = name;
+			//if (lastName == "") { lastName = name; }
+			//if (name != lastName) { count = 1; }
+		//	lastName = name;
 			
-			Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
-			newSeq.printSequence(out);
+			//Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+			//newSeq.printSequence(out);
 			
 			if (name != "") {  names.push_back(name);  }
 			
 			m->gobble(in);
-			count++;
+			//count++;
 		}
 		in.close();	
-		out.close();
+		//out.close();
 		
 		return 0;
 
diff --git a/mothurout.cpp b/mothurout.cpp
index 2b06799..c2ef698 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -438,12 +438,12 @@ string MothurOut::getline(ifstream& fileHandle) {
 	
 		string line = "";
 		
-		while (!fileHandle.eof())	{
+		while (fileHandle)	{
 			//get next character
 			char c = fileHandle.get(); 
 			
 			//are you at the end of the line
-			if ((c == '\n') || (c == '\r') || (c == '\f')){  break;	}	
+			if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;	}	
 			else {		line += c;		}
 		}
 		
diff --git a/qualityscores.cpp b/qualityscores.cpp
index 3f8722f..c9c6504 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -278,7 +278,7 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		
 		int end = windowSize;
 		int start = 0;
-		
+
 		if(seqLength < windowSize) {	return 0;	}
 			
 		while(start < seqLength){
@@ -300,6 +300,9 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		
 		if(end == -1){	end = seqLength;	}
 		
+		//failed first window
+		if (end < windowSize) { return 0; }
+			
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 80f311d..8ccb867 100644
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -186,6 +186,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
 		for (int i = 0; i < numGroups; i++) { 
 			
 			string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
+			if (outputDir != "") { options += ", outputdir=" + outputDir; }
 			
 			Command* command = new DistanceCommand(options);
 			
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index f685a42..d8a0d1d 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -497,7 +497,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			int currentSeqsDiffs = 0;
 
 			Sequence currSeq(inFASTA); m->gobble(inFASTA);
-
+			
 			QualityScores currQual;
 			if(qFileName != ""){
 				currQual = QualityScores(qFile);  m->gobble(qFile);
@@ -546,7 +546,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 					else if(qRollAverage != 0)	{	success = currQual.stripQualRollingAverage(currSeq, qRollAverage);	}
 					else if(qWindowAverage != 0){	success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);	}
 					else						{	success = 1;				}
-					
+				
 					//you don't want to trim, if it fails above then scrap it
 					if ((!qtrim) && (origLength != currSeq.getNumBases())) {  success = 0; }
 					
-- 
2.39.2