1.23.0

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index e266b98837f4a787975319c7e098904cae552209..40a4c8499a599207b56831c91e6f0f41c023eb2c 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -2150,7 +2150,9 @@ void ShhherCommand::setOTUs(){
 void ShhherCommand::writeQualities(vector<int> otuCounts){
        
        try {
-               string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string qualityFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
 
                ofstream qualityFile;
                m->openOutputFile(qualityFileName, qualityFile);
@@ -2255,8 +2257,9 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
-               
-               string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string fastaFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
                ofstream fastaFile;
                m->openOutputFile(fastaFileName, fastaFile);
                
@@ -2302,7 +2305,9 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
 
 void ShhherCommand::writeNames(vector<int> otuCounts){
        try {
-               string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string nameFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
                ofstream nameFile;
                m->openOutputFile(nameFileName, nameFile);
                
@@ -2338,7 +2343,9 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
 
 void ShhherCommand::writeGroups(){
        try {
-               string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string fileRoot = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.'));
                string groupFileName = fileRoot + ".shhh.groups";
                ofstream groupFile;
                m->openOutputFile(groupFileName, groupFile);
@@ -2361,7 +2368,9 @@ void ShhherCommand::writeGroups(){
 
 void ShhherCommand::writeClusters(vector<int> otuCounts){
        try {
-               string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+               string otuCountsFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);