some changes while testing 1.9

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 07e946b78eb8d7d56c7d09a91fd2fb90fc8564a5..43ec945ad49e45ba933b866ac55995ed3e11e62d 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -199,7 +199,7 @@ int RemoveSeqsCommand::execute(){
 int RemoveSeqsCommand::readFasta(){
        try {
                if (outputDir == "") {  outputDir += hasPath(fastafile);  }
-               string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -245,7 +245,7 @@ int RemoveSeqsCommand::readFasta(){
 int RemoveSeqsCommand::readList(){
        try {
                if (outputDir == "") {  outputDir += hasPath(listfile);  }
-               string outputFileName = getRootName(listfile) + "pick" +  getExtension(listfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -316,8 +316,8 @@ int RemoveSeqsCommand::readList(){
 int RemoveSeqsCommand::readName(){
        try {
                if (outputDir == "") {  outputDir += hasPath(namefile);  }
-               string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
-               string outputFileName2 = getRootName(namefile) + "dups.accnos";
+               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
+               string outputFileName2 = outputDir + getRootName(getSimpleName(namefile)) + "dups.accnos";
 
                ofstream out2;
                if (dups) {      openOutputFile(outputFileName2, out2); }
@@ -415,7 +415,7 @@ int RemoveSeqsCommand::readName(){
 int RemoveSeqsCommand::readGroup(){
        try {
                if (outputDir == "") {  outputDir += hasPath(groupfile);  }
-               string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -460,7 +460,7 @@ int RemoveSeqsCommand::readGroup(){
 int RemoveSeqsCommand::readAlign(){
        try {
                if (outputDir == "") {  outputDir += hasPath(alignfile);  }
-               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+               string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);