Only sort mothur generated files

Bug Fix

Makefile

@@ -14,8 +14,8 @@ USEREADLINE ?= yes
 USEBOOST ?= yes
 BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"4/05/2016\""
-VERSION = "\"1.37.0\""
+RELEASE_DATE = "\"4/18/2016\""
+VERSION = "\"1.37.1\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION
@@ -54,7 +54,7 @@ else
 endif
 
     LIBS += -lboost_iostreams -lz
-    CXXFLAGS += -DUSE_BOOST
+    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
 endif
 
 #

makefile-internal

@@ -1,7 +1,7 @@
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
 USEBOOST ?= yes
-RELEASE_DATE = "\"4/05/2015\""
+RELEASE_DATE = "\"4/11/2015\""
 VERSION = "\"1.37.0\""
 
 # Optimize to level 3:
@@ -10,7 +10,7 @@ VERSION = "\"1.37.0\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     #if you are a mac user use the following line
-    #TARGET_ARCH += -arch x86_64
+    TARGET_ARCH += -arch x86_64
 
     #if you using cygwin to build Windows the following line
     #CXX = x86_64-w64-mingw32-g++
@@ -40,12 +40,12 @@ ifeq  ($(strip $(USEBOOST)),yes)
     BOOST_INCLUDE_DIR="/usr/local/include"
     BOOST_LIBRARY_DIR="/usr/local/lib"
 
-    CXXFLAGS += -DUSE_BOOST
+    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
 
     LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a
 
     #if mac
-    LIBS += ${BOOST_LIBRARY_DIR}/zlib.a
+    LIBS += -lz
 
     #if linux or windows
     #LIBS += ${BOOST_LIBRARY_DIR}/libz.a

source/classifier/phylosummary.cpp

@@ -454,7 +454,7 @@ void PhyloSummary::print(ofstream& out, string output){
         
         //print labels
         if (output == "detail") {   out << "taxlevel\trankID\ttaxon\tdaughterlevels\ttotal";  }
-        else                    {   out << "taxon\ttotal";  }
+        else                    {   out << "taxonomy\ttotal";  }
         
         if (printlevel == -1) { printlevel = maxLevel; }
         else if (printlevel > maxLevel) { m->mothurOut("[WARNING]: Your printlevel is greater than your maxlevel, adjusting your printlevel to " + toString(maxLevel) + "\n"); printlevel = maxLevel; }
@@ -501,46 +501,42 @@ void PhyloSummary::print(ofstream& out, string output){
                 if (output == "detail") {
                     out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << (tree[0].total/(double) tree[0].total);
                 }else{
-                    //if (totalChildrenInTree == 0) { //leaf node - we want to print it. Use rank to find full taxonomy
-                        //out << findTaxon(tree[0].rank) << '\t' << tree[0].total;
-                   // }
+                    out << tree[0].name << "\t" << (tree[0].total/(double) tree[0].total);
                 }
                 
-                if ((output == "detail")) {
-                    if (groupmap != NULL) {
+                
+                if (groupmap != NULL) {
+                    for (int i = 0; i < mGroups.size(); i++) {
+                        double thisNum = tree[0].groupCount[mGroups[i]];
+                        thisNum /= (double) groupmap->getNumSeqs(mGroups[i]);
+                        out  << '\t' << thisNum;
+                    }
+                }else if ( ct != NULL) {
+                    if (ct->hasGroupInfo()) {
                         for (int i = 0; i < mGroups.size(); i++) {
                             double thisNum = tree[0].groupCount[mGroups[i]];
-                            thisNum /= (double) groupmap->getNumSeqs(mGroups[i]);
+                            thisNum /= (double) ct->getGroupCount(mGroups[i]);
                             out  << '\t' << thisNum;
                         }
-                    }else if ( ct != NULL) {
-                        if (ct->hasGroupInfo()) {
-                            for (int i = 0; i < mGroups.size(); i++) {
-                                double thisNum = tree[0].groupCount[mGroups[i]];
-                                thisNum /= (double) ct->getGroupCount(mGroups[i]);
-                                out  << '\t' << thisNum;
-                            }
-                        }
                     }
-                    out << endl;
                 }
+                out << endl;
+               
                 
             }else {
                 if (output == "detail") {
                     out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total;
                 }else{
-                    if (totalChildrenInTree == 0) { //leaf node - we want to print it. Use rank to find full taxonomy
-                        out << findTaxon(tree[0].rank) << '\t' << tree[0].total;
-                    }
+                    out << tree[0].name << '\t' << tree[0].total;
                 }
-                if ((output == "detail")) {
-                    if (groupmap != NULL) {
-                        for (int i = 0; i < mGroups.size(); i++) {  out  << '\t'<< tree[0].groupCount[mGroups[i]]; }
-                    }else if ( ct != NULL) {
-                        if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out  << '\t' << tree[0].groupCount[mGroups[i]]; } }
-                    }
-                    out << endl;
+                
+                if (groupmap != NULL) {
+                    for (int i = 0; i < mGroups.size(); i++) {  out  << '\t'<< tree[0].groupCount[mGroups[i]]; }
+                }else if ( ct != NULL) {
+                    if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out  << '\t' << tree[0].groupCount[mGroups[i]]; } }
                 }
+                out << endl;
+                
             }
         
         

source/commands/clusterdoturcommand.cpp

@@ -366,7 +366,7 @@ void ClusterDoturCommand::printData(string label, map<string, int>& counts){
         if(countfile != "") {
             oldList.print(listFile, counts);
         }else {
-            oldList.print(listFile);
+            oldList.print(listFile, true);
         }
 
 	}

source/commands/clustersplitcommand.cpp

@@ -677,7 +677,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
 				
 				//print to new file
 				list->setLabel(thisLabel);
-				list->print(outFilled);
+				list->print(outFilled, true);
 		
 				//update labelBin
 				labelBin[orderFloat[l]] += list->getNumBins();
@@ -832,7 +832,7 @@ void ClusterSplitCommand::printData(ListVector* oldList){
 		oldRAbund.print(outRabund);
 		oldRAbund.getSAbundVector().print(outSabund);
 	
-		oldList->print(outList);
+		oldList->print(outList, true);
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClusterSplitCommand", "printData");

source/commands/getgroupscommand.cpp

@@ -700,7 +700,7 @@ int GetGroupsCommand::readList(){
 				wroteSomething = true;
                 newList.setLabels(newBinLabels);
                 newList.printHeaders(out);
-				newList.print(out);
+				newList.print(out, false);
 			}
 			
 			m->gobble(in);

source/commands/getlineagecommand.cpp

@@ -595,7 +595,7 @@ int GetLineageCommand::readList(){
 				wroteSomething = true;
 				newList.setLabels(newBinLabels);
                 newList.printHeaders(out);
-				newList.print(out);
+				newList.print(out, false);
 			}
 			
 			m->gobble(in);

source/commands/getotulabelscommand.cpp

@@ -554,7 +554,7 @@ int GetOtuLabelsCommand::readList(){
             wroteSomething = true;
             newList.setLabels(newLabels);
             newList.printHeaders(out);
-            newList.print(out);
+            newList.print(out, false);
         }
 		out.close();
 		

source/commands/getseqscommand.cpp

@@ -793,7 +793,7 @@ int GetSeqsCommand::readList(){
 				wroteSomething = true;
 				newList.setLabels(newBinLabels);
                 newList.printHeaders(out);
-				newList.print(out);
+				newList.print(out, false);
 			}
 			
 			m->gobble(in);

source/commands/makecontigscommand.cpp

@@ -2550,7 +2550,7 @@ int MakeContigsCommand::setNameType(string forwardFile, string reverseFile, char
         }else { //compressed files
 #ifdef USE_BOOST
             m->openInputFileBinary(forwardFile, inForward, inFF);
-            m->openInputFileBinary(reverseFile, inForward, inRF);
+            m->openInputFileBinary(reverseFile, inReverse, inRF);
             
             if (delim == '>') {
                 Sequence fread(inFF);