changed how we name the make.group groups file, and filter file in filter.seqs, finis...

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index aa26d296e614adf04d69a2d73fb341dd798205a0..4f48d9ce03b64ec2a5c1f52d4d3ef2feaab9d8a5 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -246,7 +246,7 @@ int Bellerophon::getChimeras() {
                numSeqsPerProcessor = iters / processors;
                
                //each process hits this only once
-               int startPos = pid * numSeqsPerProcessor;
+               unsigned long int startPos = pid * numSeqsPerProcessor;
                if(pid == processors - 1){
                                numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
                }
@@ -326,7 +326,7 @@ int Bellerophon::getChimeras() {
                                int numSeqsPerProcessor = iters / processors;
                                
                                for (int i = 0; i < processors; i++) {
-                                       int startPos = i * numSeqsPerProcessor;
+                                       unsigned long int startPos = i * numSeqsPerProcessor;
                                        if(i == processors - 1){
                                                numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
                                        }
@@ -665,7 +665,7 @@ int Bellerophon::writePrefs(string file, linePair tempLine) {
        try {
        
                ofstream outTemp;
-               openOutputFile(file, outTemp);
+               m->openOutputFile(file, outTemp);
                
                //lets you know what part of the pref matrix you are writing
                outTemp << tempLine.start << '\t' << tempLine.num << endl;
@@ -695,12 +695,12 @@ int Bellerophon::readPrefs(string file) {
        try {
        
                ifstream inTemp;
-               openInputFile(file, inTemp);
+               m->openInputFile(file, inTemp);
                
                int start, num;
                
                //lets you know what part of the pref matrix you are writing
-               inTemp >> start >> num;  gobble(inTemp);
+               inTemp >> start >> num;  m->gobble(inTemp);
                
                for (int i = start; i < num; i++) {
                        
@@ -710,7 +710,7 @@ int Bellerophon::readPrefs(string file) {
                        
                                inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
                                inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
-                               gobble(inTemp);
+                               m->gobble(inTemp);
                        }
                }