added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 207328203a24088c111054de2b157fae9235876c..4965cfd75e06c9f8ba8157056922514581e3e10e 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -303,7 +303,7 @@ int SffInfoCommand::execute(){
                
                for (int s = 0; s < filenames.size(); s++) {
                        
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
                        
                        int start = time(NULL);
                        
@@ -319,7 +319,7 @@ int SffInfoCommand::execute(){
                
                if (sfftxtFilename != "") {  parseSffTxt(); }
                
-               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
+               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
                
                //set fasta file as new current fastafile
                string current = "";
@@ -466,7 +466,7 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        //read offset
                        char buffer2 [8];
                        in.read(buffer2, 8);
-                       header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
+                       header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
                        
                        //read index length
                        char buffer3 [4];
@@ -513,8 +513,8 @@ int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
                        delete[] tempBuffer2;
                                
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
                        in.seekg(spot);
                        
                }else{
@@ -581,8 +581,8 @@ int SffInfoCommand::readHeader(ifstream& in, Header& header){
                        decodeName(header.timestamp, header.region, header.xy, header.name);
                        
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{
@@ -634,8 +634,8 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
                        }
        
                        /* Pad to 8 chars */
-                       unsigned long int spotInFile = in.tellg();
-                       unsigned long int spot = (spotInFile + 7)& ~7;
+                       unsigned long long spotInFile = in.tellg();
+                       unsigned long long spot = (spotInFile + 7)& ~7;
                        in.seekg(spot);
                        
                }else{