added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index e008ce47d2153530af1c0ab09a585a94d4963662..40dd09b9820b9689ab4d30ba9f5666ceb2e9573b 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -298,7 +298,6 @@ SffInfoCommand::SffInfoCommand(string option)  {
 //**********************************************************************************************************************
 int SffInfoCommand::execute(){
        try {
-               
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int s = 0; s < filenames.size(); s++) {
@@ -406,7 +405,9 @@ int SffInfoCommand::extractSffInfo(string input, string accnos){
                        //read data
                        seqRead read; 
                        readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
-                               
+            bool okay = sanityCheck(readheader, read);
+            if (!okay) { break; }
+            
                        //if you have provided an accosfile and this seq is not in it, then dont print
                        if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
                        
@@ -609,7 +610,7 @@ int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, i
                                in.read(buffer, 2);
                                read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
                        }
-       
+            
                        //read flowIndex
                        read.flowIndex.resize(numBases);
                        for (int i = 0; i < numBases; i++) {  
@@ -741,11 +742,39 @@ int SffInfoCommand::printHeader(ofstream& out, Header& header) {
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
+       try {
+        bool okay = true;
+        string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
+        
+        if (header.clipQualLeft > read.bases.length()) {
+            okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
+        }
+        if (header.clipQualRight > read.bases.length()) {
+            okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
+        }
+        if (header.clipQualLeft > read.qualScores.size()) {
+            okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
+        }
+        if (header.clipQualRight > read.qualScores.size()) {
+            okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
+        }
+        
+        if (okay == false) {
+            m->mothurOut(message); m->mothurOutEndLine();
+        }
+        
+               return okay;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SffInfoCommand", "sanityCheck");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
-               
                out << "Flowgram: ";
                for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
                
@@ -775,10 +804,9 @@ int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& hea
 //**********************************************************************************************************************
 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
-               
                string seq = read.bases;
                
-               if (trim) {
+        if (trim) {
                        if(header.clipQualRight < header.clipQualLeft){
                                seq = "NNNN";
                        }