limit the number of number of random sequence if too many non ACGT se…

…quences

enveomics/References.cpp

@@ -61,16 +61,21 @@ void References::intializeReferences(FastqReader &fastqReader) {
   double kerr;
   unsigned long long int hashcode;
   size_t i = 0;
+  size_t error_seq = 0;
+  size_t error_seq_limit = 3 * this->refSize;
   // deal with shorter reads then kmer length
   for(i=0;i<this->refSize;i++) {
     fastqReader.getRandomSeq(temp);
     //Hashcode for forward kmer
+    if(error_seq > error_seq_limit)
+	error("Sequence file has low quality with many non ACGT bases"); 
     if(temp.sequence.length() < this->ksize)
       error("Reads are required to have a minimum length of kmer size");
     kmer = temp.sequence.substr(0,this->ksize);
     flag = getHashCode(kmer,hashcode);
     if(flag == -1) {
         i--;
+        error_seq++;
         continue;
     }
     refKmerMap[hashcode] = 0;
@@ -95,14 +100,19 @@ void References::intializeReferences(FastaReader &fastaReader) {
   int flag;
   unsigned long long int hashcode;
   size_t i = 0;
+  size_t error_seq = 0;
+  size_t error_seq_limit = 3 * this->refSize;
   for(i=0;i<this->refSize;i++) {
     fastaReader.getRandomSeq(temp);
+    if(error_seq > error_seq_limit)
+        error("Sequence file has low quality with many non ACGT bases");
     if(temp.sequence.length() < this->ksize)
         error("Reads are required to have a minimum length of kmer size");
     kmer = temp.sequence.substr(0,this->ksize);
     flag = getHashCode(kmer, hashcode);
     if(flag == -1) {
       i--;
+      error_seq++;
       continue;
     }
     refKmerMap[hashcode] = 0;