fixed at in single

Author: grenaud

src/leeHom.cpp

@@ -1531,16 +1531,16 @@ bool checkForWritingLoopFQ(fqwriters * onereadgroup,int * lastWrittenChunk,Merge
 			    }
 			}
 
-			onereadgroup->singlef<<"@"<<dataToWrite->dataToProcess->at(i).d1<<" " <<dataToWrite->dataToProcess->at(i).cmt<<endl << dataToWrite->dataToProcess->at(i).s1 <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1 <<endl;
+			onereadgroup->singlef<<""<<dataToWrite->dataToProcess->at(i).d1<<" " <<dataToWrite->dataToProcess->at(i).cmt<<endl << dataToWrite->dataToProcess->at(i).s1 <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1 <<endl;
 			continue;
 		    }
 
 		    if(dataToWrite->dataToProcess->at(i).sequence != ""){ //new sequence
 			mtr->incrementCounttrimmed();
-			onereadgroup->single<<"@"<<dataToWrite->dataToProcess->at(i).d1<<" "<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).sequence <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).quality<<endl;
+			onereadgroup->single<<""<<dataToWrite->dataToProcess->at(i).d1<<" "<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).sequence <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).quality<<endl;
 		    }else{
 			mtr->incrementCountnothing();
-			onereadgroup->single<<"@"<<dataToWrite->dataToProcess->at(i).d1<<" "<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1       <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1     <<endl;
+			onereadgroup->single<<""<<dataToWrite->dataToProcess->at(i).d1<<" "<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1       <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1     <<endl;
 		    }
 		}
 
@@ -2501,13 +2501,13 @@ int main (int argc, char *argv[]) {
 
 			    if(dataToWrite->dataToProcess->at(i).sequence != ""){ //new sequence
 				mtr->incrementCounttrimmed();
-				onereadgroup.single<<"@"<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).sequence <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).quality<<endl;
+				onereadgroup.single<<""<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).sequence <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).quality<<endl;
 			    }else{
 				mtr->incrementCountnothing();
 				if(trimKey){
-				    onereadgroup.single<<"@"<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1.substr( key1.length() )<<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1.substr( key1.length() )<<endl;
+				    onereadgroup.single<<""<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1.substr( key1.length() )<<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1.substr( key1.length() )<<endl;
 				}else{
-				    onereadgroup.single<<"@"<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1                        <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1                        <<endl;
+				    onereadgroup.single<<""<<dataToWrite->dataToProcess->at(i).d1<<""<<dataToWrite->dataToProcess->at(i).cmt <<endl << dataToWrite->dataToProcess->at(i).s1                        <<endl<<"+"<<endl << dataToWrite->dataToProcess->at(i).q1                        <<endl;
 				}
 			    }
 			}

test/fq_s.head60out.md5sum_

@@ -0,0 +1 @@
+3504df19437c13450a66aa9956984e34  -

test/fq_s.md5sum_

@@ -0,0 +1 @@
+93e864afaccc151873fe00279c832a3f  -

test/test.sh

@@ -21,7 +21,7 @@ else
 fi
 
 
-echo -n "Running on fastq format:"
+echo -n "Running on paired-end fastq format:"
 ../src/leeHom  -fqo out -fq1 ../testData/rawAncientDNA.f1.gz -fq2 ../testData/rawAncientDNA.f2.gz |& md5sum > fq.md5sum
 echo -e " ${GREEN}ok${NC}"
 
@@ -33,7 +33,6 @@ else
     echo -e " ${RED}test failed${NC}"
     exit 1
 fi
-
 zcat out.fq.gz |head -n 60 |md5sum > fq.head60out.md5sum
 
 echo -n "testing output md5sum:"
@@ -46,6 +45,34 @@ else
 fi
 
 
+
+
+echo -n "Running on single-end fastq format:"
+../src/leeHom  -fqo out_s -fq1 ../testData/rawAncientDNA.f1.gz |& md5sum > fq_s.md5sum
+echo -e " ${GREEN}ok${NC}"
+
+echo -n "testing md5sum:"
+if diff fq_s.md5sum fq_s.md5sum_ > /dev/null
+then
+    echo -e " ${GREEN}test passed${NC}"
+else
+    echo -e " ${RED}test failed${NC}"
+    exit 1
+fi
+zcat out_s.fq.gz |head -n 60 |md5sum > fq_s.head60out.md5sum
+
+echo -n "testing output md5sum:"
+if diff fq_s.head60out.md5sum fq_s.head60out.md5sum_ > /dev/null
+then
+    echo -e " ${GREEN}test passed${NC}"
+else
+    echo -e " ${RED}test failed${NC}"
+    exit 1
+fi
+
+
+
+
 echo -n "Running ancient DNA mode:"
 ../src/leeHom --ancientdna -f AGATCGGAAGAGCACACGTCTGAACTCCAG -s GGAAGAGCGTCGTGTAGGGAAAGAGTGTAG   -o out.bam ../testData/rawAncientDNA.bam |& md5sum > bamanc.md5sum
 echo -e " ${GREEN}ok${NC}"