added traces for debug

src/FqBaseBackend.cpp

@@ -16,7 +16,7 @@
 
 #include "FqBaseBackend.h"
 
-//#define DEBUG
+#define DEBUG
 #ifdef DEBUG
 #include <cassert>
 #include <iostream>
@@ -135,7 +135,9 @@ int FqBaseBackend::getRead(const unsigned long& offset, char * fq_record) {
     char * pchar;
 
     if (i_f_desc==-1) throw std::runtime_error("No open file currently associated to this backend");
-
+#ifdef DEBUG
+    cout<<"going to read record at offset: "<<offset<<endl;
+#endif
     int res=lseek(i_f_desc,offset,SEEK_SET);
     if (res==-1) {
         // err(errno,"fseek problem when trying to retrieve dna string.");
@@ -146,6 +148,9 @@ int FqBaseBackend::getRead(const unsigned long& offset, char * fq_record) {
         throw errno;
     }
     nread=read(i_f_desc,fq_record,MAX_FQ_RECORD_LENGTH);
+#ifdef DEBUG
+    assert(*(fq_record)=='@');
+#endif
     nb_lines=0;
     i=1;
     pchar=fq_record;

src/read_utils.cpp

@@ -16,6 +16,7 @@
 #include "srp.h"
 #include "read_utils.h"
 #include "rock_commons.h"
+#define DEBUG
 
 #ifdef DEBUG
 #include <cassert>
@@ -82,6 +83,9 @@ void getDNASeqstr(FqBaseBackend* fq_files_be [],
     f_id2=fid_stored &mask_fid;
 
     unsigned long offset1=j*UINT_MAX+sr.read_a1;
+#ifdef DEBUG
+    cout<<"getting record at offset: "<<offset1<<endl;
+#endif
     try {
         getFqRecord(fq_files_be,f_id1,offset1,dna_seqs[0].fq_record_buf);
         processFqRecord(p_dna_seqs);