diff --git a/src/FqAuxBackend.cpp b/src/FqAuxBackend.cpp
index 7e78a1750a2d60535f918ee453aca5448927e31a..c237db37941aca75d728d6bcaa282ee2e95048f7 100644
--- a/src/FqAuxBackend.cpp
+++ b/src/FqAuxBackend.cpp
@@ -20,7 +20,7 @@
#include <iostream>
using namespace std;
-//#define DEBUG
+// #define DEBUG
int FqAuxBackend::getNextRead(rinfo * p_nr) {
rinfo nr;
@@ -95,7 +95,7 @@ int FqAuxBackend::processBuffer(rinfo * p_nr) {
#ifdef DEBUG
store_id:
{ if (is_id==1) {
- if (*pchar!='\/') current_id[idx_id]=*pchar;
+ if (*pchar!='/' and *pchar!=' ') current_id[idx_id]=*pchar;
else current_id[idx_id]='\0';
idx_id+=1;
}
diff --git a/src/FqBaseBackend.cpp b/src/FqBaseBackend.cpp
index bd841c40d459ab29bb124e85d400086f92340f40..96d7f89846aad0979a50524e69ddab0dee70227e 100644
--- a/src/FqBaseBackend.cpp
+++ b/src/FqBaseBackend.cpp
@@ -140,6 +140,9 @@ int FqBaseBackend::getRead(const unsigned long& offset, char * fq_record) {
if (res==-1) {
// err(errno,"fseek problem when trying to retrieve dna string.");
// add exception for debug
+#ifdef DEBUG
+ cout<<"Couldn't get read at offset: "<<offset<<endl;
+#endif
throw errno;
}
nread=read(i_f_desc,fq_record,MAX_FQ_RECORD_LENGTH);
diff --git a/src/FqMainBackend.cpp b/src/FqMainBackend.cpp
index c68b2afe67b34a9be09a8c36932b064f5f9e022a..e43408c0a9f6a51f3551734a2444e36cfe145b9d 100644
--- a/src/FqMainBackend.cpp
+++ b/src/FqMainBackend.cpp
@@ -44,7 +44,7 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
int st,s;
int cnt,nread;
long cur_offset;
- int nb_read_oper=0;
+ // int nb_read_oper=0;
mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
//cout<<"INT_MAX="<<INT_MAX<<endl;
// cout<<filename<<endl;
@@ -68,7 +68,7 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
}
/* for each read, we want : offset, filenb, total quality score. */
while ((nread=read(f_single,buf,FqBaseBackend::bufsize))!=0) {
- nb_read_oper++;
+ // nb_read_oper++;
//cout<<"BE1: read operation nbr: "<<nb_read_oper<<endl;
//printf("going to call ftell on : %p \n",fp);
//cur_offset=ftell(fp); // don't know why but it seems that this doesn't work under linux; always returns 0...
@@ -81,16 +81,18 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
}
-
-void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned long cur_offset) {
- int cnt=0;
- unsigned int s;
- static unsigned int st;
- static int num_l_in_rec; /* counter to know on which line inside the fastq record we are */
- static int qual_score=0;
- static unsigned long rstart_offset;
#ifdef DEBUG
- static int nb_start;
+
+#define init_debug 1
+#define on_record_new 2
+#define on_record_end 3
+#define on_buf_end 4
+#define on_line_end 5
+#define on_store_read_id 6
+#define on_record_end_pe 7
+
+void FqMainBackend::debug_processBuf(int evt,int& cnt,int& nread,char * pchar,unsigned long& rstart_offset) { // put all the bebug stuff in a separate method so that processBuf is shorter and more "lisible".
+ static int nb_start; // number of fq record start and stop found in current buffer.
static int nb_stop;
static int tot_nb_stop=0;
static int tot_nb_start=0;
@@ -100,6 +102,58 @@ void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned
nb_start=0;
nb_stop=0;
}
+
+ switch(evt) {
+ case on_record_new:
+ cout<<"nread="<<nread<<endl;
+ cout<<"cnt="<<cnt<<endl;
+ cout<<"rstart_offset="<<rstart_offset<<endl;
+ is_id=1;
+ idx_id=0;
+ nb_start++;
+ break;
+ case on_line_end:
+ is_id=0;
+ break;
+ case on_record_end:
+ nb_stop++;
+ cout<<"just finished processing : "<<endl;
+ cout<<current_id<<endl;
+ break;
+ case on_store_read_id:
+ if (is_id==1) {
+ if (*pchar!='/' and *pchar !=' ') current_id[idx_id]=*pchar;
+ else current_id[idx_id]='\0';
+ idx_id+=1;
+ }
+ break;
+ case on_buf_end:
+ std::cout<<" Main BE position in buffer "<<cnt<<endl;
+ assert(cnt==nread);
+ cout<<"Main BE Found "<<nb_start<<" and "<<nb_stop<<" start/stop of record in this buffer."<<endl;
+ tot_nb_start+=nb_start;
+ tot_nb_stop+=nb_stop;
+ cout<<"Main BE Total cumulated number of start: "<<tot_nb_start<<" Total number of stop: "<<tot_nb_stop<<endl;
+ break;
+ case on_record_end_pe:
+ cout<<p_auxFqProcessor->current_id<<endl;
+ assert(strcmp(current_id,p_auxFqProcessor->current_id)==0);
+ break;
+ }
+ }
+#endif
+
+
+void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned long cur_offset) {
+ int cnt=0;
+ unsigned int s;
+ static unsigned int st;
+ static int num_l_in_rec; /* counter to know on which line inside the fastq record we are */
+ static int qual_score=0;
+ static unsigned long rstart_offset;
+ int limit_case=0;
+#ifdef DEBUG
+ debug_processBuf(init_debug,cnt,nread,NULL,rstart_offset);
#endif
char * pchar=buf;
while (cnt<=nread-1) {
@@ -107,40 +161,33 @@ void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned
case k_read_id_start:
if (qual_score) goto inc_score;
else {
- rstart_offset=cur_offset-nread+cnt;
+ rstart_offset=cur_offset-nread+cnt;
#ifdef DEBUG
- cout<<"nread="<<nread<<endl;
- cout<<"cnt="<<cnt<<endl;
- cout<<"rstart_offset="<<rstart_offset<<endl;
- is_id=1;
- idx_id=0;
- nb_start++;
+ debug_processBuf(on_record_new,cnt,nread,NULL,rstart_offset);
#endif
- // rstart_offset=cur_offset-nread+cnt;
- num_l_in_rec=1; }
- break;
+ num_l_in_rec=1; }
+ break;
case k_read_qual_start:
qual_score=1;
st=0;
break;
case '\n':
#ifdef DEBUG
- is_id=0;
+ debug_processBuf(on_line_end,cnt,nread,pchar,rstart_offset);
#endif
num_l_in_rec+=1;
if (num_l_in_rec==5) {
- // std::cout<<"BE1 position in buffer "<<cnt+1<<endl; //add 1 to compare value with BE2.
qual_score=0;/* end of fastq record */
rpos rp=init_rpos(f_id,rstart_offset);
+#ifdef DEBUG
+ debug_processBuf(on_record_end,cnt,nread,pchar,rstart_offset);
+#endif
if (p_auxFqProcessor!=NULL) {
rinfo pe2info;
int eof=p_auxFqProcessor->getNextRead(&pe2info);
assert(!eof); // There should be the same number of reads in both PE files.
-
- // if (eof) cout<<"warning, reached eof in file PE2 after: "<<nb_read_PE1<<" reads in PE1"<<endl;
st+=pe2info.score;
unsigned long j=rstart_offset/UINT_MAX;
- // if (pe2info.rstart_offset/UINT_MAX!=j) throw std::runtime_error("Inconsistency between offset values in PE files!");
if (pe2info.rstart_offset/UINT_MAX!=j) {
std::stringstream ss;
ss<<"Inconsistency between offset values in PE files! offset1=";
@@ -149,34 +196,25 @@ void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned
ss<<pe2info.rstart_offset;
// throw std::runtime_error(ss.str()); // "limit case. For the moment, skip read, will see later how to handle it.
std::cout<<ss.str()<<std::endl;
+ limit_case=1;
} else {
update_rpos(pe2info.f_id,pe2info.rstart_offset,j,&rp);
}
#ifdef DEBUG
- nb_stop++;
- cout<<"Just processed : "<<endl;
- if (strcmp(current_id,"NS500443:42:H3MH2AFXX:1:11208:4026:13258")==0) {
- cout<<"put breakpoint here"<<endl;
- }
- cout<<current_id<<endl;
- cout<<p_auxFqProcessor->current_id<<endl;
- assert(strcmp(current_id,p_auxFqProcessor->current_id)==0);
+ debug_processBuf(on_record_end_pe,cnt,nread,pchar,rstart_offset);
#endif
}
- i_dim& ref_i_dim=(*p_scoreReadStruct)[st/K_SCORE_NORM_FACTOR];
- k_dim& ref_k_dim=ref_i_dim[rstart_offset/UINT_MAX];
- ref_k_dim.push_back(rp); }
-
+ if (!limit_case) { // skip limit_case for the moment and see how it impacts perfs on loading data.
+ i_dim& ref_i_dim=(*p_scoreReadStruct)[st/K_SCORE_NORM_FACTOR];
+ k_dim& ref_k_dim=ref_i_dim[rstart_offset/UINT_MAX];
+ ref_k_dim.push_back(rp);
+ } else std::cout<<"skipping limit case read"<<std::endl; // debug stuff, TODO remove it.
+ limit_case=0;
+ }
break;
default:
#ifdef DEBUG
- store_id:
- { if (is_id==1) {
- if (*pchar!='\/') current_id[idx_id]=*pchar;
- else current_id[idx_id]='\0';
- idx_id+=1;
- }
- }
+ store_id: debug_processBuf(on_store_read_id,cnt,nread,pchar,rstart_offset);
#endif
inc_score:
{ if (qual_score==1) {
@@ -191,13 +229,7 @@ void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned
cnt++;
}
#ifdef DEBUG
- std::cout<<"BE1 position in buffer "<<cnt<<endl;
- if (cnt==nread) {
- cout<<"BE1 Found "<<nb_start<<" and "<<nb_stop<<" start/stop of record in this buffer."<<endl;
- tot_nb_start+=nb_start;
- tot_nb_stop+=nb_stop;
- cout<<"BE1 Total cumulated number of start: "<<tot_nb_start<<" Total number of stop: "<<tot_nb_stop<<endl;
- }
+ debug_processBuf(on_buf_end,cnt,nread,pchar,rstart_offset);
#endif
}
diff --git a/src/FqMainBackend.h b/src/FqMainBackend.h
index 6ef5565f62676b68c27bf31a79f0f979d9cb68f4..db7414e12ff2262db36f3d37bef0152cd4cd3cbe 100644
--- a/src/FqMainBackend.h
+++ b/src/FqMainBackend.h
@@ -21,6 +21,8 @@ class FqMainBackend : public FqBaseBackend {
srp * p_scoreReadStruct; /* Where we store information about the reads. */
char current_id[50];
+ void debug_processBuf(int evt,int& cnt,int& nread,char * pchar, unsigned long &);
+
friend void test_processInputFiles();
public:
diff --git a/src/read_utils.cpp b/src/read_utils.cpp
index 0639f4195a19fac9bb5a83f3dbfe4906220ce697..496e9ae3086ee9dd3b045146419118ce3b95ec7b 100644
--- a/src/read_utils.cpp
+++ b/src/read_utils.cpp
@@ -26,7 +26,12 @@
void getFqRecord(FqBaseBackend* fq_files_be[],const unsigned char& f_id,const unsigned long& offset,
char * fq_record) {
FqBaseBackend * be=fq_files_be[f_id-1];
- be->getRead(offset,fq_record);
+ try {
+ be->getRead(offset,fq_record);
+ } catch (int e) {
+ cout<<"couldn't retrieve read at offset: "<<offset<<endl;
+ throw e;
+ }
}