diff --git a/src/FqAuxBackend.cpp b/src/FqAuxBackend.cpp
index f97f7857e0c1c248a93ca501f47d5a36bad4c942..26912250b7e89aa6cc47f66329b976f637bd2013 100644
--- a/src/FqAuxBackend.cpp
+++ b/src/FqAuxBackend.cpp
@@ -12,17 +12,24 @@
#include <unistd.h>
#include <errno.h>
#include <err.h>
+#include <stdlib.h>
#include "FqAuxBackend.h"
+#include <iostream>
+using namespace std;
+
+//#define DEBUG
int FqAuxBackend::getNextRead(rinfo * p_nr) {
rinfo nr;
int rfound=0;
int eof=0;
-
while (!rfound) {
- if (pos_in_buf>=nread-1) readBuffer();
+ if (nread==0 || (pos_in_buf>=nread)) {
+ // if (pos_in_buf==nread-1) cout<<"BE2 : last char of buf before reading new buffer: "<<buf[pos_in_buf]<<endl;
+ readBuffer();
+ }
if (nread==0) { eof=1; break;}
rfound=processBuffer(p_nr);
}
@@ -37,30 +44,63 @@ int FqAuxBackend::processBuffer(rinfo * p_nr) {
static unsigned long rstart_offset;
char * pchar=buf+pos_in_buf;
int rfound=0;
+#ifdef DEBUG
+ static int tot_nb_start=0;
+ static int tot_nb_stop=0;
+ static int nb_stop=0;
+ static int nb_start=0;
+
+ static int idx_id;
+ static int is_id=0;
+ if (pos_in_buf==0) {
+ nb_start=0;
+ nb_stop=0;
+ }
+#endif
while (pos_in_buf<=nread-1 && !rfound) {
switch (*pchar){
- case k_read_id_start: {
+ case k_read_id_start:
+ if (qual_score) goto inc_score;
+ else {
+#ifdef DEBUG
+ is_id=1;
+ idx_id=0;
+ nb_start++;
+#endif
+ //cout<<k_read_id_start<<" found in PE2."<<endl;
rstart_offset=cur_offset-nread+pos_in_buf;
num_l_in_rec=1; }
break;
- case k_read_qual_start: {
+ case k_read_qual_start:
qual_score=1;
- st=0;}
+ st=0;
break;
- case '\n': {
+ case '\n':
num_l_in_rec+=1;
- if (num_l_in_rec==5) {qual_score=0;/* end of fastq record */
- // debug stuff
- /*printf("\nquality score is : %d \n",st);
- printf("read start_offset is %lu \n",rstart_offset);*/
+#ifdef DEBUG
+ is_id=0;
+#endif
+ if (num_l_in_rec==5) { qual_score=0;/* end of fastq record */
+#ifdef DEBUG
+ nb_stop++;
+#endif
p_nr->f_id=f_id;
p_nr->score=st;
p_nr->rstart_offset=rstart_offset;
rfound=1;
}
- }
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;
+ }
+ }
+#endif
+ inc_score:
{ if (qual_score==1) {
s=(int)*pchar;
s-=k_phred_32;
@@ -71,6 +111,15 @@ int FqAuxBackend::processBuffer(rinfo * p_nr) {
pchar++;
pos_in_buf++;
}
+#ifdef DEBUG
+ std::cout<<"BE2, position in buffer: "<<pos_in_buf<<endl;
+ if (pos_in_buf==nread) {
+ cout<<"BE2 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<<"BE2 Total cumulated number of start char found: "<<tot_nb_start<< " Total number of stop: "<<tot_nb_stop<<endl;
+ }
+#endif
return rfound;
}
@@ -102,13 +151,19 @@ void FqAuxBackend::openFile(char * ficname, unsigned char id) {
if (fp2==NULL) {
err(errno,"cannot open file: %s.",filename);
}
-
+ buf=(char *) malloc(bufsize*sizeof(char));
+ if (buf==NULL) {
+ err(errno,"cannot allocate memory: %lu bytes.",bufsize);
+ }
+ pos_in_buf=bufsize; // do that to force first reading in buffer.
}
void FqAuxBackend::closeFile() {
if (filename!=NULL) {
close(f_pe2);
filename=NULL;
+ free(buf);
+ buf=NULL;
}
}
diff --git a/src/FqAuxBackend.h b/src/FqAuxBackend.h
index bc767e6c1c98960879a264c8f1c325feea2d9909..badb2ee563ba93f36bef92477f88ba4cf08f6875 100644
--- a/src/FqAuxBackend.h
+++ b/src/FqAuxBackend.h
@@ -9,22 +9,25 @@
#define FQAUXBACKEND_H_
#include "srp.h"
-const size_t bufsize=10240;
+const size_t bufsize=6048000; // It seems that I can't have a much bigger value than that or else my objects construction throws exception. Strange.
+// const size_t bufsize=500000; //try that in valgrind
class FqAuxBackend {
char * filename;
unsigned char f_id;
- char buf[bufsize];
- int nread;
+ size_t nread;
int f_pe2; // for calling read
FILE * fp2; // for calling ftell
unsigned long cur_offset;
- int pos_in_buf;
+ char * buf;
void readBuffer();
int processBuffer(rinfo * p_nr);
public:
+
+ size_t pos_in_buf;
+ char current_id[50];
FqAuxBackend() {
filename=NULL;
@@ -33,7 +36,7 @@ public:
f_id=0;
cur_offset=0;
nread=0;
- pos_in_buf=bufsize; // do that to force first reading in buffer.
+ buf=NULL;
}
void openFile(char * ficname, unsigned char id);
diff --git a/src/FqMainBackend.cpp b/src/FqMainBackend.cpp
index c8d4214adf2d8d9f180d5bfcfad195b1fbd29aa3..30ae15071c4d0747bfa0ff1e1520fd9d3b25b83b 100644
--- a/src/FqMainBackend.cpp
+++ b/src/FqMainBackend.cpp
@@ -13,10 +13,17 @@
#include <err.h>
#include <limits.h>
#include <assert.h>
+#include <stdlib.h>
+
+// for debug only. TODO : remove that.
+#include <iostream>
+using namespace std;
#include "FqMainBackend.h"
#include "srp.h"
+//#define DEBUG
+
rpos init_rpos(unsigned char f_id, unsigned long rstart_offset) {
rpos rp;
rp.fileid=f_id <<4;
@@ -33,13 +40,23 @@ void update_rpos(unsigned char f_id,unsigned long rstart_offset,unsigned long j,
}
+
+FqMainBackend::FqMainBackend(srp * io_sr) {
+ p_auxFqProcessor=NULL;
+ p_scoreReadStruct=io_sr;
+}
+
+
void FqMainBackend::processFile(char * filename,unsigned char f_id) {
FILE * fp;
int st,s;
int cnt,nread;
- unsigned long cur_offset;
+ long cur_offset;
+ int nb_read_oper=0;
mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
- char buf[bufsize];
+ //cout<<"INT_MAX="<<INT_MAX<<endl;
+ // cout<<filename<<endl;
+
int f_single=open(filename,O_RDONLY,mode);
if (f_single==-1) {
err(errno,"cannot open file: %s.",filename);
@@ -49,66 +66,128 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
if (fp==NULL) {
err(errno,"cannot open file: %s.",filename);
}
-
+ cur_offset=ftell(fp);
+ char* buf=(char *) malloc(bufsize*sizeof(char));
+ if (buf==NULL) {
+ err(errno,"cannot allocate memory: %lu bytes.",bufsize);
+ }
/* for each read, we want : offset, filenb, total quality score. */
while ((nread=read(f_single,buf,bufsize))!=0) {
- // printf("%s",buf);
+ 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);
- processBuf((char *)&buf,nread,f_id,cur_offset);
+ processBuf((char *)buf,nread,f_id,cur_offset);
}
close(f_single);
-
+ free(buf);
}
+
void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned long cur_offset) {
int cnt=0;
+ // debug stuff, TODO: remove it
+ // static int nb_read_PE1=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;
+ static int nb_stop;
+ static int tot_nb_stop=0;
+ static int tot_nb_start=0;
+ static int idx_id;
+ static int is_id=0;
+ if (cnt==0) {
+ nb_start=0;
+ nb_stop=0;
+ }
+#endif
char * pchar=buf;
while (cnt<=nread-1) {
switch (*pchar){
- case k_read_id_start: {
+ case k_read_id_start:
+ if (qual_score) goto inc_score;
+ else {
+#ifdef DEBUG
+ is_id=1;
+ idx_id=0;
+ nb_start++;
+#endif
rstart_offset=cur_offset-nread+cnt;
num_l_in_rec=1; }
break;
- case k_read_qual_start: {
+ case k_read_qual_start:
qual_score=1;
- st=0;}
+ st=0;
break;
- case '\n': {
+ case '\n':
+#ifdef DEBUG
+ is_id=0;
+#endif
num_l_in_rec+=1;
- if (num_l_in_rec==5) {qual_score=0;/* end of fastq record */
- // debug stuff
- /*printf("\nquality score is : %d \n",st);
- printf("read start_offset is %lu \n",rstart_offset);*/
+ 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);
+ // nb_read_PE1++; // TODO: remove, this is debug stuff
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/INT_MAX;
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);
+#endif
}
i_dim& ref_i_dim=(*p_scoreReadStruct)[st/K_SCORE_NORM_FACTOR];
k_dim& ref_k_dim=ref_i_dim[rstart_offset/INT_MAX];
ref_k_dim.push_back(rp); }
- }
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;
+ }
+ }
+#endif
+ inc_score:
{ if (qual_score==1) {
s=(int)*pchar;
s-=k_phred_32;
st+=s;
}
}
+ break;
}
pchar++;
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;
+ }
+#endif
}
diff --git a/src/FqMainBackend.h b/src/FqMainBackend.h
index 610a6a3b7be85d1de7fe1f7ff8c9a3659cb13dad..38a9bf30f70da4f1b823c018c89f8a535917dadf 100644
--- a/src/FqMainBackend.h
+++ b/src/FqMainBackend.h
@@ -13,17 +13,15 @@
#include "FqAuxBackend.h"
#include "FqConstants.h"
+
class FqMainBackend {
FqAuxBackend * p_auxFqProcessor; /* Another fastq processor component is necessary for handling the case of PE reads.*/
srp * p_scoreReadStruct; /* Where we store information about the reads. */
+ char current_id[50];
public:
- FqMainBackend(srp * io_sr) {
- p_scoreReadStruct=io_sr;
- p_auxFqProcessor=NULL;
- }
-
-
+
+ FqMainBackend(srp*);
void setAuxProcessor(FqAuxBackend* fq2ndProc) {
p_auxFqProcessor=fq2ndProc;
diff --git a/src/fqreader.cpp b/src/fqreader.cpp
index 182a1d738c43be73808bb3e43ccb6816f2162023..7b8169f1536e35aba574015fc8e20199c18b3dc9 100644
--- a/src/fqreader.cpp
+++ b/src/fqreader.cpp
@@ -17,6 +17,8 @@
#include "FqMainBackend.h"
+
+
/*
typedef struct {
char buf[bufsize];
@@ -40,12 +42,19 @@ void processSingleFile(char * fq_s,unsigned char f_id, srp* io_sr) {
/* Processes 1 pair of files containing PE reads.*/
void processPEFiles(char * fq_1, unsigned char f_id1,char * fq_2, unsigned char f_id2,srp * io_sr ) {
- FqMainBackend be_fq1=FqMainBackend(io_sr);
- FqAuxBackend be_fq2=FqAuxBackend();
+ FqAuxBackend be_fq2;
+ FqMainBackend be_fq1(io_sr);
+
be_fq2.openFile(fq_2,f_id2);
be_fq1.setAuxProcessor(&be_fq2);
be_fq1.processFile(fq_1,f_id1);
be_fq2.closeFile();
}
+/*
+ * This function processes the content of an rpos structure and returns the character string "ATCG" corresponding to the read record.
+ * PE reads are concatenated.
+ */
+void getRead(char ** fname_id_array, const rpos& sr, unsigned int j, char ** dna_read){
+}
diff --git a/src/fqreader.h b/src/fqreader.h
index cc664c7274125cabe3b764fa456a17a220720ec8..bd823d944facebd88ffdf2ebe43d2b4fe4516925 100644
--- a/src/fqreader.h
+++ b/src/fqreader.h
@@ -8,10 +8,11 @@
#define FQREADER_H
#include "srp.h"
-
+const int read_length=1000; // this will become a parameter later.
/*void processBuf(char * buf,int nread,int cur_offset);*/
void processSingleFile(char *, unsigned char, srp*);
void processPEFiles(char * fq_1, unsigned char f_id1,char * gq_2, unsigned char f_id2,srp *io_sr );
+void getRead(char ** fname_id_array, const rpos& sr, unsigned int j, char ** read);
#endif
diff --git a/src/perf_test_fqreader.cpp b/src/perf_test_fqreader.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d6a8951486b12759b03b40ee8fda9b173f393f6c
--- /dev/null
+++ b/src/perf_test_fqreader.cpp
@@ -0,0 +1,143 @@
+/*
+ * unit_test_fqreader.cpp
+ *
+ * Created on: Dec 8, 2015
+ * Author: vlegrand
+ * unit testing for the fqreader component.
+ * Keep using assert for the moment, don't want to add a dependency on boost (or any other test framework) just for the tests.
+ */
+#include <stdio.h>
+#include <iostream>
+#include <limits.h>
+#include <assert.h>
+#include <stdlib.h>
+#include "srp.h"
+#include "fqreader.h"
+
+using namespace std;
+
+void test_processSingleFile() {
+ //printf("MAX_UINT=%u \n",UINT_MAX);
+ srp sr;
+ unsigned char f_id=1;
+ processSingleFile((char *) "../data_perf_tests/LM_single10x.fq",f_id,&sr);
+ srp::reverse_iterator rit;
+ i_dim::iterator it_offs;
+ k_dim::iterator it_struct;
+
+ int cnt_read=0;
+
+ for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
+ unsigned long score=rit->first;
+ cout << "score="<<rit->first<<endl;
+ for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
+ unsigned long offset_quotient=it_offs->first;
+ for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
+ unsigned char fid_stored=it_struct->fileid;
+ cnt_read++;
+ int tmp=fid_stored >>4;
+ cout<<" fileid="<<tmp<<" read_a1="<<it_struct->read_a1<<endl;
+ }
+ }
+ }
+ cout<<"number of reads: "<<cnt_read;
+}
+
+void test_processPEFiles() {
+ char * fq_1_test=(char *) "data/test_PE1.fq";
+ char * fq_2_test=(char *) "data/test_PE2.fq";
+
+ unsigned char f_id1=1;
+ unsigned char f_id2=2;
+
+ srp sr;
+
+ processPEFiles(fq_1_test, f_id1,fq_2_test, f_id2,&sr);
+ srp::reverse_iterator rit;
+ i_dim::iterator it_offs;
+ k_dim::iterator it_struct;
+ int cnt_read=0;
+
+ unsigned char masque=0x0F;
+
+ for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
+ // cout << "score="<<rit->first<<endl;
+ unsigned long score=rit->first;
+ if (cnt_read==0 || cnt_read==1) assert(score==10);
+ if (cnt_read==2) assert(score==9);
+ for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
+ unsigned long offset_quotient=it_offs->first;
+ assert(offset_quotient==0);
+ for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
+ unsigned char fid_stored=it_struct->fileid;
+ assert(fid_stored >>4==f_id1);
+ assert((fid_stored &masque)==f_id2);
+ if (cnt_read==0) {
+ assert(it_struct->read_a1==0);
+ assert(it_struct->read_a1==0);
+ }
+ if (cnt_read==1) {
+ //std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
+ assert(it_struct->read_a1==349);
+ assert(it_struct->read_a2==349);
+ }
+ if (cnt_read==2) {
+ // std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
+ assert(it_struct->read_a1==698);
+ assert(it_struct->read_a2==698);
+ }
+ cnt_read++;
+ /*
+ int tmp1=fid_stored >>4;
+ int tmp2=fid_stored &masque;
+ cout<<" fileid1="<<tmp1<<" read_a1="<<it_struct->read_a1<<endl;
+ cout<<" fileid2="<<tmp2<<" read_a2="<<it_struct->read_a2<<endl; */
+ }
+ }
+ }
+ assert(cnt_read==3);
+}
+
+void test_processAllFiles() {
+ char * fq_1_test=(char *) "../data_perf_tests/LM_R1_10x.fq";
+ char * fq_2_test=(char *) "../data_perf_tests/LM_R2_10x.fq";
+ char * fq_single=(char *) "../data_perf_tests/LM_single10x.fq";
+
+ unsigned char f_id1=1;
+ unsigned char f_id2=2;
+ unsigned char f_single=3;
+
+ srp sr;
+
+ processPEFiles(fq_1_test, f_id1,fq_2_test, f_id2,&sr);
+ processSingleFile(fq_single,f_single,&sr);
+
+ srp::reverse_iterator rit;
+ i_dim::iterator it_offs;
+ k_dim::iterator it_struct;
+ int cnt_read=0;
+ unsigned char masque=0x0F;
+
+ for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
+ unsigned long score=rit->first;
+ cout << "score="<<rit->first<<endl;
+ for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
+ unsigned long offset_quotient=it_offs->first;
+ assert(offset_quotient==0);
+ for (it_struct=it_offs->second.begin();it_struct!=it_offs->second.end();it_struct++) {
+ cnt_read++;
+ unsigned char fid_stored=it_struct->fileid;
+ int tmp1=fid_stored >>4;
+ int tmp2=fid_stored &masque;
+ cout<<" fileid1="<<tmp1<<" read_a1="<<it_struct->read_a1<<" fileid2="<<tmp2<<" read_a2="<<it_struct->read_a2<<endl;
+ }
+ }
+ }
+ cout<<"number of reads: "<<cnt_read;
+}
+
+int main(int argc, char **argv) {
+ // test_processSingleFile();
+ // test_processPEFiles();
+ test_processAllFiles(); /* mix PE together with single; nearly as in real life.*/
+}
diff --git a/src/unit_test_fqreader.cpp b/src/unit_test_fqreader.cpp
index 61db57c805ce0d701827f256565fede68b4287ee..64160bd84da0ceb0180be6714267a6ed1ffb1145 100644
--- a/src/unit_test_fqreader.cpp
+++ b/src/unit_test_fqreader.cpp
@@ -20,7 +20,7 @@ void test_processSingleFile() {
//printf("MAX_UINT=%u \n",UINT_MAX);
srp sr;
unsigned char f_id=1;
- processSingleFile((char *) "data/test_single.fq",f_id,&sr);
+ processSingleFile((char *) "../data/test_single.fq",f_id,&sr);
srp::reverse_iterator rit;
i_dim::iterator it_offs;
k_dim::iterator it_struct;
@@ -53,8 +53,8 @@ void test_processSingleFile() {
}
void test_processPEFiles() {
- char * fq_1_test=(char *) "data/test_PE1.fq";
- char * fq_2_test=(char *) "data/test_PE2.fq";
+ char * fq_1_test=(char *) "../data/test_PE1.fq";
+ char * fq_2_test=(char *) "../data/test_PE2.fq";
unsigned char f_id1=1;
unsigned char f_id2=2;
@@ -86,21 +86,21 @@ void test_processPEFiles() {
assert(it_struct->read_a1==0);
}
if (cnt_read==1) {
- //std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
+ std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
assert(it_struct->read_a1==349);
assert(it_struct->read_a2==349);
}
if (cnt_read==2) {
- // std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
+ std::cout<<it_struct->read_a1<<" "<<it_struct->read_a2;
assert(it_struct->read_a1==698);
assert(it_struct->read_a2==698);
}
cnt_read++;
- /*
+
int tmp1=fid_stored >>4;
int tmp2=fid_stored &masque;
cout<<" fileid1="<<tmp1<<" read_a1="<<it_struct->read_a1<<endl;
- cout<<" fileid2="<<tmp2<<" read_a2="<<it_struct->read_a2<<endl; */
+ cout<<" fileid2="<<tmp2<<" read_a2="<<it_struct->read_a2<<endl;
}
}
}
@@ -108,9 +108,9 @@ void test_processPEFiles() {
}
void test_processAllFiles() {
- char * fq_1_test=(char *) "data/test_PE1.fq";
- char * fq_2_test=(char *) "data/test_PE2.fq";
- char * fq_single=(char *) "data/test_single.fq";
+ char * fq_1_test=(char *) "../data/test_PE1.fq";
+ char * fq_2_test=(char *) "../data/test_PE2.fq";
+ char * fq_single=(char *) "../data/test_single.fq";
unsigned char f_id1=1;
unsigned char f_id2=2;
@@ -127,7 +127,7 @@ void test_processAllFiles() {
int cnt_read=0;
for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
- // cout << "score="<<rit->first<<endl;
+ //cout << "score="<<rit->first<<endl;
unsigned long score=rit->first;
if (cnt_read==0 || cnt_read==1) assert(score==10);
else if (cnt_read==2) assert(score==9);
@@ -147,8 +147,12 @@ void test_processAllFiles() {
}
int main(int argc, char **argv) {
+ cout<<"sizeof(char)"<<sizeof(char);
/*char* fq_s_test="data/test_single.fq";*/
+ cout<<"test for single file"<<endl;
test_processSingleFile();
+ cout<<"test for PE files"<<endl;
test_processPEFiles();
+ cout<<"test for both single and PE files";
test_processAllFiles(); /* mix PE together with single; nearly as in real life.*/
}