From a4a17c6b584c1b4b1435c92ae24796ae76f67cbc Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Tue, 8 Mar 2016 16:51:38 +0100
Subject: [PATCH] unit test didn't pass under linux. I don't know why but
ftell() called after read() always returns 0. Had to change for lseek.
---
src/FqAuxBackend.cpp | 3 ++-
src/FqMainBackend.cpp | 14 +++++++++++---
src/unit_test_fqreader.cpp | 4 +++-
3 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/src/FqAuxBackend.cpp b/src/FqAuxBackend.cpp
index 0e785b0..a17c28e 100644
--- a/src/FqAuxBackend.cpp
+++ b/src/FqAuxBackend.cpp
@@ -127,7 +127,8 @@ int FqAuxBackend::processBuffer(rinfo * p_nr) {
void FqAuxBackend::readBuffer() {
if ((nread=read(f_desc,buf,bufsize))!=0) {
- cur_offset=ftell(f_stream);
+ cur_offset=lseek(f_desc,0,SEEK_CUR);
+//ftell(f_stream);
pos_in_buf=0;
}
}
diff --git a/src/FqMainBackend.cpp b/src/FqMainBackend.cpp
index b259f66..72d1b15 100644
--- a/src/FqMainBackend.cpp
+++ b/src/FqMainBackend.cpp
@@ -18,6 +18,7 @@
//#define DEBUG
#ifdef DEBUG
+#include <string.h>
#include <iostream>
using namespace std;
#endif
@@ -53,7 +54,8 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
if (fp==NULL) {
err(errno,"cannot open file: %s.",filename);
}
- cur_offset=ftell(fp);
+ //cur_offset=ftell(fp);
+ //cout<<"cur_offset="<<cur_offset<<endl;
char* buf=(char *) malloc(FqBaseBackend::bufsize*sizeof(char));
if (buf==NULL) {
err(errno,"cannot allocate memory: %lu bytes.",bufsize);
@@ -63,7 +65,9 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
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);
+ //cur_offset=ftell(fp); // don't know why but it seems that this doesn't work under linux; always returns 0...
+ cur_offset = lseek(f_single, 0, SEEK_CUR);
+ //cout<<"cur_offset="<<cur_offset<<endl;
processBuf((char *)buf,nread,f_id,cur_offset);
}
close(f_single);
@@ -97,12 +101,16 @@ 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;
#ifdef DEBUG
+ cout<<"nread="<<nread<<endl;
+ cout<<"cnt="<<cnt<<endl;
+ cout<<"rstart_offset="<<rstart_offset<<endl;
is_id=1;
idx_id=0;
nb_start++;
#endif
- rstart_offset=cur_offset-nread+cnt;
+ // rstart_offset=cur_offset-nread+cnt;
num_l_in_rec=1; }
break;
case k_read_qual_start:
diff --git a/src/unit_test_fqreader.cpp b/src/unit_test_fqreader.cpp
index d40e7c2..28e8d88 100644
--- a/src/unit_test_fqreader.cpp
+++ b/src/unit_test_fqreader.cpp
@@ -7,6 +7,7 @@
* 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 <string.h>
#include <iostream>
#include <limits.h>
#include <assert.h>
@@ -38,7 +39,8 @@ void test_processSingleFile() {
assert(score==5);
for (it_offs=rit->second.begin();it_offs!=rit->second.end();it_offs++) {
unsigned long offset_quotient=it_offs->first;
- assert(offset_quotient==0);
+ cout<<"offset_quotient="<<offset_quotient<<endl;
+ 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_id);
--
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