updated path of input data files so that unit tests can also be ran with make distcheck.

src/unit_test_fqreader.cpp

@@ -26,7 +26,7 @@ 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 *) "../test/data/unit/test_single.fq",f_id,&sr);
     srp::reverse_iterator rit;
     i_dim::iterator it_offs;
     k_dim::iterator it_struct;
@@ -67,8 +67,8 @@ void test_processSingleFile() {
  */
 void test_processPEfilesWithA() {
 
-    char * fq_3_test=(char *) "../data/klebsiella_PE1.fq";
-    char * fq_4_test=(char *) "../data/klebsiella_PE2.fq";
+    char * fq_3_test=(char *) "../test/data/unit/klebsiella_PE1.fq";
+    char * fq_4_test=(char *) "../test/data/unit/klebsiella_PE2.fq";
 
     unsigned char f_id3=3;
     unsigned char f_id4=4;
@@ -124,8 +124,8 @@ void test_processPEfilesWithA() {
 }
 
 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 *) "../test/data/unit/test_PE1.fq";
+    char * fq_2_test=(char *) "../test/data/unit/test_PE2.fq";
 
     unsigned char f_id1=1;
     unsigned char f_id2=2;
@@ -205,9 +205,9 @@ void check_processAIFilesResults(srp& sr) {
 }
 
 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 *) "../test/data/unit/test_PE1.fq";
+    char * fq_2_test=(char *) "../test/data/unit/test_PE2.fq";
+    char * fq_single=(char *) "../test/data/unit/test_single.fq";
 
     unsigned char f_id1=1;
     unsigned char f_id2=2;
@@ -223,9 +223,9 @@ void test_processAllFiles() {
 
 
 void test_processInputFiles() {
-    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 *) "../test/data/unit/test_PE1.fq";
+    char * fq_2_test=(char *) "../test/data/unit/test_PE2.fq";
+    char * fq_single=(char *) "../test/data/unit/test_single.fq";
 
     IO_fq_files s;
     s.in_fq_file=fq_single;

src/unit_test_fqwriter.cpp

@@ -86,18 +86,18 @@ void test_write_PE() {
     map_id_backend[0]=be_fq1;
     map_id_backend[1]=be_fq2;
 
-    be_fq1->i_filename=(char *) "../data/klebsiella_PE1.fq";
+    be_fq1->i_filename=(char *) "../test/data/unit/klebsiella_PE1.fq";
     be_fq1->f_id=1;
     be_fq2->f_id=2;
-    be_fq2->i_filename=(char *) "../data/klebsiella_PE2.fq";
-    be_fq1->setOutputFile((char *) "../data/klebsiella_PE1_filtered.fq");
-    be_fq2->setOutputFile((char *) "../data/klebsiella_PE2_filtered.fq");
+    be_fq2->i_filename=(char *) "../test/data/unit/klebsiella_PE2.fq";
+    be_fq1->setOutputFile((char *) "../test/data/unit/klebsiella_PE1_filtered.fq");
+    be_fq2->setOutputFile((char *) "../test/data/unit/klebsiella_PE2_filtered.fq");
 
     writeFilteredFastq(map_id_backend,2, sr);
     
     // step 4 : re-read output files and check their content.
     mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
-    int f_pe1=open((char *) "../data/klebsiella_PE1_filtered.fq",O_RDONLY,mode);
+    int f_pe1=open((char *) "../test/data/unit/klebsiella_PE1_filtered.fq",O_RDONLY,mode);
     assert(f_pe1!=-1);
     char* buf=(char *) malloc(FqBaseBackend::bufsize*sizeof(char)); // test files are very small, bufsize is  enough to read them entirely.
     assert(buf!=NULL);
@@ -111,7 +111,7 @@ void test_write_PE() {
     }
 #endif
     assert(strcmp(buf,expected_content_PE1)==0);
-    int f_pe2=open((char *) "../data/klebsiella_PE2_filtered.fq",O_RDONLY,mode);
+    int f_pe2=open((char *) "../test/data/unit/klebsiella_PE2_filtered.fq",O_RDONLY,mode);
     assert(f_pe2!=-1);
     nread=read(f_pe2,buf,FqBaseBackend::bufsize);
     assert(nread<FqBaseBackend::bufsize);
@@ -126,8 +126,8 @@ void test_write_PE() {
 
     // step5 : remove output files from disk
     
-    assert(remove((char *) "../data/klebsiella_PE1_filtered.fq")==0);
-    assert(remove((char *) "../data/klebsiella_PE2_filtered.fq")==0);
+    assert(remove((char *) "../test/data/unit/klebsiella_PE1_filtered.fq")==0);
+    assert(remove((char *) "../test/data/unit/klebsiella_PE2_filtered.fq")==0);
 
 }
 

src/unit_test_read_utils.cpp

@@ -33,7 +33,7 @@ void test_getReadSingle() {
     DnaSeqStr a_seqs;
     char dna_read[MAX_READ_LENGTH];
 
-    char * fq_single2=(char *) "../data/test_single2.fq";
+    char * fq_single2=(char *) "../test/data/unit/test_single2.fq";
     FqMainBackend be_fq=FqMainBackend(&io_sr); // TODO, remove argument from constructor
     be_fq.openInputFile(fq_single2, 4);
 
@@ -85,8 +85,8 @@ void getDnaStr(FqBaseBackend * fic_map[],rpos my_struct,DnaSeqStr* a_seqs,char *
 
 void test_getReadPE() {
     rpos my_struct1,my_struct2;
-    char * fq_PE1=(char *) "../data/test_PE1_2.fq";
-    char * fq_PE2=(char *) "../data/test_PE2_2.fq";
+    char * fq_PE1=(char *) "../test/data/unit/test_PE1_2.fq";
+    char * fq_PE2=(char *) "../test/data/unit/test_PE2_2.fq";
     srp io_sr;
     unsigned int j=0;
     char dna_read[MAX_READ_LENGTH];