All tests can easily be launched by the command 'make test'

Makefile

@@ -819,8 +819,7 @@ check-syntax:
 
 
 
-#Makefile part about unit-tests
-#when you run 'make test' all unit-tests are compiled, executed and then all the executables created during the compilation will be deleted
+#Makefile part about tests
 test_SOURCE= \
 	$(CURDIR)/test/aug_suffix_tree_test.c\
 	$(CURDIR)/test/bit_vector_test.c\
@@ -838,6 +837,8 @@ test_SOURCE= \
 	$(CURDIR)/test/simpl_info_test.c\
 	$(CURDIR)/test/types_test.c\
 	$(CURDIR)/test/util_test.c\
+	$(CURDIR)/regressionTest/executePIntronTests.c\
+	$(CURDIR)/regressionTest/testPIntronOutput.c\
 
 test_EXEC= \
 	$(CURDIR)/test/aug_suffix_tree_test\
@@ -856,13 +857,18 @@ test_EXEC= \
 	$(CURDIR)/test/simpl_info_test\
 	$(CURDIR)/test/types_test\
 	$(CURDIR)/test/util_test\
+	$(CURDIR)/regressionTest/executePIntronTests\
+	$(CURDIR)/regressionTest/testPIntronOutput\
 
-CFLAGS = -l criterion -I $(INCLUDE_DIR) -I $(STREE_DIR)
+CFLAGS = -l criterion -I $(INCLUDE_DIR) -I $(STREE_DIR) -I regressionTest
 
-comp-test: $(test_EXEC) $(all_header_files) $(stree_header_files)
+comp-test:$(test_EXEC) $(all_header_files) $(stree_header_files)
 	$(CC) $(test_SOURCE) $(CFLAGS)
 
 test: $(test_EXEC)
+	#preparing files for regressionTest:
+	$(CURDIR)/regressionTest/executePIntronTests
+	#executing unitTest:
 	$(CURDIR)/test/aug_suffix_tree_test
 	$(CURDIR)/test/bit_vector_test
 	$(CURDIR)/test/bool_list_test
@@ -879,7 +885,18 @@ test: $(test_EXEC)
 	$(CURDIR)/test/simpl_info_test
 	$(CURDIR)/test/types_test
 	$(CURDIR)/test/util_test
-
+	#executing regressionTest:
+	$(CURDIR)/regressionTest/testPIntronOutput
 .PHONY: clean-test
 clean-test:
+	#cleaning unitTest temp files:
 	rm $(CURDIR)/test/*_test
+	#cleaning PIntron temp files:
+	rm $(CURDIR)/ests.txt
+	rm $(CURDIR)/genomic.txt
+	rm $(CURDIR)/pintron-log.txt
+	#cleaning regressionTest temp files:
+	rm $(CURDIR)/regressionTest/executePIntronTests
+	rm $(CURDIR)/regressionTest/testPIntronOutput
+	rm $(CURDIR)/regressionTest/output.txt
+	rm -rf $(CURDIR)/regressionTest/test*/executionOutput/

regressionTest/executePIntronTests.c

@@ -0,0 +1,161 @@
+//gcc executePIntronTests.c -o executePIntronTests -l criterion
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <criterion/criterion.h>
+#include <criterion/parameterized.h>
+#include <dirent.h>
+#include <malloc.h>
+
+char* strdup(const char* org){
+	if(org==NULL)
+		return NULL;
+	char* newstr=malloc(strlen(org)+1);
+	char* p;
+	if(newstr==NULL)
+		return NULL;
+	p=newstr;
+	while(*org)
+		*p++=*org++; //copy the string 
+	return newstr;
+}
+
+
+
+#define MAX_ROWS (256)
+#define MAX_COLUMNS (256)
+static char words1[MAX_ROWS][MAX_COLUMNS]={{'\0','\0'}};
+static char words2[MAX_ROWS][MAX_COLUMNS]={{'\0','\0'}};
+
+void bubbleSortWordsArray1(int wordCount)
+{
+	int c; //outer index through rows
+	int d; //inner index through rows
+	char swap[MAX_COLUMNS]={'\0'};
+
+	for(c=0;c<(wordCount-1);c++)
+	{
+		for(d=0;d<(wordCount-c-1);d++)
+		{
+			if(0>strcmp(words1[d],words1[d+1]))
+				{
+					//words need to be swapped
+					strcpy(swap,words1[d]);
+					strcpy(words1[d],words1[d+1]);
+					strcpy(words1[d+1],swap);
+				} 
+		}
+	}
+}
+
+void bubbleSortWordsArray2(int wordCount)
+{
+	int c; //outer index through rows
+	int d; //inner index through rows
+	char swap[MAX_COLUMNS]={'\0'};
+
+	for(c=0;c<(wordCount-1);c++)
+	{
+		for(d=0;d<(wordCount-c-1);d++)
+		{
+			if(0>strcmp(words2[d],words2[d+1]))
+				{
+					//words need to be swapped
+					strcpy(swap,words2[d]);
+					strcpy(words2[d],words2[d+1]);
+					strcpy(words2[d+1],swap);
+				}
+			}
+	}
+}
+
+char * my_strcat(char *dest, char *src)
+{
+	char *new_string = malloc(strlen(dest) + strlen(src) + 1);
+	strcpy(new_string, dest);
+	strcat(new_string, src);
+	return(new_string);
+}
+
+int main(int argc, char *argv[]){
+	system("cd regressionTest;for i in $(ls -d */); do echo ${i%%/}; done > output.txt");
+	system("make dist");
+
+	FILE * fp;
+	FILE * fpgg;
+	char * line = NULL;
+	char * linegg = NULL;
+	size_t len = 0;
+	size_t lengg = 0;
+	ssize_t read;
+	ssize_t readgg;
+
+	char *PI1="bin/pintron --bin-dir=bin/ --genomic='regressionTest/";
+	//line
+	char *PI2="/genomic.txt' --EST='regressionTest/";
+	//line
+	char *PI3="/ests.txt' --organism=human --gene=";
+	//gene.txt content extracted from test* subfolder for each test
+	//regressionTest/+line+/gene.txt
+	char *PI4=" --output='regressionTest/";
+	//line
+	char *PI5="/executionOutput/full.json' --logfile='regressionTest/";
+	//line
+	char *PI6="/executionOutput/pintron-pipeline-log.txt' general-logfile='regressionTest/";
+	//line
+	char *PI7="/executionOutput/pintron-log.txt' --gtf='regressionTest/";
+	//line
+	char *PI8="/executionOutput/pintron-all-isoforms.gtf'";
+
+	char *PI=NULL;
+
+	char *FG1="regressionTest/";
+	//line
+	char *FG2="/gene.txt";
+	//complete string:
+	char *FG=NULL;
+
+	char *MKd1="cd regressionTest/";
+	//line
+	char *MKd2="/;mkdir -p executionOutput";
+	//complete string for make missing dirs
+	char *MKdF=NULL;
+
+	fp = fopen("regressionTest/output.txt", "r");
+	while ((read = getline(&line,&len,fp)) != -1) {
+		line[strlen(line) - 1] = 0;
+
+		FG=my_strcat(FG1,line);
+		FG=my_strcat(FG,FG2);
+
+		fpgg = fopen(FG, "r");
+		while ((readgg = getline(&linegg,&lengg,fpgg)) != -1) {
+			linegg[strlen(linegg) - 1] = 0;}
+		fclose(fpgg);
+
+		MKdF=my_strcat(MKd1,line);
+		MKdF=my_strcat(MKdF,MKd2);
+		system(MKdF);
+
+		PI=my_strcat(PI1,line);
+		PI=my_strcat(PI,PI2);
+		PI=my_strcat(PI,line);
+		PI=my_strcat(PI,PI3);
+		PI=my_strcat(PI,linegg);
+		PI=my_strcat(PI,PI4);
+		PI=my_strcat(PI,line);
+		PI=my_strcat(PI,PI5);
+		PI=my_strcat(PI,line);
+		PI=my_strcat(PI,PI6);
+		PI=my_strcat(PI,line);
+		PI=my_strcat(PI,PI7);
+		PI=my_strcat(PI,line);
+		PI=my_strcat(PI,PI8);
+
+		system(PI);
+	}
+	fclose(fp);
+}
+
+

regressionTest/test-788/gene.txt

@@ -0,0 +1 @@
+AAMP