added test folder, improved compatility in makefile and fixed missing…

… library

README.md

@@ -114,7 +114,14 @@ USAGE:
 * -diffuse    Integer:   z>0 (default 4) Use 4 for everything - if using large plant genomes you can try using 1
 * -dimension  Size of the output matrix and plot. Integer:   d>0 (default 1000) Use 1000 for everything that is not full genome size, where 2000 is recommended
 
+## Test data
 
+You can test CHROMEISTER with the two mycoplasma sequences provided in the 'test-data' folder. You can do so by running the following commands (from within the test-data folder):
+
+```../bin/CHROMEISTER -query mycoplasma-232.fasta -db mycoplasma-7422.fasta -out mycoplasma-232-7422.mat -dimension 500```
+```Rscript ../bin/compute_score.R mycoplasma-232-7422.mat 500```
+
+Note: in this example we used size 500 since the two sequences are quite small.
 
 ## Help
 

src/Makefile

@@ -1,14 +1,11 @@
-CC=gcc
-CXX=g++
-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall #-DVERBOSE
+CFLAGS+=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall #-DVERBOSE
 BIN=../bin
 
 all: CHROMEISTER
 
 
-
 CHROMEISTER: CHROMEISTER.c
-	$(CC) $(CFLAGS) alignmentFunctions.c -lm commonFunctions.c -lm CHROMEISTER.c -lm -o $(BIN)/CHROMEISTER
+	gcc $(CFLAGS) alignmentFunctions.c -lm commonFunctions.c -lpthread -lm CHROMEISTER.c -lm -o $(BIN)/CHROMEISTER
 
 clean:
 	rm -rf $(BIN)/CHROMEISTER

src/commonFunctions.h

@@ -1,5 +1,6 @@
 #ifndef COMMON_FUNCTIONS_H
 #define COMMON_FUNCTIONS_H
+#include <pthread.h>
 #include "structs.h"
 /**
  * Print the error message 's' and exit(-1)