Merge branch 'master' into esa_opt

EvolBioInf · Apr 10, 2015 · 420bf0a · 420bf0a
2 parents 5403ae9 + c0df08d
commit 420bf0a
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Showing 3 changed files with 10 additions and 7 deletions.
diff --git a/src/andi.c b/src/andi.c
@@ -125,9 +125,9 @@ int main( int argc, char *argv[]){
 			case 'j':
 				FLAGS |= F_JOIN;
 				break;
-#ifdef _OPENMP
 			case 't':
 				{
+#ifdef _OPENMP
 					errno = 0;
 					char *end;
 					long unsigned int threads = strtoul( optarg, &end, 10);
@@ -149,9 +149,12 @@ int main( int argc, char *argv[]){
 					}
 
 					THREADS = threads;
+#else
+					warnx("This version of andi was built without OpenMP and thus "
+						"does not support multi threading. Ignoring -t argument.");
+#endif
 				}
 				break;
-#endif
 			case '?': /* intentional fall-through */
 			default:
 				usage();
@@ -239,7 +242,7 @@ void usage(void){
 		"  -r, --raw         Calculates raw distances; default: Jukes-Cantor corrected\n"
 		"  -v, --verbose     Prints additional information\n"
 #ifdef _OPENMP
-		"  -t <INT>          The number of threads to be used; default: 1\n"
+		"  -t <INT>          The number of threads to be used; by default, all available processors are used\n"
 #endif
 		"  -h, --help        Display this help and exit\n"
 		"      --version     Output version information and acknowledgments\n"

diff --git a/test/test_join.sh b/test/test_join.sh
@@ -11,7 +11,7 @@ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
 rm p1.fasta p2.fasta p3.fasta;
 
 
-RES=$($srcdir/src/andi -r -j S0.fasta S1.fasta |
+RES=$($srcdir/src/andi -rt 1 -j S0.fasta S1.fasta |
 	tail -n 1 |
 	awk '{print ($2 - 0.1)}' |
 	awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.01}'
@@ -33,7 +33,7 @@ tail -qn 2 p2.fasta p3.fasta > S1.fasta
 rm p2.fasta p3.fasta;
 
 
-RES=$($srcdir/src/andi -r -j S0.fasta S1.fasta |
+RES=$($srcdir/src/andi -rt1 -j S0.fasta S1.fasta |
         tail -n 1 |
         awk '{print ($2 - 0.1)}' |
         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.01}'
@@ -57,7 +57,7 @@ tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta
 rm p1.fasta p2.fasta p3.fasta;
 
 
-RES=$($srcdir/src/andi -r -j S0.fasta S1.fasta |
+RES=$($srcdir/src/andi -rt 1 -j S0.fasta S1.fasta |
         tail -n 1 |
         awk '{print ($2 - 0.1)}' |
         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.01}'

diff --git a/test/test_random.sh b/test/test_random.sh
@@ -8,7 +8,7 @@ do
 	do
 		res=$(./test/test_fasta -l $LENGTH -d $dist |
 			tee ./test/test_random.fasta |
-			./src/andi -r |
+			./src/andi -r -t 1 |
 			tail -n 1 |
 			awk -v dist=$dist '{print $2, dist}' |
 			awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.01}')