Merge branch 'bug_fixes'

Author: ch4rr0

bowtie

@@ -85,14 +85,16 @@ def main():
             if tot_size > small_index_max_size:
                 bin_spec = os.path.join(ex_path, bin_l)
         else:
-            if os.path.exists(args.index + idx_ext_l):
+            if not os.path.exists(arg + idx_ext_s)\
+                    and os.path.exists(args.index + idx_ext_l):
                 bin_spec = os.path.join(ex_path, bin_l)
         bowtie_args.insert(0, args.index)
     else:
         for arg in bowtie_args:
             if arg[0] == '-':
                 continue
-            if os.path.exists(arg + idx_ext_l):
+            if not os.path.exists(arg + idx_ext_s)\
+                    and os.path.exists(arg + idx_ext_l):
                 bin_spec = os.path.join(ex_path, bin_l)
 
     if args.debug:

ebwt_search.cpp

@@ -1566,7 +1566,7 @@ static void exactSearch(PatternComposer& _patsrc,
 			SLEEP(10);
 		}
 #else
-		for (int i = 0; i < nthreads; i++) {
+		for (int i = 0; i < nthreads - 1; i++) {
 			threads[i]->join();
 		}
 #endif
@@ -1950,7 +1950,7 @@ static void mismatchSearchFull(PatternComposer& _patsrc,
 			SLEEP(10);
 		}
 #else
-		for (int i = 0; i < nthreads; i++) {
+		for (int i = 0; i < nthreads - 1; i++) {
 			threads[i]->join();
 		}
 #endif
@@ -2453,7 +2453,7 @@ static void twoOrThreeMismatchSearchFull(
 			SLEEP(10);
 		}
 #else
-		for (int i = 0; i < nthreads; i++) {
+		for (int i = 0; i < nthreads - 1; i++) {
 			threads[i]->join();
 		}
 #endif
@@ -3011,7 +3011,7 @@ static void seededQualCutoffSearchFull(
 			SLEEP(10);
 		}
 #else
-		for (int i = 0; i < nthreads; i++) {
+		for (int i = 0; i < nthreads - 1; i++) {
 			threads[i]->join();
 		}
 #endif