fix for bcalm when -out points to another directory. Also did a minor…

… change in Bank, hopefully inconsequential

gatb-core/src/gatb/bank/impl/Bank.cpp

@@ -146,9 +146,12 @@ IBank* Bank::_open_ (const std::string& uri)
     {
         result = it->factory->createBank(uri);
         DEBUG (("   factory '%s' => result=%p \n", it->name.c_str(), result ));
+
+        if (result) // if one of the factories produce a result, we can just stop, no need to try other factories.
+            break;
     }
 
-    if (result == 0) { throw system::Exception ("Unable to open bank '%s'", uri.c_str()); }
+    if (result == 0) { throw system::Exception ("Unable to open bank '%s' (if it is a list of files, perhaps some of the files inside don't exist)", uri.c_str()); }
 
     return result;
 }

gatb-core/src/gatb/bcalm2/bcalm_algo.cpp

@@ -1,4 +1,5 @@
 #include "bcalm_algo.hpp"
+#include <libgen.h> // for basename()
 
 /*
  * some notes: this code could be further optimized.
@@ -594,7 +595,12 @@ void bcalm2(Storage *storage,
     std::ofstream list_of_glues(prefix + ".glue"); 
     for (unsigned int i = 0; i < (unsigned int)nb_threads; i++)
     {
-        string glue_file = prefix + ".glue." + std::to_string(i);
+
+        char* prefix_copy = strdup (prefix.c_str());
+        std::string prefix_base (basename(prefix_copy)); // posix basename() may alter the string
+        free (prefix_copy);
+
+        string glue_file = prefix_base + ".glue." + std::to_string(i);
         if (nb_seqs_in_glue[i])
         {
             list_of_glues << glue_file << endl;

gatb-core/src/gatb/system/impl/FileSystemCommon.cpp

@@ -110,7 +110,7 @@ IFileSystem::Path FileSystemCommon::getTemporaryDirectory ()
 ** INPUT   :
 ** OUTPUT  :
 ** RETURN  :
-** REMARKS :
+** REMARKS : Warning! this method isn't exactly basename() as you'd expect in C++. It returns the base name but cuts everything after the last dot.
 *********************************************************************/
 IFileSystem::Path FileSystemCommon::getBaseName (const Path& path, bool cutToFirstDot)
 {