Add 'bam copy' command.

bam/utils/system.py

@@ -123,3 +123,27 @@ def is_compressed_filetype(filepath):
         # '.gz', '.tgz',
         # '.zip',
         }
+
+
+def is_subdir(path, directory):
+    """
+    Returns true if *path* in a subdirectory of *directory*.
+    """
+    import os
+    from os.path import normpath, normcase
+    path = normpath(normcase(path))
+    directory = normpath(normcase(directory))
+
+    if isinstance(directory, bytes):
+        sep_i = ord(os.sep)
+        sep = os.sep.encode('ascii')
+    else:
+        sep_i = os.sep
+        sep = os.sep
+
+    directory = directory.rstrip(sep)
+    if len(path) > len(directory):
+        if path.startswith(directory):
+            return (path[len(directory)] == sep_i)
+    return False
+