Updating recursion directory naming behavior.

The previous commit fixed the bug associated with 2 subtree
decomposition recursions trying to write to the same directory.
However, the global 'RECURSION_INDEX' attribute of the class
SateAlignerJob was continuing to increment between sate
iterations. This did not cause any problems, but left a less
intuitive recursion directory taxonomy.

This commit adds the 'reset_recursion_index' option to
SateAlignerJob.__init__, which is used by sate.satejob each
time a new iteration begins. As a result the recursion indices
start at 0 for each sate iteration.

Author: joaks1

Diff for: sate/satealignerjob.py

@@ -65,6 +65,7 @@ def __init__(self,
                 tree,
                 tmp_base_dir,
                 tmp_dir_par=None,
+                reset_recursion_index=False,
                 **kwargs):
         self._job_lock = Lock()
         TreeHolder.__init__(self, multilocus_dataset.dataset)
@@ -86,6 +87,8 @@ def __init__(self,
         self.tmp_dir_par = tmp_dir_par
         if self.tmp_dir_par == None:
             self.tmp_dir_par = self.tmp_base_dir
+        if reset_recursion_index:
+            self.__class__.RECURSION_INDEX = 0
 
     def configuration(self):
         d = {}

Diff for: sate/satejob.py

@@ -356,6 +356,7 @@ def run(self, tmp_dir_par, sate_products=None):
                                          sate_team=self.sate_team,
                                          tree=tree_for_aligner,
                                          tmp_base_dir=curr_tmp_dir_par,
+                                         reset_recursion_index=True,
                                          **configuration)
                 self.sate_aligner_job = aligner
                 aligner.launch_alignment(break_strategy=break_strategy,