Respect high --keep setting

unicycler/spades_func.py

@@ -68,7 +68,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi
         reads = (short1, short2, short_unpaired)
     else:
         reads = spades_read_correction(short1, short2, short_unpaired, spades_dir, threads,
-                                       spades_path)
+                                       spades_path, keep)
     kmer_range = get_kmer_range(short1, short2, short_unpaired, spades_dir, kmer_count, min_k_frac,
                                 max_k_frac)
     assem_dir = os.path.join(spades_dir, 'assembly')
@@ -200,7 +200,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi
     return assembly_graph
 
 
-def spades_read_correction(short1, short2, unpaired, spades_dir, threads, spades_path):
+def spades_read_correction(short1, short2, unpaired, spades_dir, threads, spades_path, keep):
     """
     This runs SPAdes with the --only-error-correction option.
     """
@@ -309,7 +309,8 @@ def spades_read_correction(short1, short2, unpaired, spades_dir, threads, spades
     if using_unpaired_reads and not corrected_u_exists:
         quit_with_error('SPAdes read error correction failed. '
                         'See spades_assembly/read_correction/spades.log for more info.')
-    shutil.rmtree(read_correction_dir, ignore_errors=True)
+    if keep < 3:
+        shutil.rmtree(read_correction_dir, ignore_errors=True)
 
     if not using_paired_reads:
         corrected_1 = None

unicycler/string_graph.py

@@ -202,7 +202,6 @@ def remove_branching_paths(self):
         else:
             log.log('No links needed removal', verbosity=2)
 
-
     def segment_leads_directly_to_contig_in_both_directions(self, seg_name):
         if self.segments[seg_name].contig:
             return True