obi import: better checking of whether to import quality

python/obitools3/commands/import.pyx

@@ -105,7 +105,6 @@ def run(config):
     output = open_uri(config['obi']['outputURI'],
                       input=False,
                       newviewtype=v)
-                      #quality=get_quality)  # TODO
     if output is None:
         raise Exception("Could not create output view")
         
@@ -130,11 +129,15 @@ def run(config):
     else: 
         raise NotImplementedError()
 
+    get_quality = config["obi"]["noquality"]
+    
     # Save basic columns in variables for optimization
     if NUC_SEQS_view :
         id_col = view[b"ID"]            # TODO use macros or globals for column names
         def_col = view[b"DEFINITION"]
         seq_col = view[b"NUC_SEQ"]
+        if get_quality:
+            qual_col = view[b"QUALITY"]
         
     dcols = {}
         
@@ -144,18 +147,9 @@ def run(config):
         pb(i)
                         
         if NUC_SEQS_view: 
-            
-            # Check if there is a sequencing quality associated     # TODO
-            if i == 0:
-                get_quality = b"QUALITY" in entry
-                if get_quality:
-                    Column.new_column(view, b"QUALITY", OBI_QUAL)
-                    qual_col = view[b"QUALITY"]
-            
             id_col[i] = entry.id
             def_col[i] = entry.definition
             seq_col[i] = entry.seq
-            
             if get_quality :
                 qual_col[i] = entry.quality