Various non-important fixes and comments

doc/sphinx/build_dir.txt

-build/lib.macosx-10.6-intel-3.4

python/obitools3/commands/import.pyx

@@ -70,7 +70,6 @@ def run(config):
     cdef   Column      def_col
     cdef   Column      seq_col
     cdef   Column      qual_col
-    cdef   Column      taxid_col
     cdef   Column      old_column
     cdef   bint        rewrite
     cdef   dict        dcols

python/obitools3/commands/ls.pyx

@@ -26,12 +26,3 @@ def run(config):
     
     print(repr(input[1]))
      
-     
-     
-     
- 
-     
-     
-     
-     
-         
\ No newline at end of file

python/obitools3/commands/uniq.pyx

@@ -37,7 +37,7 @@ def addOptions(parser):
     group.add_argument('--merge-ids', '-e',
                        action="store_true", dest="uniq:mergeids",
                        default=False,
-                       help="ONLY WORKING ON SMALL SETS FOR NOW Add the merged key with all ids of merged sequences.")
+                       help="ONLY WORKING ON SMALL SETS FOR NOW Add the merged key with all ids of merged sequences.")  # TODO ?
    
     group.add_argument('--category-attribute', '-c',
                         action="append", dest="uniq:categories",

python/obitools3/dms/view/view.pyx

@@ -601,7 +601,7 @@ cdef class Line_selection(list):
         
     cpdef View materialize(self,
                            object view_name,
-                           object comments=""):
+                           object comments=b""):
 
         cdef bytes view_name_b = tobytes(view_name)
         cdef bytes comments_b

src/encode.c

@@ -307,7 +307,7 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
 			break;
 		default:
 			obi_set_errno(OBI_ENCODE_ERROR);
-			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
+			obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC), sequence: %s", seq);
 			return NULL;
 		}
 	}

src/obi_clean.c

@@ -57,7 +57,6 @@
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
 static int create_output_columns(Obiview_p o_view,
-								 Obiview_p i_view,
 								 OBIDMS_column_p sample_column,
 								 int sample_count);
 
@@ -85,7 +84,6 @@ static inline int idxcmp(const void* idx1, const void* idx2);
  ************************************************************************/
 
 static int create_output_columns(Obiview_p o_view,
-								 Obiview_p i_view,
 								 OBIDMS_column_p sample_column,
 								 int sample_count)
 {
@@ -279,7 +277,7 @@ int obi_clean(const char* dms_name,
 	sample_count = (sample_column->header)->nb_elements_per_line;
 
 	// Create the output columns
-	if (create_output_columns(o_view, i_view, sample_column, sample_count) < 0)
+	if (create_output_columns(o_view, sample_column, sample_count) < 0)
 	{
 		obidebug(1, "\nError creating the output columns");
 		return -1;

src/obi_clean.h

@@ -67,7 +67,7 @@
  * @retval 0 if the operation was successfully completed.
  * @retval -1 if an error occurred.
  *
- * @since April 2017
+ * @since April 2018
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
 int obi_clean(const char* dms_name,

src/obiavl.h

@@ -33,7 +33,7 @@
 #define MAX_NB_OF_AVLS_IN_GROUP (1000)						/**< The maximum number of AVL trees in a group.	// TODO discuss
                               	  	 	 	 	 	 	 	 */
 #define MAX_NODE_COUNT_PER_AVL (10000000)					/**< The maximum number of nodes in an AVL tree.
-															 *   Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
+															 *   Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss. Try 30M?
                               	  	 	 	 	 	 	 	 */
 #define MAX_DATA_SIZE_PER_AVL (1073741824)		            /**< The maximum size of the data referred to by an AVL tree in a group.
  	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   Only used to decide when to create a new AVL in a group.

src/obidmscolumn.h

@@ -372,7 +372,6 @@ int obi_truncate_column(OBIDMS_column_p column);
 int obi_enlarge_column(OBIDMS_column_p column);
 
 
-
 /*
  * @brief Sets the data in a column to the specified value.
  *