obi clean: option to only keep heads now works, fixed a bug where last

sequence was not properly labelled, and code is cleaned, fixed and error
checked

src/obi_clean.c

@@ -41,13 +41,40 @@
  *
  **************************************************************************/
 
-// TODO
+
+/**
+ * Internal function creating the output columns for the obiclean algorithm.
+ *
+ * @param o_view A pointer on the output view.
+ * @param i_view A pointer on the input view.
+ * @param sample_column A pointer on the column where sample counts are kept.
+ * @param sample_count The number of different samples.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since April 2018
+ * @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);
 
 
+/**
+ * @brief Internal function comparing two indexes (int64_t).
+ *
+ * @param idx1 A pointer on the first index.
+ * @param idx2 A pointer on the second index.
+ *
+ * @returns -1 if idx1 < idx2,
+ * 			1 if idx1 > idx2,
+ * 			and 0 if idx1 == idx2.
+ *
+ * @since April 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
 static inline int idxcmp(const void* idx1, const void* idx2);
 
 
@@ -125,7 +152,6 @@ static inline int idxcmp(const void* idx1, const void* idx2)
  **********************************************************************/
 
 
-// TODO comment
 int obi_clean(const char* dms_name,
 		      const char* i_view_name,
 			  const char* sample_column_name,
@@ -136,10 +162,12 @@ int obi_clean(const char* dms_name,
 			  bool heads_only,
 			  int thread_count)
 {
+	char* 			o_view_name_temp;
 	float 			p;
-	index_t         i, j;
+	index_t         i, j, l;
 	index_t         seq_count;
 	index_t*  		index_array;
+	index_t*  		line_selection;
 	double          score;
 	bool            above_threshold;
 	int             lcs_length;
@@ -174,8 +202,6 @@ int obi_clean(const char* dms_name,
 	OBIDMS_column_p singletoncount_column = NULL;
 	OBIDMS_column_p samplecount_column = NULL;
 
-	// TODO other columns
-
 	void* no;
 	void* yes;
 	void* key_p;
@@ -184,11 +210,13 @@ int obi_clean(const char* dms_name,
 	int reference = 0;
 	bool similarity_mode = false;
 
-	char* seq1;
-	char* seq2;
-
 	// Open DMS
 	dms = obi_dms(dms_name);
+	if (dms == NULL)
+	{
+		obidebug(1, "\nError opening the DMS");
+		return -1;
+	}
 
 	// Open input view
 	i_view = obi_open_view(dms, i_view_name);
@@ -226,11 +254,25 @@ int obi_clean(const char* dms_name,
 		}
 	}
 
-	// Create the output view
+	// Create the output view, or a temporary one if heads only
-	o_view = obi_clone_view(dms, i_view, o_view_name, NULL, o_view_comments);
+	if (heads_only)
+	{
+		o_view_name_temp = calloc((strlen(o_view_name)+strlen("_temp")+1), sizeof(char));
+		if (o_view_name_temp == NULL)
+		{
+			obidebug(1, "\nError allocating memory for the name of a temporary output view in obiclean");
+			return -1;
+		}
+		o_view_name_temp = strcpy(o_view_name_temp, o_view_name);
+		strcat(o_view_name_temp, "_temp");
+		o_view = obi_clone_view(dms, i_view, o_view_name_temp, NULL, o_view_comments);
+	}
+	else
+		o_view = obi_clone_view(dms, i_view, o_view_name, NULL, o_view_comments);
+
 	if (o_view == NULL)
 	{
-		obidebug(1, "\nError creating the output view");
+		obidebug(1, "\nError creating the output view in obiclean");
 		return -1;
 	}
 
@@ -238,16 +280,48 @@ int obi_clean(const char* dms_name,
 
 	// Create the output columns
 	if (create_output_columns(o_view, i_view, sample_column, sample_count) < 0)
-		// TODO
+	{
+		obidebug(1, "\nError creating the output columns");
 		return -1;
+	}
 
 	// Get the created output columns
 	status_column = obi_view_get_column(o_view, CLEAN_STATUS_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean status column");
+		return -1;
+	}
 	head_column = obi_view_get_column(o_view, CLEAN_HEAD_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean head column");
+		return -1;
+	}
 	internalcount_column = obi_view_get_column(o_view, CLEAN_INTERNALCOUNT_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean internal count column");
+		return -1;
+	}
 	headcount_column = obi_view_get_column(o_view, CLEAN_HEADCOUNT_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean head count column");
+		return -1;
+	}
 	singletoncount_column = obi_view_get_column(o_view, CLEAN_SINGLETONCOUNT_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean singleton count column");
+		return -1;
+	}
 	samplecount_column = obi_view_get_column(o_view, CLEAN_SAMPLECOUNT_COLUMN_NAME);
+	if (status_column == NULL)
+	{
+		obidebug(1, "\nError getting the obiclean sample count column");
+		return -1;
+	}
 
 	// Build kmer tables
 	ktable = hash_seq_column(i_view, iseq_column, 0);
@@ -262,30 +336,50 @@ int obi_clean(const char* dms_name,
 
 	// Allocate arrays of pointers to binary trees
 	yes_trees = (void**) calloc(seq_count, sizeof(void*));
+	if (yes_trees == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for 'yes' binary trees");
+		return -1;
+	}
 	no_trees = (void**) calloc(seq_count, sizeof(void*));
+	if (no_trees == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for 'no' binary trees");
+		return -1;
+	}
 
 	// Allocate and fill index array for the binary trees to reference (they don't copy the data)
 	index_array = (index_t*) malloc(seq_count * sizeof(index_t));
+	if (index_array == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for the index array");
+		return -1;
+	}
 	for (i=0; i < seq_count; i++)
 		index_array[i]=i;
 
 	// Initialize all sequences to singletons or NA if no sequences in that sample
-	for (i=0; i < (seq_count - 1); i++)
+	for (i=0; i<seq_count; i++)
 	{
 		for (sample=0; sample < sample_count; sample++)
 		{
-			if (obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample) != OBIInt_NA)
+			if (obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample) != OBIInt_NA)  // Only initialize samples where there are some sequences
 			{
 				if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 's') < 0)
-				// TODO
+				{
+					obidebug(1, "\nError initializing all sequences to singletons");
 					return -1;
+				}
 			}
 		}
 	}
 
 	for (sample=0; sample < sample_count; sample++)
 	{
-		for (i=0; i < (seq_count - 1); i++)
+		for (i=0; i< (seq_count-1); i++)
 		{
 			if (i%1000 == 0)
 			{
@@ -301,8 +395,6 @@ int obi_clean(const char* dms_name,
 				return -1;
 			}
 
-			seq1 = obi_get_seq_with_elt_idx_and_col_p_in_view(i_view, iseq_column, i, 0);
-
 			// Get count for this sample
 			s1_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample);
 
@@ -316,8 +408,6 @@ int obi_clean(const char* dms_name,
 					return -1;
 				}
 
-				seq2 = obi_get_seq_with_elt_idx_and_col_p_in_view(i_view, iseq_column, j, 0);
-
 				// Get count for this sample
 				s2_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, j, sample);
 
@@ -326,6 +416,7 @@ int obi_clean(const char* dms_name,
 						((((s1_count >= s2_count) && (((double) s2_count / (double) s1_count) <= max_ratio))) ||
 						(((s2_count >= s1_count) && (((double) s1_count / (double) s2_count) <= max_ratio)))))
 				{
+
 					yes=NULL;
 					no=NULL;
 					no = tfind(index_array+j, &(no_trees[i]), idxcmp);
@@ -333,7 +424,7 @@ int obi_clean(const char* dms_name,
 						yes = tfind(index_array+j, &(yes_trees[i]), idxcmp);
 
 					above_threshold = false;
-					if ((no == NULL) && (yes == NULL))			//never compared
+					if ((no == NULL) && (yes == NULL))	// never compared before
 					{
 						// Check if the sequences are identical in a quick way (same index in the same indexer)
 						if (obi_get_index_with_elt_idx_and_col_p_in_view(i_view, iseq_column, i, 0) == obi_get_index_with_elt_idx_and_col_p_in_view(i_view, iseq_column, j, 0))
@@ -354,38 +445,74 @@ int obi_clean(const char* dms_name,
 					if (yes || above_threshold)
 					{
 						if (yes == NULL)
-							// put seqs in their 'yes' trees
+						// Put in 'yes' tree of 1st sequence
-							key_p = tsearch(index_array+j, &(yes_trees[i]), idxcmp);   // TODO error checking
+						{
+							key_p = tsearch(index_array+j, &(yes_trees[i]), idxcmp);
+							if (key_p == NULL)
+							{
+								obidebug(1, "\nError adding an index in a binary tree");
+								return -1;
+							}
+						}
+
 						// label as head or internal
 						if (s1_count >= s2_count)
 						{
 							if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample) == 's')	// seq can become head ONLY if it's a singleton
-								obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h');
+							{
+								if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h') < 0)
+									return -1;
+							}
 							// Otherwise it's an internal
-							obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i');
+							if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i') < 0)
+								return -1;
 						}
 						else
 						{
 							if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample) == 's')	// seq can become head ONLY if it's a singleton
-								obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h');
+								{
-							obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i');
+									if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h') < 0)
+										return -1;
+								}
+							if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i') < 0)
+								return -1;
 						}
 					}
 					else if (no == NULL)
-					// put in 'no' tree of both sequences  // TODO why just one then???
+					// Put in 'no' tree of 1st sequence
-						key_p = tsearch(index_array+j, &(no_trees[i]), idxcmp);   // TODO error checking
+					{
+						key_p = tsearch(index_array+j, &(no_trees[i]), idxcmp);
+						if (key_p == NULL)
+						{
+							obidebug(1, "\nError adding an index in a binary tree");
+							return -1;
+						}
+					}
 				}
-				free(seq2);
 			}
-			free(seq1);
 		}
 	}
 
 	free_kmer_tables(ktable, seq_count);
+	free(index_array);
+	free(yes_trees);
+	free(no_trees);
 
 	fprintf(stderr, "\n");
 
-	for (i=0; i < (seq_count - 1); i++)
+	if (heads_only)
+	{
+		line_selection = malloc((o_view->infos)->line_count * sizeof(index_t));
+		if (line_selection == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for line selection");
+			return -1;
+		}
+		l=0;
+	}
+
+	for (i=0; i<seq_count; i++)
 	{
 		if (i%1000 == 0)
 		{
@@ -404,7 +531,14 @@ int obi_clean(const char* dms_name,
 			// Check if head or singleton in at least one sample
 			status = obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample);
 			if ((!head) && ((status == 'h') || (status == 's')))
+			{
 				head = true;
+				if (heads_only)
+				{
+					line_selection[l] = i;
+					l++;
+				}
+			}
 
 			if (status == 's')
 			{
@@ -424,23 +558,42 @@ int obi_clean(const char* dms_name,
 
 		}
 
-		if (obi_set_bool_with_elt_idx_and_col_p_in_view(o_view, head_column, i, 0, head) < 0)
+		if (!heads_only  || (heads_only && head))  // Label only if sequence is going to be kept in final view
-			// TODO
+		{
-			return -1;
+			if (obi_set_bool_with_elt_idx_and_col_p_in_view(o_view, head_column, i, 0, head) < 0)
+				return -1;
+			if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, singletoncount_column, i, 0, singleton_count) < 0)
+				return -1;
+			if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, internalcount_column, i, 0, internal_count) < 0)
+				return -1;
+			if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, headcount_column, i, 0, head_count) < 0)
+				return -1;
+			if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, samplecount_column, i, 0, ind_sample_count) < 0)
+				return -1;
+		}
+	}
 
-		if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, singletoncount_column, i, 0, singleton_count) < 0)
+	// Flag the end of the line selection
-			// TODO
+	if (heads_only)
-			return -1;
+		line_selection[l] = -1;
-		if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, internalcount_column, i, 0, internal_count) < 0)
-			// TODO
-			return -1;
-		if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, headcount_column, i, 0, head_count) < 0)
-			// TODO
-			return -1;
-		if (obi_set_int_with_elt_idx_and_col_p_in_view(o_view, samplecount_column, i, 0, ind_sample_count) < 0)
-			// TODO
-			return -1;
 
+	// Create new view with line selection if heads only
+	if (heads_only)
+	{
+		if (obi_save_and_close_view(o_view) < 0)
+		{
+			obidebug(1, "\nError closing the temporary output view");
+			return -1;
+		}
+		o_view = obi_clone_view_from_name(dms, o_view_name_temp, o_view_name, line_selection, o_view_comments);
+		if (o_view == NULL)
+		{
+			obidebug(1, "\nError cloning the temporary output view to make the final output view");
+			return -1;
+		}
+
+		free(o_view_name_temp);
+		free(line_selection);
 	}
 
 	// Close views
@@ -449,6 +602,7 @@ int obi_clean(const char* dms_name,
 		obidebug(1, "\nError closing the input view after aligning");
 		return -1;
 	}
+
 	if (obi_save_and_close_view(o_view) < 0)
 	{
 		obidebug(1, "\nError closing the output view after aligning");