C obi_lcs: fixed checking for identical sequences when aligning 2

columns

src/obi_lcs.c

@@ -70,7 +70,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
 /**
  * @brief Internal function printing the result of one alignment to the output view.
  *
- * @param output_view A pointer on the writable view where the columns should be created.
+ * @param output_view A pointer on the writable view where the result should be written.
  * @param line The line in the output view where the result should be written.
  * @param idx1_column A pointer on the column where the index referring to the line of the first sequence aligned in the input view should be written.
  * @param idx2_column A pointer on the column where the index referring to the line of the second sequence aligned in the input view should be written.
@@ -85,7 +85,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
  * @param seq2_column A pointer on the column where the second sequence aligned should be written.
  * @param seq1_idx The index of the sequence of the first sequence aligned.
  * @param seq2_idx The index of the sequence of the second sequence aligned.
- * @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view.		// Count columns not implement yet
+ * @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view.
  * @param count1_column A pointer on the column where the count of the first sequence aligned should be written.
  * @param count2_column A pointer on the column where the count of the second sequence aligned should be written.
  * @param count1 The count of the first sequence aligned.
@@ -448,7 +448,7 @@ int obi_lcs_align_one_column(const char* dms_name,
 
 	// Open the sequence column to align
 	// If a column name wasn't given, open default sequence column
-	if (strcmp(seq_column_name, "") == 0)
+	if (strcmp(seq_column_name, "") == 0)  // TODO check for NULL
 	{
 		if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
 			iseq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN);
@@ -997,13 +997,13 @@ int obi_lcs_align_two_columns(const char* dms_name,
 					score = blob1->length_decoded_value;
 			}
 
-			else // the sequences aren't identical
+			else // the sequences aren't identical or we don't know
 			{
 				// kmer filter (offset for the index of the kmer table of the 2nd sequence because the kmer tables of the 2 sequence columns are concatenated in one)
-				align_filters(ktable, blob1, blob2, i, seq1_count+j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, false);
+				align_filters(ktable, blob1, blob2, i, seq1_count+j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, !same_indexer);
 
 				// Compute alignment score
-				if ((threshold == 0) || (score == -1.0))	// no threshold, or filter passed: align
+				if ((score < 0) && ((threshold == 0) || (score == -1.0)))	// (sequences are not identical), and (no threshold, or filter passed): align
 					score = obiblob_sse_banded_lcs_align(blob1, blob2, threshold, normalize, reference, similarity_mode, &lcs_length, &ali_length);
 
 				// TODO check this