C: new function to build a reference database with LCA and score

metadata for the taxonomic assignment of sequences

src/build_reference_db.h

+/****************************************************************************************************
+ * Header file for functions to build reference databases for the taxonomic assignment of sequences *
+ ****************************************************************************************************/
+
+/**
+ * @file build_reference_db.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date November 15th 2018
+ * @brief Header file for the functions for the taxonomic assignment of sequences.
+ */
+
+
+#ifndef BUILD_REFERENCE_DB_H_
+#define BUILD_REFERENCE_DB_H_
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+
+#define LCA_TAXID_COLUMN_NAME "LCA_TAXID"
+#define LCA_TAXID_ARRAY_COLUMN_NAME "LCA_TAXID"
+#define LCA_SCORE_ARRAY_COLUMN_NAME "LCA_SCORE"
+
+
+/**
+ * @brief Building of reference databases for the taxonomic assignment of sequences.
+ *
+ * Note: The columns where the results are written are automatically named and created.
+ *
+ * @param dms_name The name of the DMS.
+ * @param refs_view_name The name of the view containing the reference sequences annotated with their taxids.
+ * @param taxonomy_name The name of the taxonomy stored in the DMS.
+ * @param o_view_name The name of the final reference database to create.
+ * @param o_view_comments The comments to associate with the final reference database to create.
+ * @param threshold The threshold (similarity score in identity percentage) at which the database should be created.
+ *                  The output database contains the Lowest Common Ancestor and associated highest similarity score for each
+ *                  sequence with the sequences with a similarity equal or greater than this threshold.
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since November 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int build_reference_db(const char* dms_name,
+					   const char* refs_view_name,
+					   const char* taxonomy_name,
+					   const char* o_view_name,
+					   const char* o_view_comments,
+					   double threshold);
+
+
+#endif /* BUILD_REFERENCE_DB_H_ */
+