Commit f942dd85 by Celine Mercier

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

metadata for the taxonomic assignment of sequences
parent 730ea99f
/****************************************************************************************************
* 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_ */
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