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