86 lines
3.2 KiB
C
Executable File
86 lines
3.2 KiB
C
Executable File
/*************************************************************************************************
|
|
* Header file for functions tagging a set of sequences for PCR/sequencing errors identification *
|
|
*************************************************************************************************/
|
|
|
|
/**
|
|
* @file obi_clean.h
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
* @date April 9th 2018
|
|
* @brief Header file for the functions tagging a set of sequences for PCR/sequencing errors identification.
|
|
*/
|
|
|
|
|
|
#ifndef OBI_CLEAN_H_
|
|
#define OBI_CLEAN_H_
|
|
|
|
|
|
#include <stdlib.h>
|
|
#include <stdio.h>
|
|
#include <stdbool.h>
|
|
|
|
#include "obidms.h"
|
|
#include "obiview.h"
|
|
#include "obidmscolumn.h"
|
|
#include "obitypes.h"
|
|
|
|
|
|
/**
|
|
* @brief Names and comments of columns automatically created in the output view when aligning.
|
|
*
|
|
* @since April 2018
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
#define CLEAN_STATUS_COLUMN_NAME "obiclean_status"
|
|
#define CLEAN_HEAD_COLUMN_NAME "obiclean_head"
|
|
#define CLEAN_SAMPLECOUNT_COLUMN_NAME "obiclean_samplecount"
|
|
#define CLEAN_HEADCOUNT_COLUMN_NAME "obiclean_headcount"
|
|
#define CLEAN_INTERNALCOUNT_COLUMN_NAME "obiclean_internalcount"
|
|
#define CLEAN_SINGLETONCOUNT_COLUMN_NAME "obiclean_singletoncount"
|
|
|
|
#define CLEAN_STATUS_COLUMN_COMMENTS ""
|
|
#define CLEAN_HEAD_COLUMN_COMMENTS ""
|
|
#define CLEAN_SAMPLECOUNT_COLUMN_COMMENTS ""
|
|
#define CLEAN_HEADCOUNT_COLUMN_COMMENTS ""
|
|
#define CLEAN_INTERNALCOUNT_COLUMN_COMMENTS ""
|
|
#define CLEAN_SINGLETONCOUNT_COLUMN_COMMENTS ""
|
|
|
|
|
|
/**
|
|
* @brief Tags a set of sequences for PCR/sequencing errors identification
|
|
*
|
|
* Note: The columns where the results are written are automatically named and created.
|
|
*
|
|
* @param dms A pointer on an OBIDMS.
|
|
* @param i_view_name The name of the input view.
|
|
* @param sample_column_name The name of the OBI_STR column in the input view where the sample information is kept.
|
|
* NULL or "" (empty string) if there is no sample information.
|
|
* @param o_view_name The name of the output view where the results should be written (should not already exist).
|
|
* @param o_view_comments The comments that should be associated with the output view.
|
|
* @param threshold Similarity threshold expressed as a number of differences.
|
|
* Only sequence pairs with a similarity above the threshold are clustered.
|
|
* @param max_ratio Maximum ratio between the counts of two sequences so that the less abundant one can be considered
|
|
* as a variant of the more abundant one.
|
|
* @param heads_only If true, only cluster heads are printed to the output view.
|
|
* @param thread_count Number of threads to use (Not available yet) TODO
|
|
*
|
|
* @returns A value indicating the success of the operation.
|
|
* @retval 0 if the operation was successfully completed.
|
|
* @retval -1 if an error occurred.
|
|
*
|
|
* @since April 2018
|
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
*/
|
|
int obi_clean(const char* dms_name,
|
|
const char* i_view_name,
|
|
const char* sample_column_name,
|
|
const char* o_view_name,
|
|
const char* o_view_comments,
|
|
double threshold,
|
|
double max_ratio,
|
|
bool heads_only,
|
|
int thread_count);
|
|
|
|
|
|
#endif /* OBI_CLEAN_H_ */
|
|
|