obi clean: first version

src/obi_clean.h

@@ -0,0 +1,85 @@
+/*************************************************************************************************
+ * 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 2017
+ * @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_ */
+