obitools3/src/obi_align.c

/****************************************************************************
 * Sequence alignment functions				                                *
 ****************************************************************************/

/**
 * @file obi_align.c
 * @author Celine Mercier
 * @date May 4th 2016
 * @brief Functions handling sequence alignments.
 */


#include <stdlib.h>
#include <stdio.h>
#include <stdbool.h>

#include "obidebug.h"
#include "obierrno.h"
#include "obitypes.h"
#include "obiview.h"
#include "sse_banded_LCS_alignment.h"


#define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)


// TODO
// use openMP pragmas
// option pour ecrire en stdint?
// check NUC_SEQS view type? and score type (int or float if normalize)
// what's with multiple sequences/line columns?
// make function that put blobs in int16


int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column,
						 Obiview_p score_view, OBIDMS_column_p id1_column, OBIDMS_column_p id2_column, OBIDMS_column_p score_column,
						 double threshold, bool normalize, int reference, bool similarity_mode)
{
	index_t i, j, k;
	index_t seq_count;
	char* seq1;
	char* seq2;
	const char* id1;
	const char* id2;
	double score;
	OBIDMS_column_p id_column;

	k = 0;

	if ((seq_column->header)->returned_data_type != OBI_SEQ)
	{
		obi_set_errno(OBI_ALIGN_ERROR);
		obidebug(1, "\nTrying to align a column of a different type than OBI_SEQ");
		return -1;
	}

	if ((normalize && ((score_column->header)->returned_data_type != OBI_FLOAT)) ||
			(!normalize && ((score_column->header)->returned_data_type != OBI_INT)))
	{
		obi_set_errno(OBI_ALIGN_ERROR);
		obidebug(1, "\nTrying to store alignment scores in a column of an inappropriate type");
		return -1;
	}

	// Get the ID column pointer
	id_column = obi_view_get_column(seq_view, ID_COLUMN);

	seq_count = (seq_column->header)->lines_used;

	for (i=0; i < (seq_count - 1); i++)
	{
		for (j=i+1; j < seq_count; j++)
		{
			//fprintf(stderr, "\ni=%lld, j=%lld, k=%lld", i, j, k);

			seq1 = obi_get_seq_with_elt_idx_and_col_p_in_view(seq_view, seq_column, i, 0);
			seq2 = obi_get_seq_with_elt_idx_and_col_p_in_view(seq_view, seq_column, j, 0);

			if ((seq1 == NULL) || (seq2 == NULL))
			{
				obidebug(1, "\nError retrieving sequences to align");
				return -1;
			}

			// TODO kmer filter

			// Compute alignment score
			score = generic_sse_banded_lcs_align(seq1, seq2, threshold, normalize, reference, similarity_mode);

			// Get sequence ids
			id1 = obi_get_str_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0);
			id2 = obi_get_str_with_elt_idx_and_col_p_in_view(seq_view, id_column, j, 0);

			// Write sequence ids in output view
			if (obi_set_str_with_elt_idx_and_col_p_in_view(score_view, id1_column, k, 0, id1) < 0)
			{
				obidebug(1, "\nError writing id1 in a column");
				return -1;
			}

			if (obi_set_str_with_elt_idx_and_col_p_in_view(score_view, id2_column, k, 0, id2) < 0)
			{
				obidebug(1, "\nError writing id2 in a column");
				return -1;
			}

			// Write score in output view
			if (normalize)
			{
				if (obi_set_float_with_elt_idx_and_col_p_in_view(score_view, score_column, k, 0, (obifloat_t) score) < 0)
				{
					obidebug(1, "\nError writing alignment score in a column");
					return -1;
				}
			}
			else
			{
				if (obi_set_int_with_elt_idx_and_col_p_in_view(score_view, score_column, k, 0, (obiint_t) score) < 0)
				{
					obidebug(1, "\nError writing alignment score in a column");
					return -1;
				}
			}

			free(seq1);
			free(seq2);

			k++;
		}
	}

	return 0;
}


// TODO discuss if 2 input views or 2 columns or both possible
//int obi_align_two_columns(Obiview_p seq_view, OBIDMS_column_p seq_column_1, OBIDMS_column_p seq_column_2,	// TODO it's implied both seq columns are in the same view but maybe it shouldn't
//						  Obiview_p score_view, OBIDMS_column_p score_column,
//						  double threshold, bool normalize, int reference, bool similarity_mode)
//{
//	index_t i, j, k;
//	index_t seq_count_1;
//	index_t seq_count_2;
//	char* seq1;
//	char* seq2;
//	double score;
//
//	k = 0;
//
//	if (((seq_column_1->header)->returned_data_type != OBI_SEQ) || ((seq_column_2->header)->returned_data_type != OBI_SEQ))
//	{
//		obi_set_errno(OBI_ALIGN_ERROR);
//		obidebug(1, "\nTrying to align a column of a different type than OBI_SEQ");
//		return -1;
//	}
//
//	if ((normalize && ((score_column->header)->returned_data_type != OBI_FLOAT)) ||
//			(!normalize && ((score_column->header)->returned_data_type != OBI_INT)))
//	{
//		obi_set_errno(OBI_ALIGN_ERROR);
//		obidebug(1, "\nTrying to store alignment scores in a column of an inappropriate type");
//		return -1;
//	}
//
//	seq_count_1 = (seq_column_1->header)->lines_used;
//	seq_count_2 = (seq_column_2->header)->lines_used;
//
//	for (i=0; i < (seq_count_1 - 1); i++)
//	{
//		for (j=0; j < seq_count_2; j++)
//		{
//			//fprintf(stderr, "\ni=%lld, j=%lld, k=%lld", i, j, k);
//
//			seq1 = obi_get_seq_with_elt_idx_and_col_p_in_view(seq_view, seq_column_1, i, 0);
//			seq2 = obi_get_seq_with_elt_idx_and_col_p_in_view(seq_view, seq_column_2, j, 0);
//
//			if ((seq1 == NULL) || (seq2 == NULL))
//			{
//				obidebug(1, "\nError retrieving sequences to align");
//				return -1;
//			}
//
//			// TODO kmer filter
//
//			score = generic_sse_banded_lcs_align(seq1, seq2, threshold, normalize, reference, similarity_mode);
//
//			if (normalize)
//			{
//				if (obi_set_float_with_elt_idx_and_col_p_in_view(score_view, score_column, k, 0, (obifloat_t) score) < 0)
//				{
//					obidebug(1, "\nError writing alignment score in a column");
//					return -1;
//				}
//			}
//			else
//			{
//				if (obi_set_int_with_elt_idx_and_col_p_in_view(score_view, score_column, k, 0, (obiint_t) score) < 0)
//				{
//					obidebug(1, "\nError writing alignment score in a column");
//					return -1;
//				}
//			}
//
//			free(seq1);
//			free(seq2);
//
//			k++;
//		}
//	}
//
//	return 0;
//}