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"
#include "upperband.h"
#include "obiblob.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?


int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, const char* seq_name,
						 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;
	const char*     id1;
	const char*     id2;
	double          score;
	OBIDMS_column_p id_column;
	Kmer_table_p    ktable;
	Obi_blob_p      blob1;
	Obi_blob_p   	blob2;
	int				lcs_min;
	index_t         seq_idx;

	k = 0;

	// If no sequence column is given and the view has the type NUC_SEQS_VIEW, the default sequence column is aligned
	if ((seq_column == NULL) && (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0))
	{
		seq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN);
		if (seq_column == NULL)
			return -1;
	}
	// Check that the given sequence column contains nucleotide sequences
	else 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 element index from element name to compute it only once
	if (seq_name != NULL)
	{
		seq_idx = obi_column_get_element_index_from_name(seq_column, seq_name);
		if (seq_idx == OBIIdx_NA)
		{
			obidebug(1, "\nError getting the sequence index in a column line when aligning");
			return -1;
		}
	}
	else
		seq_idx = 0;

	// Build kmer tables
	ktable = hash_seq_column(seq_view, seq_column, seq_idx);
	if (ktable == NULL)
	{
		obi_set_errno(OBI_ALIGN_ERROR);
		obidebug(1, "\nError building kmer tables before aligning");
		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++)
	{
		if (i%100 == 0)
			fprintf(stderr,"\rDone : %f %%       ", (i / (float) seq_count)*100);

		for (j=i+1; j < seq_count; j++)
		{
			blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, seq_column, i, seq_idx);
			blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, seq_column, j, seq_idx);

			if ((blob1 == NULL) || (blob2 == NULL))
			{
				obidebug(1, "\nError retrieving sequences to align");
				return -1;
			}

			// Check if the sequences are identical in a quick way (same index in the same indexer)
			if (obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, seq_column, i, seq_idx) == obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, seq_column, j, seq_idx))
			{
				if (similarity_mode && normalize)
					score = 1.0;
				else if (!similarity_mode)
					score = 0.0;
				else
					score = blob1->length_decoded_value;
			}

			else // the sequences aren't identical
			{
				// kmer filter
				align_filters(ktable, blob1, blob2, i, j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, false);

				// Compute alignment score
				if ((threshold == 0) || (score == -1.0))	// no threshold, or filter passed: align
					score = obiblob_sse_banded_lcs_align(blob1, blob2, threshold, normalize, reference, similarity_mode);
			}

			if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))
			{	// Print result

				// Get sequence ids
				id1 = obi_get_str_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0);	// TODO Could there be multiple IDs per line?
				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;
					}
				}

				k++;
			}
		}
	}

	free_kmer_tables(ktable, seq_count);

	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;
//}