110 lines
2.9 KiB
C
110 lines
2.9 KiB
C
/****************************************************************************
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* Sequence alignment functions *
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****************************************************************************/
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/**
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* @file obi_align.c
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* @author Celine Mercier
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* @date May 4th 2016
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* @brief Functions handling sequence alignments.
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*/
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#include <stdlib.h>
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#include <stdio.h>
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#include <stdbool.h>
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#include "obidebug.h"
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#include "obierrno.h"
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#include "obitypes.h"
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#include "obiview.h"
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#include "sse_banded_LCS_alignment.h"
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#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
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// TODO
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// use openMP pragmas : garder scores en memoire et ecrire a la fin? (normalement c bon avec index)
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// tout ecrire en stdint?
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// check NUC_SEQS and score type (int or float if normalize)
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// what's with multiple sequence/line columns?
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// make function that put blobs in int16
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int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
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{
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index_t i, j, k;
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index_t seq_count;
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char* seq1;
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char* seq2;
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double score;
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k = 0;
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if ((seq_column->header)->returned_data_type != OBI_SEQ)
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{
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obi_set_errno(OBI_ALIGN_ERROR);
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obidebug(1, "\nTrying to align a column of a different type than OBI_SEQ");
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return -1;
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}
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if ((normalize && ((score_column->header)->returned_data_type != OBI_FLOAT)) ||
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(!normalize && ((score_column->header)->returned_data_type != OBI_INT)))
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{
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obi_set_errno(OBI_ALIGN_ERROR);
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obidebug(1, "\nTrying to store alignment scores in a column of an inappropriate type");
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return -1;
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}
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seq_count = (seq_column->header)->lines_used;
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for (i=0; i < (seq_count - 1); i++)
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{
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for (j=i+1; j < seq_count; j++)
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{
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//fprintf(stderr, "\ni=%lld, j=%lld, k=%lld", i, j, k);
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seq1 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, i, 0);
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seq2 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, j, 0);
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if ((seq1 == NULL) || (seq2 == NULL))
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{
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obidebug(1, "\nError retrieving sequences to align");
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return -1;
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}
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// TODO filter
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score = generic_sse_banded_lcs_align(seq1, seq2, threshold, normalize, reference, similarity_mode);
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if (normalize)
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{
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if (obi_column_set_obifloat_with_elt_idx_in_view(score_view, score_column, k, 0, (obifloat_t) score) < 0)
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{
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obidebug(1, "\nError writing alignment score in a column");
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return -1;
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}
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}
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else
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{
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if (obi_column_set_obiint_with_elt_idx_in_view(score_view, score_column, k, 0, (obiint_t) score) < 0)
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{
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obidebug(1, "\nError writing alignment score in a column");
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return -1;
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}
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}
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k++;
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}
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}
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return 0;
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}
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int obi_align_two_columns(OBIDMS_column_p seq_column_1, OBIDMS_column_p seq_column_2, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
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{
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// TODO
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return 0;
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}
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