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obitools3/src/obi_align.c

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/****************************************************************************
* LCS sequence alignment functions *
****************************************************************************/
/**
* @file obi_align.c
* @author Celine Mercier (celine.mercier@metabarcoding.org)
* @date May 4th 2016
* @brief Functions handling LCS sequence alignments.
*/
//#define OMP_SUPPORT // TODO
#ifdef OMP_SUPPORT
#include <omp.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <stdbool.h>
#include "obi_align.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?)
/**************************************************************************
*
* D E C L A R A T I O N O F T H E P R I V A T E F U N C T I O N S
*
**************************************************************************/
/**
* @brief Internal function creating the columns where the alignment results are written.
*
* @param output_view A pointer on the writable view where the columns should be created.
* @param id1_indexer_name The name of the indexer where the id of the 1st sequence aligned is indexed.
* @param id2_indexer_name The name of the indexer where the id of the 2nd sequence aligned is indexed.
* @param seq1_indexer_name The name of the indexer where the 1st sequence aligned is indexed (needed only if print_seq is True).
* @param seq2_indexer_name The name of the indexer where the 2nd sequence aligned is indexed (needed only if print_seq is True).
* @param print_seq A boolean indicating whether the aligned sequences should be copied in the output view.
* @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view.
* @param normalize Whether the score should be normalized with the reference sequence length.
* @param reference The reference length. 0: The alignement length; 1: The longest sequence's length; 2: The shortest sequence's length.
* @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since December 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int create_alignment_output_columns(Obiview_p output_view,
const char* id1_indexer_name,
const char* id2_indexer_name,
const char* seq1_indexer_name,
const char* seq2_indexer_name,
bool print_seq, bool print_count,
bool normalize, int reference, bool similarity_mode);
/**
* @brief Internal function printing the result of one alignment to the output view.
*
* @param output_view A pointer on the writable view where the columns should be created.
* @param line The line in the output view where the result should be written.
* @param idx1_column A pointer on the column where the index referring to the line of the first sequence aligned in the input view should be written.
* @param idx2_column A pointer on the column where the index referring to the line of the second sequence aligned in the input view should be written.
* @param idx1 The index referring to the line of the first sequence aligned in the input view.
* @param idx2 The index referring to the line of the second sequence aligned in the input view.
* @param id1_column A pointer on the column where the identifier of the first sequence aligned should be written.
* @param id2_column A pointer on the column where the identifier of the second sequence aligned should be written.
* @param id1_idx The index of the identifier of the first sequence aligned.
* @param id2_idx The index of the identifier of the second sequence aligned.
* @param print_seq A boolean indicating whether the aligned sequences should be copied in the output view.
* @param seq1_column A pointer on the column where the first sequence aligned should be written.
* @param seq2_column A pointer on the column where the second sequence aligned should be written.
* @param seq1_idx The index of the sequence of the first sequence aligned.
* @param seq2_idx The index of the sequence of the second sequence aligned.
* @param print_count A boolean indicating whether the aligned sequence counts should be copied in the output view. // Count columns not implement yet
* @param count1_column A pointer on the column where the count of the first sequence aligned should be written.
* @param count2_column A pointer on the column where the count of the second sequence aligned should be written.
* @param count1 The count of the first sequence aligned.
* @param count2 The count of the second sequence aligned.
* @param ali_length_column A pointer on the column where the alignment length should be written.
* @param ali_length The alignment length.
* @param lcs_length_column A pointer on the column where the LCS length should be written.
* @param lcs_length The LCS length.
* @param score_column A pointer on the column where the score should be written.
* @param score The alignment score.
* @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length.
* @param normalize Whether the score should be normalized with the reference sequence length.
* @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
*
* @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred.
*
* @since December 2016
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int print_alignment_result(Obiview_p output_view,
index_t line,
OBIDMS_column_p idx1_column,
OBIDMS_column_p idx2_column,
index_t idx1,
index_t idx2,
OBIDMS_column_p id1_column,
OBIDMS_column_p id2_column,
index_t id1_idx,
index_t id2_idx,
bool print_seq,
OBIDMS_column_p seq1_column,
OBIDMS_column_p seq2_column,
index_t seq1_idx,
index_t seq2_idx,
// bool print_count,
// OBIDMS_column_p count1_column,
// OBIDMS_column_p count2_column,
// int count1,
// int count2,
OBIDMS_column_p ali_length_column,
int ali_length,
OBIDMS_column_p lcs_length_column,
int lcs_length,
OBIDMS_column_p score_column,
double score,
int reference,
bool normalize,
bool similarity_mode);
/************************************************************************
*
* D E F I N I T I O N O F T H E P R I V A T E F U N C T I O N S
*
************************************************************************/
static int create_alignment_output_columns(Obiview_p output_view,
const char* id1_indexer_name,
const char* id2_indexer_name,
const char* seq1_indexer_name,
const char* seq2_indexer_name,
bool print_seq, bool print_count,
bool normalize, int reference, bool similarity_mode)
{
// Create the column for the ids of the 1st sequence aligned
if (obi_view_add_column(output_view, ID1_COLUMN_NAME, -1, ID1_COLUMN_NAME, OBI_STR, 0, 1, NULL, id1_indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence ids when aligning");
return -1;
}
// Create the column for the ids of the 2nd sequence aligned
if (obi_view_add_column(output_view, ID2_COLUMN_NAME, -1, ID2_COLUMN_NAME, OBI_STR, 0, 1, NULL, id2_indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1;
}
// Create the column for the index (in the input view) of the first sequences aligned
if (obi_view_add_column(output_view, IDX1_COLUMN_NAME, -1, IDX1_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence indices when aligning");
return -1;
}
// Create the column for the index (in the input view) of the second sequences aligned
if (obi_view_add_column(output_view, IDX2_COLUMN_NAME, -1, IDX2_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, IDX2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence indices when aligning");
return -1;
}
// Create the column for the LCS length
if (obi_view_add_column(output_view, LCS_LENGTH_COLUMN_NAME, -1, LCS_LENGTH_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, LCS_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the LCS length when aligning");
return -1;
}
// Create the column for the alignment length if it is computed
if ((reference == ALILEN) && (normalize || !similarity_mode))
{
if (obi_view_add_column(output_view, ALI_LENGTH_COLUMN_NAME, -1, ALI_LENGTH_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, ALI_LENGTH_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the column for the alignment length when aligning");
return -1;
}
}
// Create the column for the alignment score
if (normalize)
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, SCORE_COLUMN_NAME, OBI_FLOAT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
}
}
else
{
if (obi_view_add_column(output_view, SCORE_COLUMN_NAME, -1, SCORE_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, SCORE_COLUMN_NAME, true) < 0)
{
obidebug(1, "\nError creating the column for the score when aligning");
return -1;
}
}
if (print_seq)
{
// Create the column for the first sequences aligned
if (obi_view_add_column(output_view, SEQ1_COLUMN_NAME, -1, SEQ1_COLUMN_NAME, OBI_SEQ, 0, 1, NULL, seq1_indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1;
}
// Create the column for the second sequences aligned
if (obi_view_add_column(output_view, SEQ2_COLUMN_NAME, -1, SEQ2_COLUMN_NAME, OBI_SEQ, 0, 1, NULL, seq2_indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1;
}
}
// if (print_count) // TODO count columns not implemented yet
// {
// // Create the column for the count of the first sequences aligned
// if (obi_view_add_column(output_view, COUNT1_COLUMN_NAME, -1, COUNT1_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT1_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the first column for the sequence counts when aligning");
// return -1;
// }
//
// // Create the column for the count of the second sequences aligned
// if (obi_view_add_column(output_view, COUNT2_COLUMN_NAME, -1, COUNT2_COLUMN_NAME, OBI_INT, 0, 1, NULL, NULL, NULL, -1, COUNT2_COLUMN_COMMENTS, true) < 0)
// {
// obidebug(1, "\nError creating the second column for the sequence counts when aligning");
// return -1;
// }
// }
return 0;
}
static int print_alignment_result(Obiview_p output_view,
index_t line,
OBIDMS_column_p idx1_column,
OBIDMS_column_p idx2_column,
index_t idx1,
index_t idx2,
OBIDMS_column_p id1_column,
OBIDMS_column_p id2_column,
index_t id1_idx,
index_t id2_idx,
bool print_seq,
OBIDMS_column_p seq1_column,
OBIDMS_column_p seq2_column,
index_t seq1_idx,
index_t seq2_idx,
// bool print_count,
// OBIDMS_column_p count1_column,
// OBIDMS_column_p count2_column,
// int count1,
// int count2,
OBIDMS_column_p ali_length_column,
int ali_length,
OBIDMS_column_p lcs_length_column,
int lcs_length,
OBIDMS_column_p score_column,
double score,
int reference,
bool normalize,
bool similarity_mode)
{
// Write line indices of the input view in the output view (to easily refer to the input sequences from the output view)
if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, idx1_column, line, 0, idx1) < 0)
{
obidebug(1, "\nError writing idx1 in a column");
return -1;
}
if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, idx2_column, line, 0, idx2) < 0)
{
obidebug(1, "\nError writing idx2 in a column");
return -1;
}
// Write ids in output view
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id1_column, line, 0, id1_idx) < 0)
{
obidebug(1, "\nError writing id1 in a column");
return -1;
}
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id2_column, line, 0, id2_idx) < 0)
{
obidebug(1, "\nError writing id2 in a column");
return -1;
}
// Write the sequences if needed
if (print_seq)
{
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, seq1_column, line, 0, seq1_idx) < 0)
{
obidebug(1, "\nError writing seq1 in a column");
return -1;
}
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, seq2_column, line, 0, seq2_idx) < 0)
{
obidebug(1, "\nError writing seq2 in a column");
return -1;
}
}
// // Write the counts if needed // TODO count columns not implemented yet
// if (print_count)
// {
// if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, count1_column, line, 0, count1) < 0)
// {
// obidebug(1, "\nError writing count1 in a column");
// return -1;
// }
//
// if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, count2_column, line, 0, count2) < 0)
// {
// obidebug(1, "\nError writing count2 in a column");
// return -1;
// }
// }
// Write the alignment length if it was computed
if ((reference == ALILEN) && (normalize || !similarity_mode))
{
if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, ali_length_column, line, 0, ali_length) < 0)
{
obidebug(1, "\nError writing alignment length in a column");
return -1;
}
}
// Write the LCS length
if (obi_set_int_with_elt_idx_and_col_p_in_view(output_view, lcs_length_column, line, 0, lcs_length) < 0)
{
obidebug(1, "\nError writing LCS length in a column");
return -1;
}
// Write score
if (normalize)
{
if (obi_set_float_with_elt_idx_and_col_p_in_view(output_view, score_column, line, 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(output_view, score_column, line, 0, (obiint_t) score) < 0)
{
obidebug(1, "\nError writing alignment score in a column");
return -1;
}
}
return 0;
}
/**********************************************************************
*
* D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S
*
**********************************************************************/
int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char* seq_column_name, const char* seq_elt_name,
const char* id_column_name,
const char* output_view_name, const char* output_view_comments,
bool print_seq, bool print_count,
double threshold, bool normalize, int reference, bool similarity_mode,
int thread_count)
{
index_t i, j, k;
index_t seq_count;
index_t id1_idx, id2_idx;
index_t seq1_idx, seq2_idx;
double score;
int lcs_length;
int ali_length;
Kmer_table_p ktable;
Obi_blob_p blob1;
Obi_blob_p blob2;
int lcs_min;
index_t seq_elt_idx;
Obiview_p seq_view = NULL;
Obiview_p output_view = NULL;
OBIDMS_column_p iseq_column = NULL;
OBIDMS_column_p id_column = NULL;
OBIDMS_column_p id1_column = NULL;
OBIDMS_column_p id2_column = NULL;
OBIDMS_column_p seq1_column = NULL;
OBIDMS_column_p seq2_column = NULL;
//OBIDMS_column_p count1_column = NULL;
//OBIDMS_column_p count2_column = NULL;
OBIDMS_column_p idx1_column = NULL;
OBIDMS_column_p idx2_column = NULL;
OBIDMS_column_p lcs_length_column = NULL;
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
k = 0;
// Open input view
seq_view = obi_open_view(dms, seq_view_name);
if (seq_view == NULL)
{
obidebug(1, "\nError opening the input view to align");
return -1;
}
// Open the sequence column to align
// If a column name wasn't given, open default sequence column
if (strcmp(seq_column_name, "") == 0)
{
if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
iseq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no column given to align");
return -1;
}
}
else
iseq_column = obi_view_get_column(seq_view, seq_column_name);
if (iseq_column == NULL)
{
obidebug(1, "\nError getting the column to align");
return -1;
}
// Check column type
if ((iseq_column->header)->returned_data_type != OBI_SEQ)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: column given to align is not an OBI_SEQ column");
return -1;
}
// Get element index of the sequence to align in each line to compute it only once
if ((strcmp(seq_elt_name, "") != 0) && (seq_elt_name != NULL))
{
seq_elt_idx = obi_column_get_element_index_from_name(iseq_column, seq_elt_name);
if (seq_elt_idx == OBIIdx_NA)
{
obidebug(1, "\nError getting the sequence index in a column line when aligning");
return -1;
}
}
else
seq_elt_idx = 0;
// Open the ID column, containing the identifiers of the sequences to align
// If a column name wasn't given, open default ID column
if (strcmp(id_column_name, "") == 0)
{
if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
id_column = obi_view_get_column(seq_view, ID_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no ID column given");
return -1;
}
}
else
id_column = obi_view_get_column(seq_view, id_column_name);
if (id_column == NULL)
{
obidebug(1, "\nError getting the ID column");
return -1;
}
// Create the output view
output_view = obi_new_view(dms, output_view_name, NULL, NULL, output_view_comments);
if (output_view == NULL)
{
obidebug(1, "\nError creating the output view when aligning");
return -1;
}
// Create the output columns
if (create_alignment_output_columns(output_view,
(id_column->header)->indexer_name, (id_column->header)->indexer_name,
(iseq_column->header)->indexer_name, (iseq_column->header)->indexer_name,
print_seq, print_count, normalize, reference, similarity_mode) < 0)
return -1;
id1_column = obi_view_get_column(output_view, ID1_COLUMN_NAME);
id2_column = obi_view_get_column(output_view, ID2_COLUMN_NAME);
idx1_column = obi_view_get_column(output_view, IDX1_COLUMN_NAME);
idx2_column = obi_view_get_column(output_view, IDX2_COLUMN_NAME);
lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME);
if ((reference == ALILEN) && (normalize || !similarity_mode))
ali_length_column = obi_view_get_column(output_view, ALI_LENGTH_COLUMN_NAME);
score_column = obi_view_get_column(output_view, SCORE_COLUMN_NAME);
if (print_seq)
{
seq1_column = obi_view_get_column(output_view, SEQ1_COLUMN_NAME);
seq2_column = obi_view_get_column(output_view, SEQ2_COLUMN_NAME);
}
// if (print_count) // TODO count columns not implemented yet
// {
// count1_column = obi_view_get_column(seq_view, COUNT1_COLUMN_NAME);
// count2_column = obi_view_get_column(seq_view, COUNT2_COLUMN_NAME);
// }
// Build kmer tables
ktable = hash_seq_column(seq_view, iseq_column, seq_elt_idx);
if (ktable == NULL)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError building kmer tables before aligning");
return -1;
}
seq_count = (seq_view->infos)->line_count;
#ifdef OMP_SUPPORT
omp_set_num_threads(thread_count);
#pragma omp parallel for
#endif
for (i=0; i < (seq_count - 1); i++)
{
if (i%100 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) seq_count)*100);
// Get first id idx
id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0); // TODO Could there be multiple IDs per line?
// Get first sequence and its index
seq1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, i, seq_elt_idx);
blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, i, seq_elt_idx);
if (blob1 == NULL)
{
obidebug(1, "\nError retrieving sequences to align");
return -1;
}
for (j=i+1; j < seq_count; j++)
{
// Get second sequence and its index
seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_idx);
blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_idx);
if (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, iseq_column, i, seq_elt_idx) == obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, iseq_column, j, seq_elt_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, &lcs_length, &ali_length);
}
if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))
{ // Print result
// Get second id idx
id2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, j, 0);
if (print_alignment_result(output_view, k,
idx1_column, idx2_column, i, j,
id1_column, id2_column, id1_idx, id2_idx,
print_seq, seq1_column, seq2_column, seq1_idx, seq2_idx,
//print_count, count1_column, count2_column, count1, count2,
ali_length_column, ali_length,
lcs_length_column, lcs_length,
score_column, score,
reference, normalize, similarity_mode) < 0)
return -1;
k++;
}
}
}
// Close views
if (obi_save_and_close_view(seq_view) < 0)
{
obidebug(1, "\nError closing the input view after aligning");
return -1;
}
if (obi_save_and_close_view(output_view) < 0)
{
obidebug(1, "\nError closing the output view after aligning");
return -1;
}
free_kmer_tables(ktable, seq_count);
return 0;
}
int obi_lcs_align_two_columns(OBIDMS_p dms,
const char* seq1_view_name,
const char* seq2_view_name,
const char* seq1_column_name,
const char* seq2_column_name,
const char* seq1_elt_name,
const char* seq2_elt_name,
const char* id1_column_name,
const char* id2_column_name,
const char* output_view_name, const char* output_view_comments,
bool print_seq, bool print_count,
double threshold, bool normalize, int reference, bool similarity_mode)
{
index_t i, j, k;
index_t seq1_count;
index_t seq2_count;
index_t id1_idx, id2_idx;
index_t seq1_idx, seq2_idx;
double score;
int lcs_length;
int ali_length;
Kmer_table_p ktable;
Obi_blob_p blob1;
Obi_blob_p blob2;
int lcs_min;
index_t seq1_elt_idx;
index_t seq2_elt_idx;
bool same_indexer;
Obiview_p seq1_view = NULL;
Obiview_p seq2_view = NULL;
Obiview_p output_view = NULL;
OBIDMS_column_p i_seq1_column = NULL;
OBIDMS_column_p i_seq2_column = NULL;
OBIDMS_column_p i_id1_column = NULL;
OBIDMS_column_p i_id2_column = NULL;
OBIDMS_column_p id1_column = NULL;
OBIDMS_column_p id2_column = NULL;
OBIDMS_column_p seq1_column = NULL;
OBIDMS_column_p seq2_column = NULL;
//OBIDMS_column_p count1_column = NULL;
//OBIDMS_column_p count2_column = NULL;
OBIDMS_column_p idx1_column = NULL;
OBIDMS_column_p idx2_column = NULL;
OBIDMS_column_p lcs_length_column = NULL;
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
k = 0;
// Open the first input view
seq1_view = obi_open_view(dms, seq1_view_name);
if (seq1_view == NULL)
{
obidebug(1, "\nError opening the first input view to align");
return -1;
}
// Open the second input view. Same as 1st if ""
if (strcmp(seq2_view_name, "") == 0)
seq2_view = seq1_view;
else
{
seq2_view = obi_open_view(dms, seq2_view_name);
if (seq2_view == NULL)
{
obidebug(1, "\nError opening the second input view to align");
return -1;
}
}
// Open the first sequence column to align
// If a column name wasn't given, open default sequence column
if (strcmp(seq1_column_name, "") == 0)
{
if (strcmp((seq1_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
i_seq1_column = obi_view_get_column(seq1_view, NUC_SEQUENCE_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no first column given to align");
return -1;
}
}
else
i_seq1_column = obi_view_get_column(seq1_view, seq1_column_name);
if (i_seq1_column == NULL)
{
obidebug(1, "\nError getting the first column to align");
return -1;
}
// Check column type
if ((i_seq1_column->header)->returned_data_type != OBI_SEQ)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: first column given to align is not an OBI_SEQ column");
return -1;
}
// Open the second sequence column to align
// If a column name wasn't given, open default sequence column
if (strcmp(seq2_column_name, "") == 0)
{
if (strcmp((seq2_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
i_seq2_column = obi_view_get_column(seq2_view, NUC_SEQUENCE_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no second column given to align");
return -1;
}
}
else
i_seq2_column = obi_view_get_column(seq2_view, seq2_column_name);
if (i_seq2_column == NULL)
{
obidebug(1, "\nError getting the second column to align");
return -1;
}
// Check that the sequence columns are not both the default NUC_SEQ column of the same view
if (i_seq1_column == i_seq2_column)
{
obidebug(1, "\nError: trying to align a column with itself (default NUC_SEQ column of the same view)");
return -1;
}
// Check column type
if ((i_seq2_column->header)->returned_data_type != OBI_SEQ)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: second column given to align is not an OBI_SEQ column");
return -1;
}
// Get element index of the sequence to align in each line of the first column to compute it only once
if ((strcmp(seq1_elt_name, "") != 0) && (seq1_elt_name != NULL))
{
seq1_elt_idx = obi_column_get_element_index_from_name(i_seq1_column, seq1_elt_name);
if (seq1_elt_idx == OBIIdx_NA)
{
obidebug(1, "\nError getting the sequence index in a column line when aligning");
return -1;
}
}
else
seq1_elt_idx = 0;
// Get element index of the sequence to align in each line of the second column to compute it only once
if ((strcmp(seq2_elt_name, "") != 0) && (seq2_elt_name != NULL))
{
seq2_elt_idx = obi_column_get_element_index_from_name(i_seq2_column, seq2_elt_name);
if (seq2_elt_idx == OBIIdx_NA)
{
obidebug(1, "\nError getting the sequence index in a column line when aligning");
return -1;
}
}
else
seq2_elt_idx = 0;
// Open the first ID column, containing the identifiers of the first sequence to align
// If a column name wasn't given, open default ID column
if (strcmp(id1_column_name, "") == 0)
{
if (strcmp((seq1_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
i_id1_column = obi_view_get_column(seq1_view, ID_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no first ID column given");
return -1;
}
}
else
i_id1_column = obi_view_get_column(seq1_view, id1_column_name);
if (i_id1_column == NULL)
{
obidebug(1, "\nError getting the first ID column");
return -1;
}
// Open the second ID column, containing the identifiers of the second sequence to align
// If a column name wasn't given, open default ID column
if (strcmp(id2_column_name, "") == 0)
{
if (strcmp((seq2_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
i_id2_column = obi_view_get_column(seq2_view, ID_COLUMN);
else
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError: no second ID column given");
return -1;
}
}
else
i_id2_column = obi_view_get_column(seq2_view, id2_column_name);
if (i_id2_column == NULL)
{
obidebug(1, "\nError getting the second ID column");
return -1;
}
// Create the output view
output_view = obi_new_view(dms, output_view_name, NULL, NULL, output_view_comments);
if (output_view == NULL)
{
obidebug(1, "\nError creating the output view when aligning");
return -1;
}
// Create the output columns
if (create_alignment_output_columns(output_view,
(i_id1_column->header)->indexer_name, (i_id2_column->header)->indexer_name,
(i_seq1_column->header)->indexer_name, (i_seq2_column->header)->indexer_name,
print_seq, print_count, normalize, reference, similarity_mode) < 0)
return -1;
id1_column = obi_view_get_column(output_view, ID1_COLUMN_NAME);
id2_column = obi_view_get_column(output_view, ID2_COLUMN_NAME);
idx1_column = obi_view_get_column(output_view, IDX1_COLUMN_NAME);
idx2_column = obi_view_get_column(output_view, IDX2_COLUMN_NAME);
lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME);
if ((reference == ALILEN) && (normalize || !similarity_mode))
ali_length_column = obi_view_get_column(output_view, ALI_LENGTH_COLUMN_NAME);
score_column = obi_view_get_column(output_view, SCORE_COLUMN_NAME);
if (print_seq)
{
seq1_column = obi_view_get_column(output_view, SEQ1_COLUMN_NAME);
seq2_column = obi_view_get_column(output_view, SEQ2_COLUMN_NAME);
}
// if (print_count) // TODO count columns not implemented yet
// {
// count1_column = obi_view_get_column(seq_view, COUNT1_COLUMN_NAME);
// count2_column = obi_view_get_column(seq_view, COUNT2_COLUMN_NAME);
// }
// Check if the sequence columns share the same indexer (allows for quick checking of sequence equality)
if (strcmp((i_seq1_column->header)->indexer_name, (i_seq2_column->header)->indexer_name) == 0)
same_indexer = true;
else
same_indexer = false;
// Build kmer tables
ktable = hash_two_seq_columns(seq1_view, i_seq1_column, seq1_elt_idx, seq2_view, i_seq2_column, seq2_elt_idx);
if (ktable == NULL)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError building kmer tables before aligning");
return -1;
}
// TODO check this
if (!similarity_mode && normalize && (threshold > 0))
threshold = 1.0 - threshold;
seq1_count = (seq1_view->infos)->line_count;
seq2_count = (seq2_view->infos)->line_count;
for (i=0; i < seq1_count; i++)
{
if (i%100 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) seq1_count)*100);
// Get id index of first sequence
id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq1_view, i_id1_column, i, 0); // TODO Could there be multiple IDs per line?
// Get first sequence and its index
seq1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq1_view, i_seq1_column, i, seq1_elt_idx);
blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq1_view, i_seq1_column, i, seq1_elt_idx);
if (blob1 == NULL)
{
obidebug(1, "\nError retrieving sequences to align");
return -1;
}
for (j=0; j < seq2_count; j++)
{
// Get second sequence and its index
seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);
blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);
if (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 (same_indexer && (seq1_idx == seq2_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 (offset for the index of the kmer table of the 2nd sequence because the kmer tables of the 2 sequence columns are concatenated in one)
align_filters(ktable, blob1, blob2, i, seq1_count+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, &lcs_length, &ali_length);
// TODO check this
// if (print && !lcsmode && normalize)
// score = 1.0 - score;
}
if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))
{ // Print result
// Get second id idx
id2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_id2_column, j, 0);
if (print_alignment_result(output_view, k,
idx1_column, idx2_column, i, j,
id1_column, id2_column, id1_idx, id2_idx,
print_seq, seq1_column, seq2_column, seq1_idx, seq2_idx,
//print_count, count1_column, count2_column, count1, count2,
ali_length_column, ali_length,
lcs_length_column, lcs_length,
score_column, score,
reference, normalize, similarity_mode) < 0)
return -1;
k++;
}
}
}
// Close views
if (seq2_view != seq1_view)
{
if (obi_save_and_close_view(seq2_view) < 0)
{
obidebug(1, "\nError closing the second input view after aligning");
return -1;
}
}
if (obi_save_and_close_view(seq1_view) < 0)
{
obidebug(1, "\nError closing the first input view after aligning");
return -1;
}
if (obi_save_and_close_view(output_view) < 0)
{
obidebug(1, "\nError closing the output view after aligning");
return -1;
}
free_kmer_tables(ktable, seq1_count + seq2_count);
return 0;
}
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