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Refactored alignment code for minimum redundancy between the function

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that aligns 1 column and the function that aligns 2 columns
This commit is contained in:
Celine Mercier
2016-12-13 17:18:12 +01:00
parent 8afb1644e9
commit 9b24818fe2
1 changed files with 368 additions and 178 deletions
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546
src/obi_align.c
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@ -31,6 +31,360 @@
// use openMP pragmas
/**************************************************************************
*
* 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,
@ -140,114 +494,30 @@ int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char
}
// Create the output columns
// 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, (id_column->header)->indexer_name, NULL, -1, ID1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequence ids when aligning");
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);
// 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, (id_column->header)->indexer_name, NULL, -1, ID2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequence ids when aligning");
return -1;
}
id2_column = obi_view_get_column(output_view, ID2_COLUMN_NAME);
// 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;
}
idx1_column = obi_view_get_column(output_view, IDX1_COLUMN_NAME);
// 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;
}
idx2_column = obi_view_get_column(output_view, IDX2_COLUMN_NAME);
// 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;
}
lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME);
// Create the column for the alignment length if it is computed
lcs_length_column = obi_view_get_column(output_view, LCS_LENGTH_COLUMN_NAME);
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;
}
ali_length_column = obi_view_get_column(output_view, ALI_LENGTH_COLUMN_NAME);
}
// 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;
}
}
score_column = obi_view_get_column(output_view, SCORE_COLUMN_NAME);
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, (iseq_column->header)->indexer_name, NULL, -1, SEQ1_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the first column for the sequences when aligning");
return -1;
}
seq1_column = obi_view_get_column(output_view, SEQ1_COLUMN_NAME);
// 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, (iseq_column->header)->indexer_name, NULL, -1, SEQ2_COLUMN_COMMENTS, true) < 0)
{
obidebug(1, "\nError creating the second column for the sequences when aligning");
return -1;
}
seq2_column = obi_view_get_column(output_view, SEQ2_COLUMN_NAME);
}
// 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;
// }
// count1_column = obi_view_get_column(seq_view, COUNT1_COLUMN_NAME);
//
// // 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;
// }
// 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)
@ -301,100 +571,20 @@ int obi_lcs_align_one_column(OBIDMS_p dms, const char* seq_view_name, const char
if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))
{ // Print result // TODO make separate function maybe
// 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, k, 0, i) < 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, k, 0, j) < 0)
{
obidebug(1, "\nError writing idx2 in a column");
return -1;
}
// Get ids 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?
id2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, j, 0);
// Write ids in output view
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id1_column, k, 0, id1_idx) < 0)
{
obidebug(1, "\nError writing id1 in a column");
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;
}
if (obi_set_index_with_elt_idx_and_col_p_in_view(output_view, id2_column, k, 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, k, 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, k, 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, k, 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, k, 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, k, 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, k, 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, 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(output_view, score_column, k, 0, (obiint_t) score) < 0)
{
obidebug(1, "\nError writing alignment score in a column");
return -1;
}
}
k++;
}