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j loop with critical (untested)

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This commit is contained in:
Celine Mercier
2019-06-04 17:14:36 +02:00
parent debf59b266
commit fd0b7a9177
1 changed files with 53 additions and 60 deletions
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113
src/obi_clean.c
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@ -183,7 +183,6 @@ int obi_clean(const char* dms_name,
char status; char status;
byte_t* alignment_result_array = NULL; byte_t* alignment_result_array = NULL;
byte_t* ali_result_array = NULL;
byte_t ali_result; byte_t ali_result;
int* complete_sample_count_array = NULL; int* complete_sample_count_array = NULL;
@ -212,7 +211,6 @@ int obi_clean(const char* dms_name,
bool stop = false; bool stop = false;
int max_threads = 1; int max_threads = 1;
int thread_id = 0;
#ifdef _OPENMP #ifdef _OPENMP
max_threads = omp_get_max_threads(); max_threads = omp_get_max_threads();
@ -377,7 +375,7 @@ int obi_clean(const char* dms_name,
// Allocate alignment result array (byte at 0 if not aligned yet, // Allocate alignment result array (byte at 0 if not aligned yet,
// 1 if sequence at index has a similarity above the threshold with the current sequence, // 1 if sequence at index has a similarity above the threshold with the current sequence,
// 2 if sequence at index has a similarity below the threshold with the current sequence) // 2 if sequence at index has a similarity below the threshold with the current sequence)
alignment_result_array = (byte_t*) calloc(thread_count*seq_count, sizeof(byte_t)); alignment_result_array = (byte_t*) calloc(seq_count, sizeof(byte_t));
if (alignment_result_array == NULL) if (alignment_result_array == NULL)
{ {
obi_set_errno(OBI_MALLOC_ERROR); obi_set_errno(OBI_MALLOC_ERROR);
@ -401,43 +399,36 @@ int obi_clean(const char* dms_name,
} }
} }
#pragma omp parallel shared(seq_count, blob_array, complete_sample_count_array, alignment_result_array, stop) \
private(ali_result_array, thread_id, i, j, blob1, blob2, s1_count, s2_count, \
sample_count_array, sample, yes, no, above_threshold, ali_result, score)
for (i=0; i< (seq_count-1); i++)
{ {
if (i%1000 == 0)
#ifdef _OPENMP
thread_id = omp_get_thread_num();
ali_result_array = alignment_result_array+thread_id;
#endif
#pragma omp for schedule(dynamic, 100)
for (i=0; i< (seq_count-1); i++)
{ {
if (i%1000 == 0) p = (i/(float)seq_count)*100;
fprintf(stderr,"\rDone : %f %% ",p);
}
// Get first sequence
blob1 = blob_array[i];
// blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(i_view, iseq_column, i, 0); // slower
if (blob1 == NULL)
{
obidebug(1, "\nError retrieving sequences to align");
return -1;
}
for (sample=0; sample < sample_count; sample++)
{
sample_count_array = complete_sample_count_array+(sample*seq_count);
// Get count for this sample
s1_count = sample_count_array[i];
//s1_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample); // slower
#pragma omp parallel shared(i, seq_count, s1_count, sample, blob_array, sample_count_array, alignment_result_array, stop) \
private(j, blob2, s2_count, yes, no, above_threshold, ali_result, score)
{ {
p = (i/(float)(seq_count/(float)thread_count))*100; #pragma omp for schedule(dynamic, 100)
fprintf(stderr,"\rDone : %f %% ",p);
}
// Get first sequence
blob1 = blob_array[i];
// blob1 = obi_get_blob_with_elt_idx_and_col_p_in_view(i_view, iseq_column, i, 0); // slower
if (blob1 == NULL)
{
obidebug(1, "\nError retrieving sequences to align");
stop = true;
}
for (sample=0; sample < sample_count; sample++)
{
sample_count_array = complete_sample_count_array+(sample*seq_count);
// Get count for this sample
s1_count = sample_count_array[i];
//s1_count = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, i, sample); // slower
for (j=i+1; j < seq_count; j++) for (j=i+1; j < seq_count; j++)
{ {
// Get second sequence // Get second sequence
@ -462,7 +453,7 @@ int obi_clean(const char* dms_name,
yes = 0; yes = 0;
no = 0; no = 0;
above_threshold = false; above_threshold = false;
ali_result = ali_result_array[j]; ali_result = alignment_result_array[j];
if (ali_result > 0) // already aligned if (ali_result > 0) // already aligned
{ {
if (ali_result == 2) if (ali_result == 2)
@ -492,42 +483,47 @@ int obi_clean(const char* dms_name,
{ {
if (yes == 0) if (yes == 0)
// Set ali result as above the threshold (value 1) // Set ali result as above the threshold (value 1)
ali_result_array[j] = 1; alignment_result_array[j] = 1;
// Might be worth having arrays to read values too for some datasets but unlikely // Might be worth having arrays to read values too for some datasets but unlikely
// label as head or internal // label as head or internal
if (s1_count >= s2_count) #pragma omp critical
{ {
if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample) == 's') // seq can become head ONLY if it's a singleton if (s1_count >= s2_count)
{ {
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h') < 0) if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample) == 's') // seq can become head ONLY if it's a singleton
stop = true;
}
// Otherwise it's an internal (do nothing)
// Label other sequence as internal no matter what
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i') < 0)
stop = true;
}
else // Same thing but with sequences switched
{
if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample) == 's') // seq can become head ONLY if it's a singleton
{ {
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h') < 0) if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'h') < 0)
stop = true; stop = true;
} }
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i') < 0) // Otherwise it's an internal (do nothing)
stop = true; // Label other sequence as internal no matter what
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'i') < 0)
stop = true;
}
else // Same thing but with sequences switched
{
if (obi_get_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample) == 's') // seq can become head ONLY if it's a singleton
{
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, j, sample, 'h') < 0)
stop = true;
}
if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, i, sample, 'i') < 0)
stop = true;
}
} }
} }
else if (no == 0) else if (no == 0)
// Set ali result as above the threshold (value 2) // Set ali result as above the threshold (value 2)
ali_result_array[j] = 2; alignment_result_array[j] = 2;
} }
} }
} }
// Reset ali result array to 0 if (stop)
memset(ali_result_array, 0, seq_count); return -1;
} }
// Reset ali result array to 0
memset(alignment_result_array, 0, seq_count);
} }
free_kmer_tables(ktable, seq_count); free_kmer_tables(ktable, seq_count);
@ -537,9 +533,6 @@ int obi_clean(const char* dms_name,
fprintf(stderr, "\n"); fprintf(stderr, "\n");
if (stop)
return -1;
if (heads_only) if (heads_only)
{ {
line_selection = malloc((o_view->infos)->line_count * sizeof(index_t)); line_selection = malloc((o_view->infos)->line_count * sizeof(index_t));