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build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest

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This commit is contained in:
Celine Mercier
2020-04-28 15:56:06 +02:00
parent 1b346b54f9
commit 974528b2e6
2 changed files with 40 additions and 1 deletions
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2
python/obitools3/version.py
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@ -1,5 +1,5 @@
major = 3
minor = 0
serial= '0-beta14e'
serial= '0-beta15'
version ="%d.%02d.%s" % (major,minor,serial)

39
src/build_reference_db.c
View File

@ -477,6 +477,8 @@ int build_reference_db(const char* dms_name,
// Read alignment score
score = obi_get_float_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_score_column, i, 0);
//fprintf(stderr, "\n\ntaxid_lca=%d, score=%f, idx1=%d, idx2=%d", taxid_lca, score, idx1, idx2);
///////////////// Compute for first sequence \\\\\\\\\\\\\\\\\\\\\\\ (TODO function)
// Read arrays
@ -493,9 +495,11 @@ int build_reference_db(const char* dms_name,
// return -1;
// }
//fprintf(stderr, "\n1st sequence");
// If empty, add values
if (taxid_array_length == 0)
{
//fprintf(stderr, "\nEmpty, add value");
if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0)
{
obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@ -509,6 +513,8 @@ int build_reference_db(const char* dms_name,
}
else
{
//fprintf(stderr, "\nNot empty");
j = 0;
modified = false;
while (j < taxid_array_length)
@ -522,6 +528,9 @@ int build_reference_db(const char* dms_name,
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
//fprintf(stderr, "\nSame LCA, replace %d and %f with %d and %f", lca_taxid_array_writable[j],
// score_array_writable[j], taxid_lca, score);
// Better score for the same LCA, replace this LCA/score pair
lca_taxid_array_writable[j] = taxid_lca;
score_array_writable[j] = score;
@ -548,6 +557,8 @@ int build_reference_db(const char* dms_name,
{
if (score > score_array[j])
{
//fprintf(stderr, "\nInsert new");
memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
@ -592,10 +603,15 @@ int build_reference_db(const char* dms_name,
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
//fprintf(stderr, "\nAppend at the end");
// Append LCA
lca_taxid_array_writable[taxid_array_writable_length] = taxid_lca;
score_array_writable[score_array_writable_length] = score;
taxid_array_writable_length++;
score_array_writable_length++;
// Remove the previous (children) LCAs from the array if their score is equal or lower
while ((j>0) && (score_array_writable[j-1] <= score))
{
@ -616,6 +632,13 @@ int build_reference_db(const char* dms_name,
// Write new arrays
if (modified)
{
// fprintf(stderr, "\n\nnew array:");
// for (k=0;k<taxid_array_writable_length;k++)
// {
// lca = obi_taxo_get_taxon_with_taxid(tax, lca_taxid_array_writable[k]);
// fprintf(stderr, "\nLCA=%d, %s, score=%f", lca_taxid_array_writable[k], lca->name, score_array_writable[k]);
// }
if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx1, lca_taxid_array_writable, (uint8_t) (obi_sizeof(OBI_INT) * 8), taxid_array_writable_length) < 0)
{
obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@ -645,9 +668,13 @@ int build_reference_db(const char* dms_name,
// return -1;
// }
//fprintf(stderr, "\n2nd sequence");
// If empty, add values
if (taxid_array_length == 0)
{
//fprintf(stderr, "\nEmpty, add value");
if (obi_set_array_with_col_p_in_view(o_view, final_lca_taxid_a_column, idx2, &taxid_lca, (uint8_t) (obi_sizeof(OBI_INT) * 8), 1) < 0)
{
obidebug(1, "\nError setting a LCA taxid array in a column when building a reference database");
@ -661,6 +688,8 @@ int build_reference_db(const char* dms_name,
}
else
{
//fprintf(stderr, "\nNot empty");
j = 0;
modified = false;
while (j < taxid_array_length)
@ -674,6 +703,9 @@ int build_reference_db(const char* dms_name,
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
//fprintf(stderr, "\nSame LCA, replace %d and %f with %d and %f", lca_taxid_array_writable[j],
// score_array_writable[j], taxid_lca, score);
// Better score for the same LCA, replace this LCA/score pair
lca_taxid_array_writable[j] = taxid_lca;
score_array_writable[j] = score;
@ -700,6 +732,8 @@ int build_reference_db(const char* dms_name,
{
if (score > score_array[j])
{
//fprintf(stderr, "\nInsert new");
memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
@ -740,6 +774,8 @@ int build_reference_db(const char* dms_name,
if (j == taxid_array_length) // same or parent LCA not found, need to be appended at the end
{
//fprintf(stderr, "\nAppend at the end");
memcpy(lca_taxid_array_writable, lca_taxid_array, taxid_array_length*sizeof(obiint_t));
memcpy(score_array_writable, score_array, score_array_length*sizeof(obifloat_t));
modified = true;
@ -748,6 +784,9 @@ int build_reference_db(const char* dms_name,
lca_taxid_array_writable[taxid_array_writable_length] = taxid_lca;
score_array_writable[score_array_writable_length] = score;
taxid_array_writable_length++;
score_array_writable_length++;
// Remove the previous (children) LCAs from the array if their score is equal or lower
while ((j>0) && (score_array_writable[j-1] <= score))
{