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Fixed 2 bugs when checking qualities matching sequences predicate: now

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closing and reopening indexers so that they are mapped properly, and
fixed memory leak when reading sequences
This commit is contained in:
Celine Mercier
2018-11-19 11:05:53 +01:00
parent b0da36cb48
commit 31053591b5
1 changed files with 25 additions and 1 deletions
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26
src/obiview.c
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@ -1418,6 +1418,30 @@ static char* view_check_qual_match_seqs(Obiview_p view)
return NULL; return NULL;
} }
// Close and reopen indexers to remap them properly, because in writable mode they are mostly unmapped
if (obi_close_indexer(qual_column->indexer) < 0)
{
obidebug(1, "\nError closing the quality indexer when checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
return NULL;
}
qual_column->indexer = obi_open_avl_group(view->dms, (qual_column->header)->indexer_name);
if (qual_column->indexer == NULL)
{
obidebug(1, "\nError reopening the quality indexer when checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
return NULL;
}
if (obi_close_indexer(seq_column->indexer) < 0)
{
obidebug(1, "\nError closing the sequence indexer when checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
return NULL;
}
seq_column->indexer = obi_open_avl_group(view->dms, (seq_column->header)->indexer_name);
if (seq_column->indexer == NULL)
{
obidebug(1, "\nError reopening the sequence indexer when checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
return NULL;
}
nb_elements_per_line = (qual_column->header)->nb_elements_per_line; nb_elements_per_line = (qual_column->header)->nb_elements_per_line;
// Check that the quality and the sequence columns have the same number of elements per line // Check that the quality and the sequence columns have the same number of elements per line
if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line) if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line)
@ -1432,7 +1456,6 @@ static char* view_check_qual_match_seqs(Obiview_p view)
for (k=0; k < nb_elements_per_line; k++) for (k=0; k < nb_elements_per_line; k++)
{ {
qual = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view, qual_column, j, k, &qual_len); qual = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view, qual_column, j, k, &qual_len);
seq = obi_get_seq_with_elt_idx_and_col_p_in_view(view, seq_column, j, k); seq = obi_get_seq_with_elt_idx_and_col_p_in_view(view, seq_column, j, k);
if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA)) if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA))
{ {
@ -1449,6 +1472,7 @@ static char* view_check_qual_match_seqs(Obiview_p view)
obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name); obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
return NULL; return NULL;
} }
free(seq);
} }
} }