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Committing minor comments before merging branch with master

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This commit is contained in:
Celine Mercier
2017-07-06 10:56:39 +02:00
parent 717ee46f08
commit f03928c679
5 changed files with 14 additions and 3 deletions
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2
doc/conf.py
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@ -33,7 +33,7 @@ extensions = [
'sphinx.ext.autodoc', 'sphinx.ext.autodoc',
'sphinx.ext.todo', 'sphinx.ext.todo',
'sphinx.ext.coverage', 'sphinx.ext.coverage',
'sphinx.ext.pngmath', 'sphinx.ext.imgmath',
'sphinx.ext.ifconfig', 'sphinx.ext.ifconfig',
'sphinx.ext.viewcode', 'sphinx.ext.viewcode',
'breathe', 'breathe',

2
src/linked_list.h
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@ -90,7 +90,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx);
* @param idx The index of the node to delete. * @param idx The index of the node to delete.
* *
* @returns A pointer on the new head node of the linked list. * @returns A pointer on the new head node of the linked list.
* @retval NULL if an error occurred. * @retval NULL if an error occurred. // TODO or if list is now empty...
* *
* @since February 2017 * @since February 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)

9
src/obi_align.c
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@ -883,6 +883,10 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
return -1; return -1;
} }
// TODO check this
if (!similarity_mode && normalize && (threshold > 0))
threshold = 1.0 - threshold;
seq1_count = (seq1_view->infos)->line_count; seq1_count = (seq1_view->infos)->line_count;
seq2_count = (seq2_view->infos)->line_count; seq2_count = (seq2_view->infos)->line_count;
@ -932,6 +936,11 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
// Compute alignment score // Compute alignment score
if ((threshold == 0) || (score == -1.0)) // no threshold, or filter passed: align 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); 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)))) if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))

2
src/obiview.c
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@ -1188,6 +1188,8 @@ static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* colum
} }
} }
// TODO add line_max
if (((*line_nb_p)+1) > (view->infos)->line_count) if (((*line_nb_p)+1) > (view->infos)->line_count)
{ {
if (update_lines(view, ((*line_nb_p)+1)) < 0) if (update_lines(view, ((*line_nb_p)+1)) < 0)

2
src/upperband.c
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@ -230,7 +230,7 @@ int thresholdLCS4(int32_t reflen, int32_t lcs)
} }
Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx) Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col, index_t seq_idx) // TODO move in another file (obi_align.c)
{ {
size_t i; size_t i;
size_t seq_count; size_t seq_count;