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C obi_lcs: fixed checking for identical sequences when aligning 2

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columns
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Celine Mercier
2018-12-09 19:16:44 +01:00
parent 579f56bb54
commit 005aaeec06
1 changed files with 6 additions and 6 deletions
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12
src/obi_lcs.c
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@ -70,7 +70,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
/** /**
* @brief Internal function printing the result of one alignment to the output view. * @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 output_view A pointer on the writable view where the result should be written.
* @param line The line in the output view where the result should be written. * @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 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 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.
@ -85,7 +85,7 @@ static int create_alignment_output_columns(Obiview_p output_view,
* @param seq2_column A pointer on the column where the second 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 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 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 print_count A boolean indicating whether the aligned sequence counts should be copied in the output view.
* @param count1_column A pointer on the column where the count of the first sequence aligned should be written. * @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 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 count1 The count of the first sequence aligned.
@ -448,7 +448,7 @@ int obi_lcs_align_one_column(const char* dms_name,
// Open the sequence column to align // Open the sequence column to align
// If a column name wasn't given, open default sequence column // If a column name wasn't given, open default sequence column
if (strcmp(seq_column_name, "") == 0) if (strcmp(seq_column_name, "") == 0) // TODO check for NULL
{ {
if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0) if (strcmp((seq_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
iseq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN); iseq_column = obi_view_get_column(seq_view, NUC_SEQUENCE_COLUMN);
@ -997,13 +997,13 @@ int obi_lcs_align_two_columns(const char* dms_name,
score = blob1->length_decoded_value; score = blob1->length_decoded_value;
} }
else // the sequences aren't identical else // the sequences aren't identical or we don't know
{ {
// kmer filter (offset for the index of the kmer table of the 2nd sequence because the kmer tables of the 2 sequence columns are concatenated in one) // kmer filter (offset for the index of the kmer table of the 2nd sequence because the kmer tables of the 2 sequence columns are concatenated in one)
align_filters(ktable, blob1, blob2, i, seq1_count+j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, false); align_filters(ktable, blob1, blob2, i, seq1_count+j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, !same_indexer);
// Compute alignment score // Compute alignment score
if ((threshold == 0) || (score == -1.0)) // no threshold, or filter passed: align if ((score < 0) && ((threshold == 0) || (score == -1.0))) // (sequences are not identical), and (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 // TODO check this