obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

When aligning, it is now quickly checked whether the sequences are

Browse Source 
identical using their indexes
This commit is contained in:
Celine Mercier
2016-11-28 11:39:29 +01:00
parent 8ce6f6c80b
commit 5fb025f310
1 changed files with 19 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

18
src/obi_align.c
View File

@ -95,12 +95,26 @@ int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column,
return -1;
}
// Check if the sequences are identical in a quick way (same index in the same indexer)
if (obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, seq_column, i, 0) == obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, seq_column, j, 0))
{
if (similarity_mode && normalize)
score = 1.0;
else if (!similarity_mode)
score = 0.0;
else
score = blob1->length_decoded_value;
}
else // the sequences aren't identical
{
// kmer filter
align_filters(ktable, blob1, blob2, i, j, threshold, normalize, reference, similarity_mode, &score, &lcs_min);
align_filters(ktable, blob1, blob2, i, j, threshold, normalize, reference, similarity_mode, &score, &lcs_min, false);
// Compute alignment score
if ((threshold == 0) || (score == -1.0)) // no threshold or filter passed, and sequences not identical: 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);
}
if ((score >= 0) && (((normalize || similarity_mode) && (score >= threshold)) || ((!similarity_mode && !normalize) && (score <= threshold))))
{ // Print result