Commit da445066 by Celine Mercier

C alignment filter: added a check for sequences not being equal when the

threshold requires that they are
parent 0a407436
......@@ -355,17 +355,26 @@ void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_
*score = -2.0;
if (can_be_identical && (obi_blob_compare(seq1, seq2) == 0)) // the 2 sequences are identical.
if (can_be_identical)
{
if (similarity_mode && normalize)
*score = 1.0;
else if (!similarity_mode)
*score = 0.0;
else
*score = l1;
if (obi_blob_compare(seq1, seq2) == 0)
{
if (similarity_mode && normalize)
*score = 1.0;
else if (!similarity_mode)
*score = 0.0;
else
*score = l1;
}
}
else if ((similarity_mode && normalize && (threshold == 1.0)) ||
(!similarity_mode && (threshold == 0.0)))
{ // The sequences must be identical but are not
return;
}
else if (threshold != 0)
else if (threshold != 0.0)
{
l2 = seq2->length_decoded_value;
......
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