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C: kmer alignment: fixed a bug where scores of 0 were at

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(0+kmer_length-1) (and now setting alignment direction to None if score
is 0
This commit is contained in:
Celine Mercier
2020-06-05 16:09:33 +02:00
parent 5fbbb6d304
commit 687e42ad22
1 changed files with 12 additions and 4 deletions
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8
src/kmer_similarity.c
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@ -413,7 +413,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
return NULL; return NULL;
} }
if (max_common_kmers > 0)
score = max_common_kmers + kmer_size - 1; // aka the number of nucleotides in the longest stretch of kmers perfectly matching score = max_common_kmers + kmer_size - 1; // aka the number of nucleotides in the longest stretch of kmers perfectly matching
else
score = 0;
abs_shift = abs(best_shift); abs_shift = abs(best_shift);
// Save result in Obi_ali structure // Save result in Obi_ali structure
@ -423,10 +426,15 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
ali->shift = abs_shift; ali->shift = abs_shift;
ali->consensus_seq = NULL; ali->consensus_seq = NULL;
ali->consensus_qual = NULL; ali->consensus_qual = NULL;
if (score == 0)
ali->direction[0] = '\0';
else
{
if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs)) if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
strcpy(ali->direction, "left"); strcpy(ali->direction, "left");
else else
strcpy(ali->direction, "right"); strcpy(ali->direction, "right");
}
// Build the consensus sequence if asked // Build the consensus sequence if asked
if (build_consensus) if (build_consensus)