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C: kmer similarity: small improvements

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Celine Mercier
2019-07-06 16:30:32 +02:00
parent f765c6f41e
commit 86bfa96fbe
2 changed files with 6 additions and 14 deletions
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12
src/kmer_similarity.c
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@ -78,8 +78,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
Obi_ali_p ali = NULL;
int i, j;
bool switched_seqs;
bool left_ali;
double score = 0.0;
int score = 0;
Obi_blob_p blob1 = NULL;
Obi_blob_p blob2 = NULL;
Obi_blob_p temp_blob = NULL;
@ -397,8 +396,6 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
keep_seq2_end = true;
}
score = max_common_kmers + kmer_size - 1;
ali = (Obi_ali_p) malloc(sizeof(Obi_ali_t));
if (ali == NULL)
{
@ -407,6 +404,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
return NULL;
}
score = max_common_kmers + kmer_size - 1; // aka the number of nucleotides in the longest stretch of kmers perfectly matching
abs_shift = abs(best_shift);
// Save result in Obi_ali structure
@ -417,15 +415,9 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
ali->consensus_seq = NULL;
ali->consensus_qual = NULL;
if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
{
left_ali = true;
strcpy(ali->direction, "left");
}
else
{
left_ali = false;
strcpy(ali->direction, "right");
}
// Build the consensus sequence if asked
if (build_consensus)