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Fixed the new alignpaired end to work after ngsfilter with the 9879847

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possible cases
This commit is contained in:
Celine Mercier
2019-02-17 18:32:35 +01:00
parent 4ddd1a1c37
commit e026e9ec83
9 changed files with 151 additions and 83 deletions
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148
src/kmer_similarity.c
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@ -64,19 +64,18 @@ void obi_free_shifted_ali(Obi_ali_p ali)
Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1, index_t elt_idx1,
Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
uint8_t kmer_size,
int32_t* kmer_pos_array, int32_t* kmer_pos_array_height_p,
int32_t* shift_array, int32_t* shift_array_height_p,
int32_t* shift_count_array, int32_t* shift_count_array_length_p,
bool build_consensus)
Obiview_p view2, OBIDMS_column_p column2, index_t idx2, index_t elt_idx2,
OBIDMS_column_p qual_col1, OBIDMS_column_p qual_col2,
uint8_t kmer_size,
int32_t* kmer_pos_array, int32_t* kmer_pos_array_height_p,
int32_t* shift_array, int32_t* shift_array_height_p,
int32_t* shift_count_array, int32_t* shift_count_array_length_p,
bool build_consensus)
{
Obi_ali_p ali = NULL;
int i, j;
bool switched_seqs;
bool left_ali;
OBIDMS_column_p qual_col1;
OBIDMS_column_p qual_col2;
double score = 0.0;
Obi_blob_p blob1 = NULL;
Obi_blob_p blob2 = NULL;
@ -106,6 +105,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
int32_t overlap_len;
int32_t consensus_len;
int32_t cons_shift;
int32_t copy_start;
int32_t copy_len;
uint8_t kmer;
byte_t nuc;
uint8_t encoding;
@ -116,6 +117,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
int32_t shift_array_height = *shift_array_height_p;
int32_t shift_count_array_length = *shift_count_array_length_p;
bool free_blob1 = false;
bool keep_seq1_start;
bool keep_seq2_start;
bool keep_seq1_end;
bool keep_seq2_end;
// Check kmer size
if ((kmer_size < 1) || (kmer_size > 4))
@ -143,7 +148,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
switched_seqs = false;
len1 = blob1->length_decoded_value;
len2 = blob2->length_decoded_value;
if (len2 > len1)
if (len2 < len1)
{
switched_seqs = true;
temp_len = len1;
@ -334,7 +339,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
// Find the most represented shift
best_shift_idx = 0;
max_common_kmers = 0;
empty_part = (shift_count_array_length-1)/2 - len1;
//empty_part = (shift_count_array_length-1)/2 - len1; //TODO wrong in some cases (len1 shorter than overlap or something like that)
empty_part = 0;
for (i=empty_part; i < (shift_count_array_length - empty_part); i++) // skipping empty parts of the array
{
if (shift_count_array[i] > max_common_kmers)
@ -345,10 +351,44 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
}
best_shift = best_shift_idx - len1;
keep_seq1_start = false;
keep_seq1_end = false;
keep_seq2_start = false;
keep_seq2_end = false;
// The 873863 cases of hell
if (best_shift > 0)
overlap_len = len2 - best_shift;
else
{
overlap_len = len2 - best_shift;
if (len1 <= overlap_len)
{
overlap_len = len1;
if (! switched_seqs)
keep_seq2_end = true;
else
keep_seq2_start = true;
}
else if (switched_seqs)
{
keep_seq2_start = true;
keep_seq1_end = true;
}
}
else if (best_shift < 0)
{
overlap_len = len1 + best_shift;
if (!switched_seqs)
{
keep_seq1_start = true;
keep_seq2_end = true;
}
}
else
{
overlap_len = len1;
if ((!switched_seqs) && (len2 > len1))
keep_seq2_end = true;
}
score = max_common_kmers + kmer_size - 1;
@ -369,7 +409,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
ali->shift = abs_shift;
ali->consensus_seq = NULL;
ali->consensus_qual = NULL;
if (((best_shift < 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
if (((best_shift <= 0) && (!switched_seqs)) || ((best_shift > 0) && switched_seqs))
{
left_ali = true;
strcpy(ali->direction, "left");
@ -383,33 +423,17 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
// Build the consensus sequence if asked
if (build_consensus)
{
// Get the quality columns
qual_col1 = obi_view_get_column(view1, QUALITY_COLUMN);
if (qual_col1 == NULL)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError when computing the kmer similarity between two sequences: can't open quality column to build the consensus sequence");
return NULL;
}
qual_col2 = obi_view_get_column(view2, QUALITY_COLUMN);
if (qual_col2 == NULL)
{
obi_set_errno(OBI_ALIGN_ERROR);
obidebug(1, "\nError when computing the kmer similarity between two sequences: can't open quality column to build the consensus sequence");
return NULL;
}
// Get the quality arrays
qual1 = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view1, qual_col1, idx1, 0, &qual1_len);
if (qual1 == NULL)
{
obidebug(1, "\nError getting the blob of the 1st sequence when computing the kmer similarity between two sequences");
obidebug(1, "\nError getting the quality of the 1st sequence when computing the kmer similarity between two sequences");
return NULL;
}
qual2 = obi_get_qual_int_with_elt_idx_and_col_p_in_view(view2, qual_col2, idx2, 0, &qual2_len);
if (qual2 == NULL)
{
obidebug(1, "\nError getting the blob of the 1st sequence when computing the kmer similarity between two sequences");
obidebug(1, "\nError getting the quality of the 2nd sequence when computing the kmer similarity between two sequences");
return NULL;
}
@ -417,10 +441,10 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
if (seq1 == NULL)
seq1 = obi_blob_to_seq(blob1);
if (left_ali)
consensus_len = len1 + len2 - overlap_len;
if (! switched_seqs)
consensus_len = len2 - best_shift;
else
consensus_len = overlap_len;
consensus_len = len1 + best_shift;
// Allocate memory for consensus sequence
consensus_seq = (char*) malloc(consensus_len + 1 * sizeof(char)); // TODO keep malloced too maybe
@ -447,30 +471,27 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
// Compute consensus-relative shift for each sequence
if (best_shift > 0)
{
shift1 = best_shift;
shift2 = 0;
shift1 = 0;
shift2 = best_shift;
}
else
{
shift1 = 0;
shift2 = -(best_shift);
shift1 = -(best_shift);
shift2 = 0;
}
// If left alignment, copy first part of first sequence
if (left_ali)
// Copy first part of first or second sequence depending on cases
if (keep_seq1_start)
{
if (switched_seqs)
{
strncpy(consensus_seq, seq2, abs_shift);
memcpy(consensus_qual, qual2, abs_shift*sizeof(uint8_t));
cons_shift = abs_shift;
}
else
{
strncpy(consensus_seq, seq1, abs_shift);
memcpy(consensus_qual, qual1, abs_shift*sizeof(uint8_t));
cons_shift = abs_shift;
}
strncpy(consensus_seq, seq1, abs_shift);
memcpy(consensus_qual, qual1, abs_shift*sizeof(uint8_t));
cons_shift = abs_shift;
}
else if (keep_seq2_start)
{
strncpy(consensus_seq, seq2, abs_shift);
memcpy(consensus_qual, qual2, abs_shift*sizeof(uint8_t));
cons_shift = abs_shift;
}
else
cons_shift = 0;
@ -485,19 +506,26 @@ Obi_ali_p kmer_similarity(Obiview_p view1, OBIDMS_column_p column1, index_t idx1
consensus_qual[pos+cons_shift] = round((qual1[pos+shift1] + qual2[pos+shift2])/2); // TODO maybe use the (p1*(1-p2/3)) formula (but parenthesis bug???)
}
// If left alignment, copy last part of first sequence
if (left_ali)
// Copy last part of first or second sequence depending on cases
if (keep_seq1_end)
{
if (switched_seqs)
strncpy(consensus_seq+cons_shift+overlap_len, seq1+overlap_len, len1 - overlap_len);
memcpy(consensus_qual+cons_shift+overlap_len, qual1+overlap_len, (len1 - overlap_len)*sizeof(uint8_t));
}
if (keep_seq2_end)
{
if (best_shift <= 0)
{
strncpy(consensus_seq+cons_shift+overlap_len, seq1+overlap_len, len1-overlap_len);
memcpy(consensus_qual+cons_shift+overlap_len, qual1+overlap_len, (len1-overlap_len)*sizeof(uint8_t));
copy_start = overlap_len;
copy_len = len2 - overlap_len;
}
else
if (best_shift > 0)
{
strncpy(consensus_seq+cons_shift+overlap_len, seq2+overlap_len, len2-overlap_len);
memcpy(consensus_qual+cons_shift+overlap_len, qual2+overlap_len, (len2-overlap_len)*sizeof(uint8_t));
copy_start = overlap_len + best_shift;
copy_len = len2 - overlap_len - best_shift;
}
strncpy(consensus_seq+cons_shift+overlap_len, seq2+copy_start, copy_len);
memcpy(consensus_qual+cons_shift+overlap_len, qual2+copy_start, copy_len*sizeof(uint8_t));
}
consensus_seq[consensus_len] = '\0';