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Added an argument to specify whether the two sequences can be identical

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when applying filters before aligning
This commit is contained in:
Celine Mercier
2016-11-28 11:38:02 +01:00
parent 3e53f9418b
commit 8ce6f6c80b
2 changed files with 6 additions and 3 deletions
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7
src/upperband.c
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@ -307,8 +307,11 @@ bool is_possible(Kmer_table_p ktable, index_t idx1, index_t idx2, int l1, int l2
} }
void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin) void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2,
double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin,
bool can_be_identical)
{ // score takes value -2 if filters are not passed, -1 if filters are passed and >= 0 with max score if the 2 sequences are identical. { // score takes value -2 if filters are not passed, -1 if filters are passed and >= 0 with max score if the 2 sequences are identical.
// TODO move to obi_align.c
int l1; int l1;
int l2; int l2;
@ -316,7 +319,7 @@ void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_
*score = -2.0; *score = -2.0;
if (obi_blob_compare(seq1, seq2) == 0) // the 2 sequences are identical. TODO add bool arg indicating whether that's a possibility? if (can_be_identical && (obi_blob_compare(seq1, seq2) == 0)) // the 2 sequences are identical.
{ {
if (similarity_mode && normalize) if (similarity_mode && normalize)
*score = 1.0; *score = 1.0;

2
src/upperband.h
View File

@ -19,7 +19,7 @@ typedef struct {
Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col); Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col);
void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin); void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin, bool can_be_identical);
void free_kmer_tables(Kmer_table_p ktable, size_t count); void free_kmer_tables(Kmer_table_p ktable, size_t count);
#endif #endif