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

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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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8
src/kmer_similarity.h
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@ -33,9 +33,9 @@ typedef struct Obi_ali {
*/
int overlap_length; /**< Length of the overlap between the aligned sequences.
*/
char* consensus_seq; /**< Consensus sequence built with the computed overlap.
char* consensus_seq; /**< Consensus sequence built as to reconstruct a pairedend read.
*/
uint8_t* consensus_qual; /**< Consensus quality built with the computed overlap.
uint8_t* consensus_qual; /**< Consensus quality built as to reconstruct a pairedend read.
*/
int shift; /**< Shift chosen to align the sequences (for shifted alignment).
*/
@ -91,7 +91,7 @@ void obi_free_shifted_ali(Obi_ali_p ali);
* If needed, reallocated to a bigger size.
* @param shift_count_array_height_p A pointer on an integer corresponding to the size (number of elements)
* allocated for shift_count_array. Updated by the function as needed.
* @param build_consensus A boolean indicating whether the function should build the consensus sequence and quality. // TODO option to build consensus without quality?
* @param build_consensus A boolean indicating whether the function should build the consensus sequence and quality as to reconstruct a pairedend read. // TODO option to build consensus without quality?
*
* @returns A pointer on an Obi_ali_p structure containing the results.
* @retval NULL if an error occurred.
@ -107,6 +107,8 @@ Obi_ali_p kmer_similarity(Obiview_p view1,
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,