obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

ngsfilter and alignpairedend: paired-end reads are now correctly

Browse Source 
reversed and labeled to be aligned correctly by alignpairedend
This commit is contained in:
Celine Mercier
2019-07-23 18:56:51 +02:00
parent 1759302829
commit d99702f56f
7 changed files with 39 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
src/kmer_similarity.h
View File

@ -78,6 +78,11 @@ void obi_free_shifted_ali(Obi_ali_p ali);
* @param column2 A pointer on the column containing the second sequence.
* @param idx2 The index of the second sequence in view2.
* @param elt_idx2 The element index of the second sequence in column2.
* @param qual_col1 A pointer on the column containing the quality associated with the first sequence (in view1).
* @param qual_col2 A pointer on the column containing the quality associated with the second sequence (in view2).
* @param reversed_column A pointer on the column containing a boolean indicating whether the sequences correspond
* to paired-end reads that might have been reversed before aligning them
* (e.g. when the ngsfilter tool is used before alignpairedend).
* @param kmer_size The kmer length to use. Must be >= 1 <= 4.
* @param kmer_pos_array The array used to store kmer positions. If NULL, allocated by the function.
* If needed, reallocated to a bigger size.
@ -109,6 +114,7 @@ Obi_ali_p kmer_similarity(Obiview_p view1,
index_t elt_idx2,
OBIDMS_column_p qual_col1,
OBIDMS_column_p qual_col2,
OBIDMS_column_p reversed_column,
uint8_t kmer_size,
int32_t** kmer_pos_array_p,
int32_t* kmer_pos_array_height_p,