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

Added the kmer filter to LCS alignments, and now obiblobs containing

Browse Source 
encoded sequences are directly put in int16_t arrays for the alignment
This commit is contained in:
Celine Mercier
2016-11-18 16:29:28 +01:00
parent 08e67a090f
commit 70c49e214a
17 changed files with 653 additions and 94 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
src/sse_banded_LCS_alignment.h
View File

@ -12,6 +12,9 @@
#include <stdint.h>
#include <stdbool.h>
#include "obiblob.h"
#define ALILEN (0) // TODO enum
#define MAXLEN (1)
#define MINLEN (2)
@ -19,5 +22,6 @@
// TODO doc
int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool lcsmode);
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode);
double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double threshold, bool normalize, int reference, bool similarity_mode);
#endif