Alignpairedend: added alignment using shifting with best kmer similarity

(low level layer in C and Cython API)

python/obitools3/dms/capi/kmer_similarity.pxd

@@ -0,0 +1,42 @@
+#cython: language_level=3
+
+from obitools3.dms.capi.obiview cimport Obiview_p
+from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
+from obitools3.dms.capi.obitypes cimport index_t
+
+from libc.stdint  cimport int32_t, uint8_t
+
+
+cdef extern from "kmer_similarity.h" nogil:
+
+    struct Obi_ali_t :
+        double   score
+        int      consensus_length
+        int      overlap_length
+        char*    consensus_seq
+        uint8_t* consensus_qual
+        int      shift
+        char*    direction
+
+    ctypedef Obi_ali_t* Obi_ali_p
+
+    
+    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_height_p,
+                              bint build_consensus)

python/obitools3/dms/dms.cfiles

@@ -6,6 +6,7 @@
 ../../../src/dna_seq_indexer.c
 ../../../src/encode.c
 ../../../src/hashtable.c
+../../../src/kmer_similarity.c
 ../../../src/linked_list.c
 ../../../src/murmurhash2.c
 ../../../src/obi_lcs.c