Cython API: added API to use apat (pattern search) C library

python/obitools3/dms/capi/apat.pxd

@@ -0,0 +1,61 @@
+#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, uint32_t, uint8_t
+
+
+cdef extern from "libecoPCR/libapat/libstki.h" nogil:
+
+    struct Stacki :
+            int32_t    size
+            int32_t    top
+            int32_t    cursor
+            int32_t*   val
+
+    ctypedef Stacki* StackiPtr      
+
+
+cdef extern from "libecoPCR/libapat/apat.h" nogil:
+
+    extern int MAX_PATTERN
+
+    struct Seq :
+        char*      name
+        int32_t    seqlen
+        int32_t    seqsiz
+        int32_t    datsiz
+        int32_t    circular
+        uint8_t*   data
+        char*      cseq
+        StackiPtr* hitpos
+        StackiPtr* hiterr
+
+    ctypedef Seq* SeqPtr
+
+
+    struct Pattern :
+        int       patlen
+        int       maxerr
+        char*     cpat
+        int32_t*  patcode
+        uint32_t* smat
+        uint32_t  omask
+        bint      hasIndel
+        bint      ok
+
+    ctypedef Pattern* PatternPtr
+
+
+    int32_t ManberAll(Seq *pseq, Pattern *ppat, int patnum, int begin, int length)
+
+
+cdef extern from "libecoPCR/ecoPCR.h" nogil:
+
+    SeqPtr     ecoseq2apatseq(char* sequence, SeqPtr out, int32_t circular)
+    int32_t    delete_apatseq(SeqPtr pseq)
+    PatternPtr buildPattern(const char *pat, int32_t error_max)
+    PatternPtr complementPattern(PatternPtr pat)
+