New command: obi ecopcr

python/obitools3/dms/capi/obiecopcr.pxd

@@ -0,0 +1,28 @@
+#cython: language_level=3
+
+from obitools3.dms.capi.obidms       cimport OBIDMS_p
+from libc.stdint  cimport int32_t
+
+
+cdef extern from "obi_ecopcr.h" nogil:
+
+    int obi_ecopcr(const char* input_dms_name,
+                   const char* i_view_name,
+                   const char* taxonomy_name,
+                   const char* output_dms_name,
+                   const char* o_view_name,
+                   const char* o_view_comments,
+                   const char* primer1,
+                   const char* primer2,
+                   int error_max,
+                   int min_len,
+                   int max_len,
+                   int32_t* restrict_to_taxids,
+                   int32_t* ignore_taxids,
+                   int circular,
+                   double salt_concentration,
+                   int salt_correction_method,
+                   int keep_nucleotides,
+                   bint kingdom_mode)
+
+    

python/obitools3/dms/dms.cfiles

@@ -9,6 +9,15 @@
 ../../../src/murmurhash2.c
 ../../../src/obi_align.c
 ../../../src/obi_clean.c
+../../../src/obi_ecopcr.c
+../../../src/libecoPCR/libthermo/nnparams.c
+../../../src/libecoPCR/libapat/apat_parse.c
+../../../src/libecoPCR/libapat/apat_search.c
+../../../src/libecoPCR/libapat/libstki.c
+../../../src/libecoPCR/ecoapat.c
+../../../src/libecoPCR/ecodna.c
+../../../src/libecoPCR/ecoError.c
+../../../src/libecoPCR/ecoMalloc.c
 ../../../src/obiavl.c
 ../../../src/obiblob_indexer.c
 ../../../src/obiblob.c