Allow setting max_frag_len parameter in Aligner class

jdalsdurf · Jun 19, 2018 · 31fc0f2 · 31fc0f2
1 parent 3d3bcc2
commit 31fc0f2
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/python/mappy.pyx b/python/mappy.pyx
@@ -100,7 +100,7 @@ cdef class Aligner:
 	cdef cmappy.mm_idxopt_t idx_opt
 	cdef cmappy.mm_mapopt_t map_opt
 
-	def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None):
+	def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None):
 		cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
 		if preset is not None:
 			cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
@@ -113,6 +113,7 @@ cdef class Aligner:
 		if min_dp_score is not None: self.map_opt.min_dp_max = min_dp_score
 		if bw is not None: self.map_opt.bw = bw
 		if best_n is not None: self.map_opt.best_n = best_n
+		if max_frag_len is not None: self.map_opt.max_frag_len = max_frag_len
 
 		cdef cmappy.mm_idx_reader_t *r;
 		if fn_idx_out is None: