diff --git a/python/README.rst b/python/README.rst index 3082980..a3aad61 100644 --- a/python/README.rst +++ b/python/README.rst @@ -77,7 +77,9 @@ This constructor accepts the following arguments: * **min_chain_score**: minimum chaing score -* **bw**: chaining and alignment band width +* **bw**: chaining and alignment band width (initial chaining and extension) + +* **bw_long**: chaining and alignment band width (RMQ-based rechaining and closing gaps) * **best_n**: max number of alignments to return diff --git a/python/mappy.pyx b/python/mappy.pyx index 53eea5c..e73c4f5 100644 --- a/python/mappy.pyx +++ b/python/mappy.pyx @@ -112,7 +112,7 @@ cdef class Aligner: cdef cmappy.mm_idxopt_t idx_opt cdef cmappy.mm_mapopt_t map_opt - def __cinit__(self, fn_idx_in=None, 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, extra_flags=None, seq=None, scoring=None): + def __cinit__(self, fn_idx_in=None, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=None): self._idx = NULL cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options if preset is not None: @@ -125,6 +125,7 @@ cdef class Aligner: if min_chain_score is not None: self.map_opt.min_chain_score = min_chain_score 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 bw_long is not None: self.map_opt.bw_long = bw_long 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 if extra_flags is not None: self.map_opt.flag |= extra_flags