From 31fc0f218ad68afff7d21fc0df3cd8b87b799317 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 4 Jun 2018 15:42:14 +0200 Subject: [PATCH] Allow setting max_frag_len parameter in Aligner class --- python/mappy.pyx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/mappy.pyx b/python/mappy.pyx index 5ab92c4..cddba1d 100644 --- 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: