From 7d8bbb74a870ac98b7c09b590848c11699f6f0a4 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Fri, 15 Nov 2024 21:56:36 +0800
Subject: [PATCH] Add `sc_ambi` and `max_chain_skip` parameters to `mappy.pyx`
 (#1240)

* add sc_ambi option to cython interface

* add max_gaplen param

* set max_chain_skip to arg instead of forcing 255
---
 python/mappy.pyx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/python/mappy.pyx b/python/mappy.pyx
index 4a5adf8..474f833 100644
--- a/python/mappy.pyx
+++ b/python/mappy.pyx
@@ -113,7 +113,7 @@ 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, bw_long=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, sc_ambi=None, max_chain_skip=None):
 		self._idx = NULL
 		cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
 		if preset is not None:
@@ -138,6 +138,8 @@ cdef class Aligner:
 				self.map_opt.q2, self.map_opt.e2 = scoring[4], scoring[5]
 				if len(scoring) >= 7:
 					self.map_opt.sc_ambi = scoring[6]
+		if sc_ambi is not None: self.map_opt.sc_ambi = sc_ambi
+		if max_chain_skip is not None: self.map_opt.max_chain_skip = max_chain_skip
 
 		cdef cmappy.mm_idx_reader_t *r;