From 1b68169e355cc0cee1d0a0445b77f903f7f53607 Mon Sep 17 00:00:00 2001 From: ryanbarouki Date: Mon, 15 Dec 2025 17:08:03 +0000 Subject: [PATCH 1/2] Fix python bindings to correctly pass gap penalties to C code --- python-kalign/__init__.py | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/python-kalign/__init__.py b/python-kalign/__init__.py index 56f5686..a46596f 100644 --- a/python-kalign/__init__.py +++ b/python-kalign/__init__.py @@ -200,25 +200,23 @@ def align( gap_open = -1.0 elif not isinstance(gap_open, (int, float)): raise ValueError("gap_open must be a number") - elif gap_open > 0: - raise ValueError("gap_open must be negative or zero (penalty values)") + elif gap_open < 0: + raise ValueError("gap_open must be positive or zero") if gap_extend is None: gap_extend = -1.0 elif not isinstance(gap_extend, (int, float)): raise ValueError("gap_extend must be a number") - elif gap_extend > 0: - raise ValueError("gap_extend must be negative or zero (penalty values)") + elif gap_extend < 0: + raise ValueError("gap_extend must be positive or zero") if terminal_gap_extend is None: terminal_gap_extend = -1.0 elif not isinstance(terminal_gap_extend, (int, float)): raise ValueError("terminal_gap_extend must be a number") - elif terminal_gap_extend > 0: - raise ValueError( - "terminal_gap_extend must be negative or zero (penalty values)" - ) - + elif terminal_gap_extend < 0: + raise ValueError("terminal_gap_extend must be positive or zero") + # Handle thread count if n_threads is None: n_threads = get_num_threads() From 11d17717cb94d096c9269bc86609863f2e192cdc Mon Sep 17 00:00:00 2001 From: ryanbarouki Date: Mon, 15 Dec 2025 22:11:13 +0000 Subject: [PATCH 2/2] fix typo --- lib/src/aln_param.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/src/aln_param.c b/lib/src/aln_param.c index af447b6..5a7183d 100644 --- a/lib/src/aln_param.c +++ b/lib/src/aln_param.c @@ -82,7 +82,7 @@ int aln_param_init(struct aln_param **aln_param,int biotype , int n_threads, int ap->gpe = gpe; } - if(gpe >= 0.0){ + if(tgpe >= 0.0){ ap->tgpe = tgpe; } /* LOG_MSG("%f %f %f", ap->gpo, ap->gpe, ap->tgpe); */