From a04908b9dac2045826ca695d6f5f13fdecfafd31 Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Sat, 1 Jun 2024 22:25:17 -0500 Subject: [PATCH] fix easy scoring parameters that work well across diverse alignment problems --- src/interface/parse_args.hpp | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index 37e50069..604ebca4 100644 --- a/src/interface/parse_args.hpp +++ b/src/interface/parse_args.hpp @@ -108,14 +108,14 @@ void parse_args(int argc, {'O', "invert-filtering"}); args::ValueFlag wflambda_segment_length(alignment_opts, "N", "wflambda segment length: size (in bp) of segment mapped in hierarchical WFA problem [default: 256]", {'W', "wflamda-segment"}); args::ValueFlag wfa_score_params(alignment_opts, "mismatch,gap1,ext1", - "score parameters for the wfa alignment (affine); match score is fixed at 0 [default: 6,8,1]", + "score parameters for the wfa alignment (affine); match score is fixed at 0 [default: 2,3,1]", {"wfa-params"}); args::ValueFlag wfa_patching_score_params(alignment_opts, "mismatch,gap1,ext1,gap2,ext2", - "score parameters for the wfa patching alignment (convex); match score is fixed at 0 [default: 5,8,2,49,1]", + "score parameters for the wfa patching alignment (convex); match score is fixed at 0 [default: 3,4,2,24,1]", {"wfa-patching-params"}); //wflign parameters args::ValueFlag wflign_score_params(alignment_opts, "mismatch,gap1,ext1", - "score parameters for the wflign alignment (affine); match score is fixed at 0 [default: 4,6,1]", + "score parameters for the wflign alignment (affine); match score is fixed at 0 [default: 2,3,1]", {"wflign-params"}); args::ValueFlag wflign_max_mash_dist(alignment_opts, "N", "maximum mash distance to perform the alignment in a wflambda segment [default: adaptive with respect to the estimated identity]", {'b', "max-mash-dist"}); args::ValueFlag wflign_min_wavefront_length(alignment_opts, "N", "min wavefront length for heuristic WFlign [default: 1024]", {'j', "wflign-min-wf-len"}); @@ -282,9 +282,9 @@ void parse_args(int argc, align_parameters.wfa_gap_opening_score = params[1]; align_parameters.wfa_gap_extension_score = params[2]; } else { - align_parameters.wfa_mismatch_score = -1; - align_parameters.wfa_gap_opening_score = -1; - align_parameters.wfa_gap_extension_score = -1; + align_parameters.wfa_mismatch_score = 2; + align_parameters.wfa_gap_opening_score = 3; + align_parameters.wfa_gap_extension_score = 1; } if (!args::get(wfa_patching_score_params).empty()) { @@ -305,11 +305,11 @@ void parse_args(int argc, align_parameters.wfa_patching_gap_opening_score2 = params[3]; align_parameters.wfa_patching_gap_extension_score2 = params[4]; } else { - align_parameters.wfa_patching_mismatch_score = -1; - align_parameters.wfa_patching_gap_opening_score1 = -1; - align_parameters.wfa_patching_gap_extension_score1 = -1; - align_parameters.wfa_patching_gap_opening_score2 = -1; - align_parameters.wfa_patching_gap_extension_score2 = -1; + align_parameters.wfa_patching_mismatch_score = 3; + align_parameters.wfa_patching_gap_opening_score1 = 4; + align_parameters.wfa_patching_gap_extension_score1 = 2; + align_parameters.wfa_patching_gap_opening_score2 = 24; + align_parameters.wfa_patching_gap_extension_score2 = 1; } if (!args::get(wflign_score_params).empty()) { @@ -328,9 +328,9 @@ void parse_args(int argc, align_parameters.wflign_gap_opening_score = params[1]; align_parameters.wflign_gap_extension_score = params[2]; } else { - align_parameters.wflign_mismatch_score = -1; - align_parameters.wflign_gap_opening_score = -1; - align_parameters.wflign_gap_extension_score = -1; + align_parameters.wflign_mismatch_score = 2; + align_parameters.wflign_gap_opening_score = 3; + align_parameters.wflign_gap_extension_score = 1; } if (wflign_max_mash_dist) {