From 2e65603bf4aaa2be95e3319a7c33b120f622fa41 Mon Sep 17 00:00:00 2001 From: "Erik Garrison (aider)" Date: Sat, 9 Nov 2024 13:42:02 -0600 Subject: [PATCH] refactor: Rename --input-mapping to --align-paf and update description --- src/interface/parse_args.hpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index 0d003779..cf61348a 100644 --- a/src/interface/parse_args.hpp +++ b/src/interface/parse_args.hpp @@ -101,7 +101,7 @@ void parse_args(int argc, args::ValueFlag max_kmer_freq(mapping_opts, "INT", "maximum allowed k-mer frequency [unlimited]", {'F', "max-kmer-freq"}); args::Group alignment_opts(options_group, "Alignment:"); - args::ValueFlag input_mapping(alignment_opts, "FILE", "input PAF/SAM file for alignment", {'i', "input-mapping"}); + args::ValueFlag input_mapping(alignment_opts, "FILE", "input PAF file for alignment", {'i', "align-paf"}); args::ValueFlag wfa_params(alignment_opts, "vals", "scoring: mismatch, gap1(o,e), gap2(o,e) [6,6,2,26,1]", {'g', "wfa-params"}); @@ -607,7 +607,7 @@ void parse_args(int argc, } if (input_mapping) { - // directly use the input mapping file + // directly use the input PAF file yeet_parameters.remapping = true; map_parameters.outFileName = args::get(input_mapping); align_parameters.mashmapPafFile = args::get(input_mapping);