From c162ee345210d18e5eb6f3a129da857184e952be Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Fri, 6 Oct 2023 10:54:57 -0400 Subject: [PATCH] clean rgfa names in fasta output --- src/subcommand/paths_main.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp index 4ebf6ec26a5..58b13910f64 100644 --- a/src/subcommand/paths_main.cpp +++ b/src/subcommand/paths_main.cpp @@ -519,7 +519,7 @@ int main_paths(int argc, char** argv) { // Write as a Path in a VG chunk_to_emitter(path, *graph_emitter); } else if (extract_as_fasta) { - write_fasta_sequence(name, path_sequence(*graph, path), cout); + write_fasta_sequence(RGFACover::revert_rgfa_path_name(name, false), path_sequence(*graph, path), cout); } if (list_lengths) { cout << path.name() << "\t" << path_to_length(path) << endl; @@ -831,7 +831,8 @@ int main_paths(int argc, char** argv) { } else if (extract_as_vg) { chunk_to_emitter(path, *graph_emitter); } else if (extract_as_fasta) { - write_fasta_sequence(graph->get_path_name(path_handle), path_sequence(*graph, path), cout); + write_fasta_sequence(RGFACover::revert_rgfa_path_name(graph->get_path_name(path_handle), false), + path_sequence(*graph, path), cout); } } });