From 5f87111fb1b58e38259e00d55f0d83e275662e73 Mon Sep 17 00:00:00 2001 From: an-altosian Date: Tue, 11 Feb 2025 00:35:32 +0000 Subject: [PATCH] write geneid2name for both indexer --- src/simpleaf_commands/indexing.rs | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/simpleaf_commands/indexing.rs b/src/simpleaf_commands/indexing.rs index 4915a37..3556db1 100644 --- a/src/simpleaf_commands/indexing.rs +++ b/src/simpleaf_commands/indexing.rs @@ -577,11 +577,20 @@ simpleaf"#, std::fs::copy(t2g_file, index_t2g_path)?; } + // copy over the gene_id_to_name.tsv file to the index + let mut gene_id_to_name_out_path: Option = None; + if let Some(gene_id_to_name_file) = gene_id_to_name { + let index_id2name_path = output_index_dir.join("gene_id_to_name.tsv"); + gene_id_to_name_out_path = Some(PathBuf::from("gene_id_to_name.tsv")); + std::fs::copy(gene_id_to_name_file, index_id2name_path)?; + } + let index_json_file = output_index_dir.join("simpleaf_index.json"); let index_json = json!({ "cmd" : index_cmd_string, "index_type" : "piscem", "t2g_file" : t2g_out_path, + "gene_id_to_name_file" : gene_id_to_name_out_path, "piscem_index_parameters" : { "k" : kmer_length, "m" : minimizer_length, @@ -671,6 +680,7 @@ simpleaf"#, // copy over the gene_id_to_name.tsv file to the index let mut gene_id_to_name_out_path: Option = None; + info!("{:?}", gene_id_to_name); if let Some(gene_id_to_name_file) = gene_id_to_name { let index_id2name_path = output_index_dir.join("gene_id_to_name.tsv"); gene_id_to_name_out_path = Some(PathBuf::from("gene_id_to_name.tsv"));