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write geneid2name for both indexer #179

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Merged
rob-p merged 1 commit into from
Feb 11, 2025
Merged

write geneid2name for both indexer #179

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10 changes: 10 additions & 0 deletions src/simpleaf_commands/indexing.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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<PathBuf> = 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,
Expand Down Expand Up @@ -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<PathBuf> = 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"));
Expand Down