From a6e85856ab05d08f5e445ce8764d74ca43be148d Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 9 Jun 2023 15:05:11 +0200
Subject: [PATCH] refactor: move db::pbs into its own file, remove "db copy"
 (#115)

---
 src/db/mod.rs | 6 +-----
 src/db/pbs.rs | 3 +++
 src/main.rs   | 4 ----
 3 files changed, 4 insertions(+), 9 deletions(-)
 create mode 100644 src/db/pbs.rs

diff --git a/src/db/mod.rs b/src/db/mod.rs
index 05a84408..a187883c 100644
--- a/src/db/mod.rs
+++ b/src/db/mod.rs
@@ -4,9 +4,5 @@ pub mod compile;
 pub mod conf;
 pub mod genes;
 pub mod mk_inhouse;
+pub mod pbs;
 pub mod to_bin;
-
-/// Data structures for (de-)serialization as generated by `prost-build`.
-pub mod pbs {
-    include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs"));
-}
diff --git a/src/db/pbs.rs b/src/db/pbs.rs
new file mode 100644
index 00000000..07668675
--- /dev/null
+++ b/src/db/pbs.rs
@@ -0,0 +1,3 @@
+//! Data structures for (de-)serialization as generated by `prost-build`.
+
+include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs"));
diff --git a/src/main.rs b/src/main.rs
index 00c1343a..3239c0b2 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -54,7 +54,6 @@ struct Db {
 #[allow(clippy::large_enum_variant)]
 #[derive(Debug, Subcommand)]
 enum DbCommands {
-    Copy(annonars::db_utils::cli::copy::Args),
     Compile(db::compile::Args),
     MkInhouse(db::mk_inhouse::Args),
     Genes(Genes),
@@ -167,9 +166,6 @@ fn main() -> Result<(), anyhow::Error> {
                         db::genes::query::run(&cli.common, args)?;
                     }
                 },
-                DbCommands::Copy(args) => {
-                    annonars::db_utils::cli::copy::run(&annonars_common, args)?
-                }
             },
             Commands::Pheno(pheno) => match &pheno.command {
                 PhenoCommands::Prepare(args) => pheno::prepare::run(&cli.common, args)?,