docs: junction_annotation to junction-annotation

Author: a-frantz

src/derive/command/junction_annotation.rs

@@ -1,4 +1,4 @@
-//! Functionality relating to the `ngs derive junction_annotation` subcommand itself.
+//! Functionality relating to the `ngs derive junction-annotation` subcommand itself.
 
 use std::collections::HashMap;
 use std::path::PathBuf;
@@ -17,7 +17,7 @@ use crate::utils::formats;
 use crate::utils::formats::bam::ParsedBAMFile;
 use crate::utils::formats::utils::IndexCheck;
 
-/// Clap arguments for the `ngs derive junction_annotation` subcommand.
+/// Clap arguments for the `ngs derive junction-annotation` subcommand.
 #[derive(Args)]
 pub struct JunctionAnnotationArgs {
     /// Source BAM.
@@ -60,9 +60,9 @@ pub struct JunctionAnnotationArgs {
     count_duplicates: bool,
 }
 
-/// Main function for the `ngs derive junction_annotation` subcommand.
+/// Main function for the `ngs derive junction-annotation` subcommand.
 pub fn derive(args: JunctionAnnotationArgs) -> anyhow::Result<()> {
-    info!("Starting derive junction_annotation subcommand.");
+    info!("Starting derive junction-annotation subcommand.");
 
     let mut exons = compute::ExonSets {
         starts: HashMap::new(),

src/derive/junction_annotation.rs

@@ -1,4 +1,4 @@
-//! Supporting functionality for the `ngs derive junction_annotation` subcommand.
+//! Supporting functionality for the `ngs derive junction-annotation` subcommand.
 
 pub mod compute;
 pub mod results;

src/derive/junction_annotation/compute.rs

@@ -261,7 +261,7 @@ fn tally_junctions_and_support(junction_map: &results::JunctionsMap) -> (usize,
     (junctions, support)
 }
 
-/// Main function to summarize the results of the junction_annotation subcommand.
+/// Main function to summarize the results of the junction-annotation subcommand.
 pub fn summarize(
     results: &mut results::JunctionAnnotationResults,
     params: &JunctionAnnotationParameters,

src/derive/junction_annotation/results.rs

@@ -1,4 +1,4 @@
-//! Results related to the `ngs derive junction_annotation` subcommand.
+//! Results related to the `ngs derive junction-annotation` subcommand.
 
 use noodles::core::Position;
 use serde::ser::SerializeStruct;
@@ -82,7 +82,7 @@ impl Serialize for JunctionAnnotations {
 }
 
 /// General record metrics that are tallied as a part of the
-/// junction_annotation subcommand.
+/// junction-annotation subcommand.
 #[derive(Clone, Default, Serialize)]
 pub struct RecordMetrics {
     /// The number of records that have been fully processed.
@@ -106,7 +106,7 @@ pub struct RecordMetrics {
     pub missing_mapq: usize,
 }
 
-/// Summary statistics for the junction_annotation subcommand.
+/// Summary statistics for the junction-annotation subcommand.
 #[derive(Clone, Default, Serialize)]
 pub struct SummaryResults {
     /// The total number of junctions observed in the file.
@@ -208,6 +208,6 @@ pub struct JunctionAnnotationResults {
     /// General record metrics.
     pub records: RecordMetrics,
 
-    /// Summary statistics for the junction_annotation subcommand.
+    /// Summary statistics for the junction-annotation subcommand.
     pub summary: SummaryResults,
 }