style: prettify imports

src/derive/command/encoding.rs

@@ -1,15 +1,12 @@
 //! Functionality relating to the `ngs derive encoding` subcommand itself.
 
+use anyhow::{Context, Ok};
+use clap::Args;
+use noodles::bam;
+use num_format::{Locale, ToFormattedString};
 use std::collections::HashSet;
 use std::io::BufReader;
 use std::path::PathBuf;
-
-use anyhow::Context;
-use anyhow::Ok;
-use clap::Args;
-use noodles::bam;
-use num_format::Locale;
-use num_format::ToFormattedString;
 use tracing::info;
 
 use crate::derive::encoding::compute;

src/derive/command/endedness.rs

@@ -1,16 +1,12 @@
 //! Functionality relating to the `ngs derive endedness` subcommand itself.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
-use std::path::PathBuf;
-use std::sync::Arc;
-
 use anyhow::Context;
 use clap::Args;
-use num_format::Locale;
-use num_format::ToFormattedString;
-use tracing::info;
-use tracing::trace;
+use num_format::{Locale, ToFormattedString};
+use std::collections::{HashMap, HashSet};
+use std::path::PathBuf;
+use std::sync::Arc;
+use tracing::{info, trace};
 
 use crate::derive::endedness::compute;
 use crate::derive::endedness::compute::OrderingFlagsCounts;

src/derive/command/instrument.rs

@@ -2,8 +2,7 @@
 
 use anyhow::bail;
 use clap::Args;
-use num_format::Locale;
-use num_format::ToFormattedString;
+use num_format::{Locale, ToFormattedString};
 use std::collections::HashSet;
 use std::path::PathBuf;
 use tracing::info;

src/derive/command/junction_annotation.rs

@@ -1,15 +1,12 @@
 //! Functionality relating to the `ngs derive junction-annotation` subcommand itself.
 
-use std::collections::HashMap;
-use std::path::PathBuf;
-
 use anyhow::Context;
 use clap::Args;
 use noodles::sam::record::MappingQuality;
-use num_format::Locale;
-use num_format::ToFormattedString;
-use tracing::debug;
-use tracing::info;
+use num_format::{Locale, ToFormattedString};
+use std::collections::HashMap;
+use std::path::PathBuf;
+use tracing::{debug, info};
 
 use crate::derive::junction_annotation::compute;
 use crate::derive::junction_annotation::results::JunctionAnnotationResults;

src/derive/command/readlen.rs

@@ -1,12 +1,10 @@
 //! Functionality relating to the `ngs derive readlen` subcommand itself.
 
-use std::collections::HashMap;
-use std::path::PathBuf;
-
 use anyhow::Context;
 use clap::Args;
-use num_format::Locale;
-use num_format::ToFormattedString;
+use num_format::{Locale, ToFormattedString};
+use std::collections::HashMap;
+use std::path::PathBuf;
 use tracing::info;
 
 use crate::derive::readlen::compute;

src/derive/command/strandedness.rs

@@ -1,23 +1,17 @@
 //! Functionality relating to the `ngs derive strandedness` subcommand itself.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
-use std::fs::File;
-use std::path::PathBuf;
-
-use anyhow::bail;
-use anyhow::Context;
+use anyhow::{bail, Context};
 use clap::Args;
-use noodles::bam;
-use noodles::gff;
 use noodles::sam::record::MappingQuality;
+use noodles::{bam, gff};
 use rust_lapper::{Interval, Lapper};
-use tracing::debug;
-use tracing::info;
+use std::collections::{HashMap, HashSet};
+use std::fs::File;
+use std::path::PathBuf;
+use tracing::{debug, info};
 
-use crate::derive::strandedness::compute;
 use crate::derive::strandedness::compute::ParsedBAMFile;
-use crate::derive::strandedness::results;
+use crate::derive::strandedness::{compute, results};
 use crate::utils::formats;
 use crate::utils::read_groups::validate_read_group_info;
 

src/derive/endedness/compute.rs

@@ -1,7 +1,6 @@
 //! Module holding the logic for computing the endedness of a BAM.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
+use std::collections::{HashMap, HashSet};
 use std::ops::{Add, AddAssign};
 use std::sync::Arc;
 use tracing::warn;

src/derive/instrument/compute.rs

@@ -1,14 +1,11 @@
 //! Combines the flowcell and instrument checks into a single workflow.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
-
 use regex::Regex;
 use serde::Serialize;
+use std::collections::{HashMap, HashSet};
 use tracing::debug;
 
-use super::flowcells;
-use super::instruments;
+use crate::derive::instrument::{flowcells, instruments};
 
 /// Generalized struct for holding instrument detection results.
 #[derive(Debug, Default, Serialize)]

src/derive/instrument/flowcells.rs

@@ -1,7 +1,6 @@
 //! Knowledge about which flowcells map to which machine types.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
+use std::collections::{HashMap, HashSet};
 
 /// Encapsulates the knowledge we currently have on which flowcell patterns map
 /// to which machine types as a [`HashMap`].

src/derive/instrument/instruments.rs

@@ -1,7 +1,6 @@
 //! Knowledge about which instrument ids map to which machine types.
 
-use std::collections::HashMap;
-use std::collections::HashSet;
+use std::collections::{HashMap, HashSet};
 
 /// Encapsulates the knowledge we currently have on which instrument name patterns map
 /// to which machine types as a [`HashMap`].

src/derive/junction_annotation/compute.rs

@@ -1,14 +1,12 @@
 //! Module holding the logic for annotating junctions.
 
-use anyhow::bail;
-use anyhow::Ok;
+use anyhow::{bail, Ok};
 use noodles::core::Position;
 use noodles::sam::alignment::Record;
 use noodles::sam::record::cigar::op::Kind;
 use noodles::sam::record::MappingQuality;
 use noodles::sam::Header;
-use std::collections::HashMap;
-use std::collections::HashSet;
+use std::collections::{HashMap, HashSet};
 
 use crate::derive::junction_annotation::results;
 use crate::utils::alignment::filter_by_mapq;

src/derive/junction_annotation/results.rs

@@ -2,8 +2,7 @@
 
 use noodles::core::Position;
 use serde::ser::SerializeStruct;
-use serde::Serialize;
-use serde::Serializer;
+use serde::{Serialize, Serializer};
 use std::collections::HashMap;
 
 /// A junction is a tuple of (start, end) coordinates.

src/derive/strandedness/compute.rs

@@ -1,16 +1,18 @@
 //! Module holding the logic for computing the strandedness.
 
+use noodles::core::Region;
 use noodles::sam::record::MappingQuality;
-use noodles::{bam, core::Region, gff, sam};
+use noodles::{bam, gff, sam};
 use rand::Rng;
 use rust_lapper::Lapper;
 use std::collections::{HashMap, HashSet};
 use std::ops::{Add, AddAssign};
 use std::sync::Arc;
 
 use crate::derive::strandedness::results;
+use crate::utils::alignment::filter_by_mapq;
+use crate::utils::display::RecordCounter;
 use crate::utils::read_groups;
-use crate::utils::{alignment::filter_by_mapq, display::RecordCounter};
 
 const STRANDED_THRESHOLD: f64 = 80.0;
 const UNSTRANDED_THRESHOLD: f64 = 40.0;