feat: use NonZeroUsize for Number of Records

src/convert/command.rs

@@ -1,5 +1,6 @@
 //! Functionality related to the `ngs convert` command itself.
 
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 
 use anyhow::bail;
@@ -31,8 +32,8 @@ pub struct ConvertArgs {
     to: PathBuf,
 
     /// Number of records to process before exiting the conversion.
-    #[arg(short = 'n', long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    #[arg(short = 'n', long, value_name = "NonZeroUsize")]
+    num_records: Option<NonZeroUsize>,
 
     /// If available, the FASTA reference file used to generate the file.
     #[arg(short, long)]

src/derive/command/encoding.rs

@@ -6,6 +6,7 @@ use noodles::bam;
 use num_format::{Locale, ToFormattedString};
 use std::collections::HashSet;
 use std::io::BufReader;
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use tracing::info;
 
@@ -21,8 +22,8 @@ pub struct DeriveEncodingArgs {
     src: PathBuf,
 
     /// Examine the first `n` records in the file.
-    #[arg(short, long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    #[arg(short, long, value_name = "NonZeroUsize")]
+    num_records: Option<NonZeroUsize>,
 }
 
 /// Main function for the `ngs derive encoding` subcommand.

src/derive/command/endedness.rs

@@ -4,6 +4,7 @@ use anyhow::Context;
 use clap::Args;
 use num_format::{Locale, ToFormattedString};
 use std::collections::{HashMap, HashSet};
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use std::sync::Arc;
 use tracing::{info, trace};
@@ -24,9 +25,9 @@ pub struct DeriveEndednessArgs {
     #[arg(value_name = "BAM")]
     src: PathBuf,
 
-    /// Only examine the first n records in the file.
-    #[arg(short, long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    /// Examine the first `n` records in the file.
+    #[arg(short, long, value_name = "NonZeroUsize")]
+    num_records: Option<NonZeroUsize>,
 
     /// Distance from 0.5 split between number of f+l- reads and f-l+ reads
     /// allowed to be called 'Paired-End'. The default value of `0.0` is only appropriate

src/derive/command/instrument.rs

@@ -4,6 +4,7 @@ use anyhow::bail;
 use clap::Args;
 use num_format::{Locale, ToFormattedString};
 use std::collections::HashSet;
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use tracing::info;
 
@@ -21,9 +22,10 @@ pub struct DeriveInstrumentArgs {
     #[arg(value_name = "BAM")]
     src: PathBuf,
 
-    /// Only examine the first n records in the file.
-    #[arg(short, long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    /// Examine the first `n` records in the file.
+    /// If `0`, all records are examined.
+    #[arg(short, long, value_name = "USIZE", default_value = "10000000")]
+    num_records: usize,
 }
 
 /// Main function for the `ngs derive instrument` subcommand.
@@ -41,7 +43,10 @@ pub fn derive(args: DeriveInstrumentArgs) -> anyhow::Result<()> {
 
     // (1) Collect instrument names and flowcell names from reads within the
     // file. Support for sampling only a portion of the reads is provided.
-    let num_records = NumberOfRecords::from(args.num_records);
+    let num_records = match args.num_records {
+        0 => NumberOfRecords::All,
+        _ => NumberOfRecords::Some(NonZeroUsize::new(args.num_records).unwrap()),
+    };
     let mut counter = RecordCounter::default();
 
     for result in reader.records(&header.parsed) {

src/derive/command/readlen.rs

@@ -4,6 +4,7 @@ use anyhow::Context;
 use clap::Args;
 use num_format::{Locale, ToFormattedString};
 use std::collections::HashMap;
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use tracing::info;
 
@@ -21,9 +22,10 @@ pub struct DeriveReadlenArgs {
     #[arg(value_name = "BAM")]
     src: PathBuf,
 
-    /// Only examine the first n records in the file.
-    #[arg(short, long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    /// Examine the first `n` records in the file.
+    /// If `0`, all records are examined.
+    #[arg(short, long, value_name = "USIZE", default_value = "10000000")]
+    num_records: usize,
 
     /// Majority vote cutoff value as a fraction between [0.0, 1.0].
     #[arg(short, long, value_name = "F64", default_value = "0.7")]
@@ -46,7 +48,10 @@ pub fn derive(args: DeriveReadlenArgs) -> anyhow::Result<()> {
 
     // (1) Collect read lengths from reads within the
     // file. Support for sampling only a portion of the reads is provided.
-    let num_records = NumberOfRecords::from(args.num_records);
+    let num_records = match args.num_records {
+        0 => NumberOfRecords::All,
+        _ => NumberOfRecords::Some(NonZeroUsize::new(args.num_records).unwrap()),
+    };
     let mut counter = RecordCounter::default();
 
     for result in reader.records(&header.parsed) {

src/qc/command.rs

@@ -1,6 +1,7 @@
 //! Functionality related to the `ngs qc` command itself.
 
 use std::fs::File;
+use std::num::NonZeroUsize;
 use std::path::PathBuf;
 use std::rc::Rc;
 
@@ -50,8 +51,8 @@ pub struct QcArgs {
     /// to process per sequence in the second pass.
     ///
     /// This is generally only used for testing purposes.
-    #[arg(short = 'n', long, value_name = "USIZE")]
-    num_records: Option<usize>,
+    #[arg(short = 'n', long, value_name = "NonZeroUsize")]
+    num_records: Option<NonZeroUsize>,
 
     /// Directory to output files to. Defaults to current working directory.
     #[arg(short = 'o', long, value_name = "PATH")]

src/utils/args.rs

@@ -1,6 +1,7 @@
 //! Utilities related to the parsing of arguments.
 
 use std::fmt::Display;
+use std::num::NonZeroUsize;
 
 use noodles::{bgzf::writer::CompressionLevel, sam::record::MappingQuality};
 use tracing::debug;
@@ -17,11 +18,11 @@ pub enum NumberOfRecords {
 
     /// Designates that we should review _some_ of the records in the file. The
     /// exact count of records is stored in the `usize`.
-    Some(usize),
+    Some(NonZeroUsize),
 }
 
-impl From<Option<usize>> for NumberOfRecords {
-    fn from(num_records: Option<usize>) -> Self {
+impl From<Option<NonZeroUsize>> for NumberOfRecords {
+    fn from(num_records: Option<NonZeroUsize>) -> Self {
         match num_records {
             Some(n) => {
                 debug!("Reading a maximum of {} records.", n);

src/utils/display.rs

@@ -74,7 +74,7 @@ impl RecordCounter {
     /// (if it exists, otherwise it loops forever).
     pub fn time_to_break(&self, limit: &NumberOfRecords) -> bool {
         match limit {
-            NumberOfRecords::Some(v) => self.count >= *v,
+            NumberOfRecords::Some(v) => self.count >= <usize>::from(*v),
             NumberOfRecords::All => false,
         }
     }