Accept yes/no/y/n/t/f as boolean flag values

src/commands/clip.rs

@@ -37,7 +37,7 @@ use std::sync::atomic::{AtomicU64, Ordering};
 use super::command::Command;
 use super::common::{
     BamIoOptions, CompressionOptions, QueueMemoryOptions, SchedulerOptions, ThreadingOptions,
-    build_pipeline_config,
+    build_pipeline_config, parse_bool,
 };
 
 /// Clips reads in a BAM file to remove overlaps
@@ -100,7 +100,7 @@ pub struct Clip {
     pub sort_order: Option<String>,
 
     /// Clip overlapping read pairs
-    #[arg(long = "clip-overlapping-reads", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "clip-overlapping-reads", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub clip_overlapping_reads: bool,
 
     /// Clip reads that extend past their mate's start position
@@ -111,6 +111,7 @@ pub struct Clip {
         num_args = 0..=1,
         default_missing_value = "true",
         action = clap::ArgAction::Set,
+        value_parser = parse_bool,
     )]
     pub clip_extending_past_mate: bool,
 
@@ -131,11 +132,11 @@ pub struct Clip {
     pub read_two_three_prime: usize,
 
     /// Upgrade existing clipping to the specified clipping mode
-    #[arg(short = 'H', long = "upgrade-clipping", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'H', long = "upgrade-clipping", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub upgrade_clipping: bool,
 
     /// Automatically clip extended attributes that match read length
-    #[arg(short = 'a', long = "auto-clip-attributes", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'a', long = "auto-clip-attributes", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub auto_clip_attributes: bool,
 
     /// Output file for clipping metrics

src/commands/common.rs

@@ -104,11 +104,11 @@ pub struct ConsensusCallingOptions {
     pub min_input_base_quality: u8,
 
     /// Produce per-base tags (cd, ce) in addition to per-read tags
-    #[arg(short = 'B', long = "output-per-base-tags", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'B', long = "output-per-base-tags", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub output_per_base_tags: bool,
 
     /// Quality-trim reads before consensus calling (removes low-quality bases from ends)
-    #[arg(long = "trim", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "trim", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub trim: bool,
 
     /// Minimum consensus base quality (output consensus bases below this are masked to N)
@@ -214,7 +214,7 @@ impl Default for ReadGroupOptions {
 #[derive(Debug, Clone, Args)]
 pub struct OverlappingConsensusOptions {
     /// Consensus call overlapping bases in read pairs before UMI consensus calling
-    #[arg(long = "consensus-call-overlapping-bases", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "consensus-call-overlapping-bases", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub consensus_call_overlapping_bases: bool,
 }
 
@@ -315,7 +315,7 @@ pub struct SchedulerOptions {
     ///
     /// Shows per-step timing, throughput, contention metrics, and
     /// per-thread work distribution.
-    #[arg(long = "pipeline-stats", default_value_t = false, hide = true)]
+    #[arg(long = "pipeline-stats", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool, hide = true)]
     pub pipeline_stats: bool,
 
     /// Timeout in seconds for deadlock detection (default: 10, 0 = disabled).
@@ -329,7 +329,7 @@ pub struct SchedulerOptions {
     ///
     /// Uses progressive doubling: 2x -> 4x -> unbind, with restoration
     /// after 30s of sustained progress.
-    #[arg(long = "deadlock-recover", default_value_t = false, hide = true)]
+    #[arg(long = "deadlock-recover", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool, hide = true)]
     pub deadlock_recover: bool,
 }
 
@@ -451,7 +451,7 @@ pub struct QueueMemoryOptions {
     /// When true, total memory = queue-memory * threads. For example,
     /// --queue-memory 768 with --threads 16 allocates 12 GB total.
     /// Set to false for a fixed total memory budget regardless of thread count.
-    #[arg(long = "queue-memory-per-thread", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "queue-memory-per-thread", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub queue_memory_per_thread: bool,
 
     /// DEPRECATED: Use --queue-memory instead. Memory limit for pipeline queues in megabytes.
@@ -623,6 +623,16 @@ impl QueueMemoryOptions {
     }
 }
 
+/// Parses a boolean value from a string, accepting: true/false, yes/no, y/n, t/f
+/// (case-insensitive). Matches sopt/fgbio behavior.
+pub(crate) fn parse_bool(s: &str) -> Result<bool, String> {
+    match s.to_ascii_lowercase().as_str() {
+        "true" | "t" | "yes" | "y" => Ok(true),
+        "false" | "f" | "no" | "n" => Ok(false),
+        _ => Err(format!("Invalid boolean value '{s}'. Expected: true|false|yes|no|y|n|t|f")),
+    }
+}
+
 /// Parses a memory size string into bytes.
 ///
 /// Accepts both plain numbers (interpreted as MB) and human-readable formats like:
@@ -1208,4 +1218,76 @@ mod tests {
         let cmd = TestBoolFlags::try_parse_from(args).expect("valid CLI args should parse");
         assert_eq!(cmd.queue_memory.queue_memory_per_thread, expected);
     }
+
+    #[rstest]
+    #[case("true", true)]
+    #[case("false", false)]
+    #[case("yes", true)]
+    #[case("no", false)]
+    #[case("t", true)]
+    #[case("f", false)]
+    #[case("y", true)]
+    #[case("n", false)]
+    #[case("True", true)]
+    #[case("TRUE", true)]
+    #[case("False", false)]
+    #[case("FALSE", false)]
+    #[case("Yes", true)]
+    #[case("YES", true)]
+    #[case("No", false)]
+    #[case("NO", false)]
+    #[case("T", true)]
+    #[case("F", false)]
+    #[case("Y", true)]
+    #[case("N", false)]
+    #[case("tRuE", true)]
+    #[case("fAlSe", false)]
+    #[case("yEs", true)]
+    fn test_parse_bool_valid(#[case] input: &str, #[case] expected: bool) {
+        assert_eq!(parse_bool(input).expect("should parse"), expected);
+    }
+
+    #[rstest]
+    #[case("")]
+    #[case("tru")]
+    #[case("fals")]
+    #[case("truee")]
+    #[case("noo")]
+    #[case("yess")]
+    #[case("maybe")]
+    #[case("0")]
+    #[case("1")]
+    #[case("on")]
+    #[case("off")]
+    #[case(" true")]
+    #[case("true ")]
+    fn test_parse_bool_invalid(#[case] input: &str) {
+        assert!(parse_bool(input).is_err(), "expected error for input: {input:?}");
+    }
+
+    #[rstest]
+    #[case(&["test", "--trim", "yes"], true)]
+    #[case(&["test", "--trim", "no"], false)]
+    #[case(&["test", "--trim", "y"], true)]
+    #[case(&["test", "--trim", "n"], false)]
+    #[case(&["test", "--trim", "t"], true)]
+    #[case(&["test", "--trim", "f"], false)]
+    #[case(&["test", "--trim", "YES"], true)]
+    #[case(&["test", "--trim", "NO"], false)]
+    #[case(&["test", "--trim=yes"], true)]
+    #[case(&["test", "--trim=no"], false)]
+    fn test_extended_bool_values_in_cli(#[case] args: &[&str], #[case] expected: bool) {
+        let cmd = TestBoolFlags::try_parse_from(args).expect("valid CLI args should parse");
+        assert_eq!(cmd.consensus.trim, expected);
+    }
+
+    #[rstest]
+    #[case(&["test", "--trim", "maybe"])]
+    #[case(&["test", "--trim", "0"])]
+    #[case(&["test", "--trim", "1"])]
+    #[case(&["test", "--trim", "on"])]
+    #[case(&["test", "--trim", "off"])]
+    fn test_extended_bool_values_in_cli_invalid(#[case] args: &[&str]) {
+        assert!(TestBoolFlags::try_parse_from(args).is_err());
+    }
 }

src/commands/compare/bams.rs

@@ -38,6 +38,7 @@ use std::path::{Path, PathBuf};
 use std::thread;
 
 use crate::commands::command::Command;
+use crate::commands::common::parse_bool;
 
 use super::raw_compare::{raw_compare_structured, raw_records_byte_equal};
 
@@ -164,14 +165,14 @@ pub struct CompareBams {
     pub max_diffs: usize,
 
     /// Quiet mode - only exit code indicates result (0=equal, 1=different)
-    #[arg(short = 'q', long = "quiet")]
+    #[arg(short = 'q', long = "quiet", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub quiet: bool,
 
     /// Ignore record order when comparing in grouping mode.
     /// Required for comparing output from consensus commands (simplex/duplex/codec)
     /// when run with --threads, as parallel processing causes non-deterministic ordering.
     /// Only valid with --mode grouping.
-    #[arg(long = "ignore-order", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "ignore-order", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub ignore_order: bool,
 
     /// Initial buffer size for --ignore-order mode (number of records)

src/commands/compare/metrics.rs

@@ -3,6 +3,7 @@
 //! This is useful for comparing metrics files produced by fgbio and fgumi,
 //! which may have slightly different floating-point representations.
 
+use crate::commands::common::parse_bool;
 use anyhow::Result;
 use clap::Parser;
 use fgumi_lib::logging::OperationTimer;
@@ -69,11 +70,11 @@ pub struct CompareMetrics {
     pub max_diffs: usize,
 
     /// Quiet mode - only exit code indicates result (0=equal, 1=different)
-    #[arg(short = 'q', long = "quiet")]
+    #[arg(short = 'q', long = "quiet", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub quiet: bool,
 
     /// Verbose mode - print success message when files match
-    #[arg(short = 'v', long = "verbose")]
+    #[arg(short = 'v', long = "verbose", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub verbose: bool,
 }
 

src/commands/correct.rs

@@ -72,7 +72,7 @@ use std::sync::atomic::{AtomicU64, Ordering};
 use crate::commands::command::Command;
 use crate::commands::common::{
     BamIoOptions, CompressionOptions, QueueMemoryOptions, RejectsOptions, SchedulerOptions,
-    ThreadingOptions, build_pipeline_config,
+    ThreadingOptions, build_pipeline_config, parse_bool,
 };
 
 /// Result of matching an observed UMI to an expected UMI.
@@ -229,7 +229,7 @@ pub struct CorrectUmis {
     pub umi_tag: String,
 
     /// Don't store original UMIs in a separate tag.
-    #[arg(long)]
+    #[arg(long, default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub dont_store_original_umis: bool,
 
     /// Size of the LRU cache for UMI matching.
@@ -241,7 +241,7 @@ pub struct CorrectUmis {
     pub min_corrected: Option<f64>,
 
     /// Reverse complement UMIs before matching.
-    #[arg(long)]
+    #[arg(long, default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub revcomp: bool,
 
     /// Threading options for parallel processing.

src/commands/dedup.rs

@@ -53,7 +53,7 @@ use serde::{Deserialize, Serialize};
 use crate::commands::command::Command;
 use crate::commands::common::{
     BamIoOptions, CompressionOptions, QueueMemoryOptions, SchedulerOptions, ThreadingOptions,
-    build_pipeline_config,
+    build_pipeline_config, parse_bool,
 };
 use fgumi_lib::sort::PA_TAG;
 use fgumi_lib::sort::bam_fields;
@@ -1073,7 +1073,7 @@ pub struct MarkDuplicates {
     pub family_size_histogram: Option<PathBuf>,
 
     /// Remove duplicates instead of just marking them
-    #[arg(short = 'r', long = "remove-duplicates", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'r', long = "remove-duplicates", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub remove_duplicates: bool,
 
     /// The tag containing the raw UMI sequence
@@ -1097,7 +1097,7 @@ pub struct MarkDuplicates {
     pub min_map_q: Option<u8>,
 
     /// Include reads flagged as not passing QC
-    #[arg(short = 'n', long = "include-non-pf-reads", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'n', long = "include-non-pf-reads", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub include_non_pf_reads: bool,
 
     /// UMI grouping strategy
@@ -1126,7 +1126,7 @@ pub struct MarkDuplicates {
 
     /// Skip UMI-based grouping; group by position only. Forces identity strategy
     /// and ignores any existing UMI tags.
-    #[arg(long = "no-umi")]
+    #[arg(long = "no-umi", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub no_umi: bool,
 
     /// Scheduler and pipeline options

src/commands/downsample.rs

@@ -24,7 +24,7 @@ use std::io::Write;
 use std::path::PathBuf;
 
 use crate::commands::command::Command;
-use crate::commands::common::{BamIoOptions, CompressionOptions};
+use crate::commands::common::{BamIoOptions, CompressionOptions, parse_bool};
 
 /// MI tag for molecular identifier
 const MI_TAG: Tag = Tag::new(b'M', b'I');
@@ -76,7 +76,7 @@ pub struct Downsample {
     pub seed: Option<u64>,
 
     /// Validate that MI tags appear in consecutive groups (error if seen non-consecutively)
-    #[arg(long = "validate-mi-order", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "validate-mi-order", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub validate_mi_order: bool,
 
     /// Output file for kept family size histogram

src/commands/duplex_metrics.rs

@@ -6,6 +6,7 @@
 //! - Ideal duplex fraction calculation using proper binomial CDF
 //! - Optional interval filtering (BED or Picard interval list format) to restrict analysis to specific regions
 
+use crate::commands::common::parse_bool;
 use anyhow::{Context, Result};
 use clap::Parser;
 use fgoxide::io::DelimFile;
@@ -100,7 +101,7 @@ pub struct DuplexMetrics {
     pub min_ba_reads: usize,
 
     /// Collect duplex UMI counts (memory intensive)
-    #[arg(long = "duplex-umi-counts", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "duplex-umi-counts", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub duplex_umi_counts: bool,
 
     /// Optional intervals file to restrict analysis (BED or Picard interval list format)

src/commands/fastq.rs

@@ -3,6 +3,7 @@
 //! This tool reads a BAM file and outputs interleaved FASTQ to stdout for piping to aligners.
 //! Input should be queryname-sorted or template-coordinate sorted.
 
+use crate::commands::common::parse_bool;
 use anyhow::{Context, Result};
 use clap::Parser;
 use fgumi_lib::bam_io::create_bam_reader;
@@ -73,7 +74,7 @@ pub struct Fastq {
     pub input: PathBuf,
 
     /// Don't append /1 and /2 to read names.
-    #[arg(short = 'n', long = "no-read-suffix", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'n', long = "no-read-suffix", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub no_suffix: bool,
 
     /// Exclude reads with any of these flags present [0x900 = secondary|supplementary].

src/commands/filter.rs

@@ -41,7 +41,7 @@ use std::time::Instant;
 use crate::commands::command::Command;
 use crate::commands::common::{
     BamIoOptions, CompressionOptions, QueueMemoryOptions, SchedulerOptions, ThreadingOptions,
-    build_pipeline_config,
+    build_pipeline_config, parse_bool,
 };
 
 /// Filters and masks consensus reads based on various quality metrics.
@@ -147,15 +147,15 @@ pub struct Filter {
     pub max_no_call_fraction: f64,
 
     /// Reverse per-base tags for negative strand reads
-    #[arg(short = 'R', long = "reverse-per-base-tags", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 'R', long = "reverse-per-base-tags", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub reverse_per_base_tags: bool,
 
     /// Threading options for parallel processing
     #[command(flatten)]
     pub threading: ThreadingOptions,
 
     /// Filter templates together (all primary reads must pass)
-    #[arg(long = "filter-by-template", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(long = "filter-by-template", default_value = "true", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub filter_by_template: bool,
 
     /// Optional output BAM file for rejected reads
@@ -167,7 +167,7 @@ pub struct Filter {
     pub stats: Option<PathBuf>,
 
     /// Require single-strand agreement for duplex consensus (mask bases where AB and BA disagree)
-    #[arg(short = 's', long = "require-single-strand-agreement", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set)]
+    #[arg(short = 's', long = "require-single-strand-agreement", default_value = "false", num_args = 0..=1, default_missing_value = "true", action = clap::ArgAction::Set, value_parser = parse_bool)]
     pub require_single_strand_agreement: bool,
 
     /// Compression options for output BAM.