feat(derive): report by read group where appropriate and feasible

src/derive/command/encoding.rs

@@ -32,7 +32,7 @@ pub struct DeriveEncodingArgs {
 
 /// Main function for the `ngs derive encoding` subcommand.
 pub fn derive(args: DeriveEncodingArgs) -> anyhow::Result<()> {
-    info!("Starting derive readlen subcommand.");
+    info!("Starting derive encoding subcommand.");
 
     let file = std::fs::File::open(args.src);
     let reader = file

src/derive/command/endedness.rs

@@ -141,21 +141,21 @@ pub fn derive(args: DeriveEndednessArgs) -> anyhow::Result<()> {
         counter.get().to_formatted_string(&Locale::en)
     );
 
-    // (1.5) Validate the read group information.
+    // (2) Validate the read group information.
     let rgs_in_header_not_records = validate_read_group_info(&found_rgs, &header.parsed);
     for rg_id in rgs_in_header_not_records {
         ordering_flags.insert(Arc::new(rg_id), OrderingFlagsCounts::new());
     }
 
-    // (2) Derive the endedness based on the ordering flags gathered.
+    // (3) Derive the endedness based on the ordering flags gathered.
     let result = compute::predict(
         ordering_flags,
         read_names,
         paired_deviance,
         args.round_reads_per_template,
     );
 
-    // (3) Print the output to stdout as JSON (more support for different output
+    // (4) Print the output to stdout as JSON (more support for different output
     // types may be added in the future, but for now, only JSON).
     let output = serde_json::to_string_pretty(&result).unwrap();
     println!("{}", output);

src/derive/command/instrument.rs

@@ -1,10 +1,10 @@
 //! Functionality relating to the `ngs derive instrument` subcommand itself.
 
-use anyhow::bail;
 use clap::Args;
 use num_format::{Locale, ToFormattedString};
-use std::collections::HashSet;
+use std::collections::{HashMap, HashSet};
 use std::path::PathBuf;
+use std::sync::Arc;
 use tracing::info;
 
 use crate::derive::instrument::compute;
@@ -13,6 +13,7 @@ use crate::utils::args::NumberOfRecords;
 use crate::utils::display::RecordCounter;
 use crate::utils::formats::bam::ParsedBAMFile;
 use crate::utils::formats::utils::IndexCheck;
+use crate::utils::read_groups::{get_read_group, validate_read_group_info, ReadGroupPtr};
 
 /// Clap arguments for the `ngs derive instrument` subcommand.
 #[derive(Args)]
@@ -34,9 +35,10 @@ pub struct DeriveInstrumentArgs {
 /// Main function for the `ngs derive instrument` subcommand.
 pub fn derive(args: DeriveInstrumentArgs) -> anyhow::Result<()> {
     let src = args.src;
-    let mut instrument_names = HashSet::new();
-    let mut flowcell_names = HashSet::new();
+    let mut instrument_names: HashMap<ReadGroupPtr, HashSet<String>> = HashMap::new();
+    let mut flowcell_names: HashMap<ReadGroupPtr, HashSet<String>> = HashMap::new();
     let mut metrics = compute::RecordMetrics::default();
+    let mut found_rgs = HashSet::new();
 
     info!("Starting derive instrument subcommand.");
 
@@ -49,24 +51,25 @@ pub fn derive(args: DeriveInstrumentArgs) -> anyhow::Result<()> {
     let mut counter = RecordCounter::default();
     for result in reader.records(&header.parsed) {
         let record = result?;
+        let read_group = get_read_group(&record, Some(&mut found_rgs));
 
         if let Some(read_name) = record.read_name() {
             let name: &str = read_name.as_ref();
 
             match name.parse::<IlluminaReadName>() {
                 Ok(read) => {
-                    instrument_names.insert(read.instrument_name);
+                    instrument_names
+                        .entry(read_group.clone())
+                        .or_default()
+                        .insert(read.instrument_name);
                     metrics.found_instrument_name += 1;
                     if let Some(fc) = read.flowcell {
-                        flowcell_names.insert(fc);
+                        flowcell_names.entry(read_group).or_default().insert(fc);
                         metrics.found_flowcell_name += 1;
                     }
                 }
                 Err(_) => {
-                    bail!(
-                        "Could not parse Illumina-formatted query names for read: {}",
-                        name
-                    );
+                    metrics.bad_read_name += 1;
                 }
             }
         } else {
@@ -85,12 +88,20 @@ pub fn derive(args: DeriveInstrumentArgs) -> anyhow::Result<()> {
     );
     metrics.total_records = counter.get();
 
-    // (2) Derive the predict instrument results based on these detected
+    // (2) Validate the read group information.
+    let rgs_in_header_not_records = validate_read_group_info(&found_rgs, &header.parsed);
+    for rg_id in rgs_in_header_not_records {
+        let rg_ptr = Arc::new(rg_id);
+        instrument_names.insert(rg_ptr.clone(), HashSet::new());
+        flowcell_names.insert(rg_ptr, HashSet::new());
+    }
+
+    // (3) Derive the instrument results based on the detected
     // instrument names and flowcell names.
     let mut result = compute::predict(instrument_names, flowcell_names);
     result.records = metrics;
 
-    // (3) Print the output to stdout as JSON (more support for different output
+    // (4) Print the output to stdout as JSON (more support for different output
     // types may be added in the future, but for now, only JSON).
     let output = serde_json::to_string_pretty(&result).unwrap();
     println!("{}", output);

src/derive/command/readlen.rs

@@ -4,7 +4,9 @@ use anyhow::Context;
 use clap::Args;
 use num_format::{Locale, ToFormattedString};
 use std::collections::HashMap;
+use std::collections::HashSet;
 use std::path::PathBuf;
+use std::sync::Arc;
 use tracing::info;
 
 use crate::derive::readlen::compute;
@@ -13,6 +15,7 @@ use crate::utils::args::NumberOfRecords;
 use crate::utils::display::RecordCounter;
 use crate::utils::formats::bam::ParsedBAMFile;
 use crate::utils::formats::utils::IndexCheck;
+use crate::utils::read_groups::{get_read_group, validate_read_group_info, ReadGroupPtr};
 
 /// Clap arguments for the `ngs derive readlen` subcommand.
 #[derive(Args)]
@@ -41,7 +44,8 @@ pub fn derive(args: DeriveReadlenArgs) -> anyhow::Result<()> {
     let majority_vote_cutoff = cutoff_in_range(args.majority_vote_cutoff, 0.0..=1.0)
         .with_context(|| "Majority vote cutoff is not within acceptable range")?;
 
-    let mut read_lengths = HashMap::new();
+    let mut read_lengths: HashMap<ReadGroupPtr, HashMap<usize, usize>> = HashMap::new();
+    let mut found_rgs = HashSet::new();
 
     info!("Starting derive readlen subcommand.");
 
@@ -54,9 +58,14 @@ pub fn derive(args: DeriveReadlenArgs) -> anyhow::Result<()> {
     let mut counter = RecordCounter::default();
     for result in reader.records(&header.parsed) {
         let record = result?;
+        let read_group = get_read_group(&record, Some(&mut found_rgs));
         let len = record.sequence().len();
 
-        *read_lengths.entry(len).or_default() += 1;
+        *read_lengths
+            .entry(read_group)
+            .or_default()
+            .entry(len)
+            .or_default() += 1;
 
         counter.inc();
         if counter.time_to_break(&args.num_records) {
@@ -69,10 +78,16 @@ pub fn derive(args: DeriveReadlenArgs) -> anyhow::Result<()> {
         counter.get().to_formatted_string(&Locale::en)
     );
 
-    // (2) Derive the consensus read length based on the read lengths gathered.
-    let result = compute::predict(read_lengths, counter.get(), majority_vote_cutoff).unwrap();
+    // (2) Validate the read group information.
+    let rgs_in_header_not_records = validate_read_group_info(&found_rgs, &header.parsed);
+    for rg_id in rgs_in_header_not_records {
+        read_lengths.insert(Arc::new(rg_id), HashMap::new());
+    }
+
+    // (3) Derive the consensus read length based on the read lengths gathered.
+    let result = compute::predict(read_lengths, majority_vote_cutoff);
 
-    // (3) Print the output to stdout as JSON (more support for different output
+    // (4) Print the output to stdout as JSON (more support for different output
     // types may be added in the future, but for now, only JSON).
     let output = serde_json::to_string_pretty(&result).unwrap();
     println!("{}", output);