feat: add override_precursor_charge setting (#137)

Author: lazear

Diff for: CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [v0.15.0-alpha] (unreleased)
 ### Added
 - Initial support for searching diaPASEF data
+- `override_precursor_charge` setting that forces multiple charge states to be searched
 ### Breaking Changes
 - `precursor_ppm` field reports the non-absoluted average mass error, rather than the absoluted average mass error.
 - Don't deisotope reporter ion regions if MS2-based TMT/iTRAQ is used

Diff for: Cargo.lock

@@ -18,6 +18,7 @@ pub struct Search {
     pub precursor_tol: Tolerance,
     pub fragment_tol: Tolerance,
     pub precursor_charge: (u8, u8),
+    pub override_precursor_charge: bool,
     pub isotope_errors: (i8, i8),
     pub deisotope: bool,
     pub chimera: bool,
@@ -55,6 +56,7 @@ pub struct Input {
     max_fragment_charge: Option<u8>,
     min_matched_peaks: Option<u16>,
     precursor_charge: Option<(u8, u8)>,
+    override_precursor_charge: Option<bool>,
     isotope_errors: Option<(i8, i8)>,
     deisotope: Option<bool>,
     quant: Option<QuantOptions>,
@@ -298,6 +300,7 @@ impl Input {
             max_fragment_charge: self.max_fragment_charge,
             annotate_matches: self.annotate_matches.unwrap_or(false),
             precursor_charge: self.precursor_charge.unwrap_or((2, 4)),
+            override_precursor_charge: self.override_precursor_charge.unwrap_or(false),
             isotope_errors: self.isotope_errors.unwrap_or((0, 0)),
             deisotope: self.deisotope.unwrap_or(true),
             chimera: self.chimera.unwrap_or(false),

Diff for: crates/sage-cli/src/input.rs

@@ -262,6 +262,7 @@ impl Runner {
             max_isotope_err: self.parameters.isotope_errors.1,
             min_precursor_charge: self.parameters.precursor_charge.0,
             max_precursor_charge: self.parameters.precursor_charge.1,
+            override_precursor_charge: self.parameters.override_precursor_charge,
             max_fragment_charge: self.parameters.max_fragment_charge,
             chimera: self.parameters.chimera,
             report_psms: self.parameters.report_psms,

Diff for: crates/sage-cli/src/main.rs

@@ -26,6 +26,7 @@ fn integration() -> anyhow::Result<()> {
         max_isotope_err: 3,
         min_precursor_charge: 2,
         max_precursor_charge: 4,
+        override_precursor_charge: false,
         max_fragment_charge: Some(1),
         chimera: false,
         report_psms: 1,

Diff for: crates/sage-cli/tests/integration.rs

@@ -182,6 +182,7 @@ pub struct Scorer<'db> {
     pub max_isotope_err: i8,
     pub min_precursor_charge: u8,
     pub max_precursor_charge: u8,
+    pub override_precursor_charge: bool,
     pub max_fragment_charge: Option<u8>,
     pub chimera: bool,
     pub report_psms: usize,
@@ -346,12 +347,14 @@ impl<'db> Scorer<'db> {
             );
             self.trim_hits(&mut hits);
             hits
-        } else if let Some(charge) = precursor.charge {
+        } else if precursor.charge.is_some() && self.override_precursor_charge == false {
+            let charge = precursor.charge.unwrap();
             // Charge state is already annotated for this precusor, only search once
             let precursor_mass = mz * charge as f32;
             self.matched_peaks(query, precursor_mass, charge, self.precursor_tol)
         } else {
-            // Not all selected ion precursors have charge states annotated -
+            // Not all selected ion precursors have charge states annotated (or user has set
+            // `override_precursor_charge`)
             // assume it could be z=2, z=3, z=4 and search all three
             let mut hits = (self.min_precursor_charge..=self.max_precursor_charge).fold(
                 InitialHits::default(),