From 57c61c561a44addafe04f9b44dfd6de01cff5f95 Mon Sep 17 00:00:00 2001
From: SuhasSrinivasan <32346517+SuhasSrinivasan@users.noreply.github.com>
Date: Tue, 4 Aug 2026 23:08:12 -0700
Subject: [PATCH] Apply localize minimum coverage before aggregation

---
 modkit-core/src/localise/subcommand.rs |  1 +
 modkit-core/src/localise/util.rs       |  2 ++
 modkit/tests/test_localize.rs          | 48 ++++++++++++++++++++++++++
 3 files changed, 51 insertions(+)

diff --git a/modkit-core/src/localise/subcommand.rs b/modkit-core/src/localise/subcommand.rs
index 0a36c14..551320e 100644
--- a/modkit-core/src/localise/subcommand.rs
+++ b/modkit-core/src/localise/subcommand.rs
@@ -271,6 +271,7 @@ impl EntryLocalize {
                 .map(|gr| {
                     gr.into_localized_mod_counts(
                         &tabix_index,
+                        min_cov,
                         self.stranded_features,
                         stranded_features,
                         self.io_threads,
diff --git a/modkit-core/src/localise/util.rs b/modkit-core/src/localise/util.rs
index 54fcffb..79cc8a0 100644
--- a/modkit-core/src/localise/util.rs
+++ b/modkit-core/src/localise/util.rs
@@ -190,6 +190,7 @@ impl GenomeRegion {
     pub(super) fn into_localized_mod_counts(
         self,
         index: &HtsTabixHandler<BedMethylLine>,
+        min_coverage: u64,
         strand_rule: Option<StrandRule>,
         stranded_features: Option<StrandedFeatures>,
         io_threads: usize,
@@ -203,6 +204,7 @@ impl GenomeRegion {
         let anchor_point = self.midpoint();
         let loc_counts = bedmethyl_records
             .into_par_iter()
+            .filter(|bm| bm.valid_coverage >= min_coverage)
             .filter(|bm| {
                 stranded_features
                     .map(|f| {
diff --git a/modkit/tests/test_localize.rs b/modkit/tests/test_localize.rs
index 2225773..a62dd90 100644
--- a/modkit/tests/test_localize.rs
+++ b/modkit/tests/test_localize.rs
@@ -1,4 +1,6 @@
 use crate::common::run_modkit;
+use std::fs;
+use tempfile::tempdir;
 
 mod common;
 
@@ -9,3 +11,49 @@ fn test_localise_helps() {
     let _ = run_modkit(&["localise", "--help"])
         .expect("failed to run modkit localise help");
 }
+
+#[test]
+fn test_localize_min_coverage_filters_before_aggregation() {
+    let temp_dir = tempdir().unwrap();
+    let regions = temp_dir.path().join("regions.bed");
+    let genome_sizes = temp_dir.path().join("genome-sizes.tsv");
+    fs::write(&regions, "chr20\t9681998\t9681999\nchr20\t9838537\t9838538\n")
+        .unwrap();
+    fs::write(&genome_sizes, "chr20\t64444167\n").unwrap();
+
+    let run = |min_coverage: u64| {
+        let output = temp_dir.path().join(format!("min-{min_coverage}.tsv"));
+        let min_coverage = min_coverage.to_string();
+        run_modkit(&[
+            "localize",
+            "../tests/resources/lung_00733-m_adjacent-normal_5mc-5hmc_chr20_cpg_pileup.bed.gz",
+            "--regions",
+            regions.to_str().unwrap(),
+            "--genome-sizes",
+            genome_sizes.to_str().unwrap(),
+            "--window",
+            "1",
+            "--min-coverage",
+            &min_coverage,
+            "--threads",
+            "1",
+            "--io-threads",
+            "1",
+            "--out-file",
+            output.to_str().unwrap(),
+        ])
+        .unwrap();
+        fs::read_to_string(output).unwrap().replace("\r\n", "\n")
+    };
+
+    assert_eq!(
+        run(1),
+        "mod_code\toffset\tn_valid\tn_mod\tpercent_modified\n\
+         C\t-1\t24\t3\t12.5\n"
+    );
+    assert_eq!(
+        run(3),
+        "mod_code\toffset\tn_valid\tn_mod\tpercent_modified\n\
+         C\t-1\t23\t2\t8.695652\n"
+    );
+}