From f4b929d897613413f00825857764d7cb78bdbe7e Mon Sep 17 00:00:00 2001
From: "Erik Garrison (aider)" <erik.garrison@gmail.com>
Date: Thu, 14 Nov 2024 14:13:35 -0600
Subject: [PATCH] feat: Change default overlap threshold to 1.0 with
 short-circuit optimization

---
 src/interface/parse_args.hpp |  2 +-
 src/map/include/filter.hpp   | 44 ++++++++++++++++++++----------------
 2 files changed, 26 insertions(+), 20 deletions(-)

diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp
index ec2cb2ab..b96a23f7 100644
--- a/src/interface/parse_args.hpp
+++ b/src/interface/parse_args.hpp
@@ -364,7 +364,7 @@ void parse_args(int argc,
     if (overlap_threshold) {
         map_parameters.overlap_threshold = args::get(overlap_threshold);
     } else {
-        map_parameters.overlap_threshold = 0.5;
+        map_parameters.overlap_threshold = 1.0;
     }
 
     if (kmer_size) {
diff --git a/src/map/include/filter.hpp b/src/map/include/filter.hpp
index d8b1c3c7..324a984a 100644
--- a/src/map/include/filter.hpp
+++ b/src/map/include/filter.hpp
@@ -112,16 +112,19 @@ namespace skch
             }
             auto kit = it;
 
-            // Check for overlaps and mark bad if necessary
-            for ( ; it != L.end(); it++) {
-                if (it == L.begin()) continue;
-                int idx = *it;
-                for (auto it2 = L.begin(); it2 != kit; it2++) {
-                    double overlap = get_overlap(idx, *it2);
-                    if (overlap > overlapThreshold) {
-                        vec[idx].overlapped = 1;  // Mark as bad if it overlaps >50% with the best mapping
-                        vec[idx].discard = 1;
-                        break;
+            // Skip overlap checking if threshold is 1.0 (allow all overlaps)
+            if (overlapThreshold < 1.0) {
+                // Check for overlaps and mark bad if necessary
+                for ( ; it != L.end(); it++) {
+                    if (it == L.begin()) continue;
+                    int idx = *it;
+                    for (auto it2 = L.begin(); it2 != kit; it2++) {
+                        double overlap = get_overlap(idx, *it2);
+                        if (overlap > overlapThreshold) {
+                            vec[idx].overlapped = 1;  // Mark as bad if overlaps more than threshold
+                            vec[idx].discard = 1;
+                            break;
+                        }
                     }
                 }
             }
@@ -393,15 +396,18 @@ namespace skch
             }
             auto kit = it;
 
-            // Check for overlaps and mark bad if necessary
-            for ( ; it != L.end(); it++) {
-                if (it == L.begin()) continue;
-                int idx = *it;
-                for (auto it2 = L.begin(); it2 != kit; it2++) {
-                    if (get_overlap(idx, *it2) > overlapThreshold) {
-                        vec[idx].overlapped = 1;  // Mark as bad if it overlaps >50% with the best mapping
-                        vec[idx].discard = 1;
-                        break;
+            // Skip overlap checking if threshold is 1.0 (allow all overlaps)
+            if (overlapThreshold < 1.0) {
+                // Check for overlaps and mark bad if necessary
+                for ( ; it != L.end(); it++) {
+                    if (it == L.begin()) continue;
+                    int idx = *it;
+                    for (auto it2 = L.begin(); it2 != kit; it2++) {
+                        if (get_overlap(idx, *it2) > overlapThreshold) {
+                            vec[idx].overlapped = 1;  // Mark as bad if overlaps more than threshold
+                            vec[idx].discard = 1;
+                            break;
+                        }
                     }
                 }
             }