From a8bbb035a36383d8ed4f5e644d0bbcb312be61a4 Mon Sep 17 00:00:00 2001
From: ksahlin <ksahlin@math.su.se>
Date: Thu, 18 Apr 2024 17:23:27 +0200
Subject: [PATCH] adding syncmers at the ends of reads as seeds without
 'aucillary' (context) hash. Increases the number of seeds per read with
 2*w_min seeds'

---
 src/randstrobes.cpp | 8 ++++++++
 src/randstrobes.hpp | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/randstrobes.cpp b/src/randstrobes.cpp
index 6dc30391..be127651 100644
--- a/src/randstrobes.cpp
+++ b/src/randstrobes.cpp
@@ -158,6 +158,14 @@ Randstrobe RandstrobeIterator::get(unsigned int strobe1_index) const {
     uint64_t min_val = std::numeric_limits<uint64_t>::max();
     Syncmer strobe2 = strobe1;
 
+    if (syncmers.size() < w_start) {
+        return Randstrobe{
+                randstrobe_hash(strobe1.hash, 0, aux_len),
+                static_cast<uint32_t>(strobe1.position),
+                static_cast<uint32_t>(strobe1.position), true
+        };
+    }
+
     for (auto i = w_start; i <= w_end && syncmers[i].position <= max_position; i++) {
         assert(i < syncmers.size());
 
diff --git a/src/randstrobes.hpp b/src/randstrobes.hpp
index 070b874b..ac554f1a 100644
--- a/src/randstrobes.hpp
+++ b/src/randstrobes.hpp
@@ -126,7 +126,7 @@ class RandstrobeIterator {
     }
 
     bool has_next() {
-        return strobe1_index + w_min < syncmers.size();
+        return strobe1_index < syncmers.size();
     }
 
 private: