Add syncmers at the ends of reads as seeds without auxiliary hash

Increases the number of seeds per read by 2*w_min seeds
ksahlin · Oct 3, 2024 · 701c472 · 701c472
1 parent b6dffd1
commit 701c472
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Showing 2 changed files with 10 additions and 1 deletion.
diff --git a/src/randstrobes.cpp b/src/randstrobes.cpp
@@ -169,6 +169,15 @@ 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
@@ -126,7 +126,7 @@ class RandstrobeIterator {
     }
 
     bool has_next() {
-        return strobe1_index + w_min < syncmers.size();
+        return strobe1_index < syncmers.size();
     }
 
 private: