fix(chain): count decoy hits in fillMemCollection (decoy/transcript equal footing)

findOptChain early-returns `if (maxHits == 0)` and builds no chains. maxHits came
from fillMemCollection, which returned `maxNonDecoyHits` — the max MEM-hit count
over *non-decoy* references only. A mate that maps ONLY to a decoy (e.g. the
intronic mate of a genomic / pre-mRNA fragment, which maps uniquely to the genome
and to no transcript) therefore returned 0 and was given no chains at all. It
could never form the concordant decoy pair its (exonic) mate participates in, so
the genomic fragment leaked through as a spurious single-mate transcript orphan
instead of being attributed to the decoy.

Count hits over ALL references (transcript and decoy) so the two are chained on
equal footing — matching the salmon Rust implementation, whose chaining/consensus
considers decoy and transcript candidates together. At the default
FILTER_AFTER_CHAINING policy the only behavioral change is that decoy-only mates
are now chained (and can pair); transcript-only reads are unaffected.

Validated on SRR1039508 + GRCh38 decoy index: a fragment with one exonic mate
(maps to transcript+genome) and one intronic mate (genome only) now forms the
concordant genome pair and is correctly counted as decoy. On the 3M-read subset
C++ goes from 94.019% mapped / 42,044 decoy to 93.742% / 154,800 — matching the
Rust port's 93.749% / 154,284 (was a 0.27-pt over-report of transcript mappings).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01B7JMur5DmDpECddErpi2JS

Author: rob-p

src/MemChainer.cpp

@@ -71,7 +71,17 @@ size_t MemClusterer::fillMemCollection(std::vector<std::pair<int, pufferfish::ut
     return 0;
   }
 
-  size_t maxNonDecoyHits{0};
+  // Max MEM-hit count over ALL references (transcript AND decoy), so transcript
+  // and decoy targets are chained on equal footing. Previously this counted only
+  // non-decoy references, so a mate mapping *only* to a decoy (e.g. an intronic
+  // read of a genomic / pre-mRNA fragment) returned 0 here, and findOptChain's
+  // `if (maxHits == 0) return false` then built it no chains at all — so it could
+  // never form the concordant decoy pair its mate participates in, and the
+  // genomic fragment leaked through as a spurious transcript orphan. Counting
+  // decoy hits equally lets such a mate be chained and paired (matching the Rust
+  // implementation, whose chaining/consensus considers decoy and transcript
+  // candidates together).
+  size_t maxHits{0};
   size_t totSize{0};
   for (auto &hit : core::range<decltype(hits.begin())>(hits.begin(), hits.end())) {
     auto &refs = hit.second.refRange;
@@ -104,12 +114,13 @@ size_t MemClusterer::fillMemCollection(std::vector<std::pair<int, pufferfish::ut
         auto& refHits = trMemMap[encodeRefKey(tid, refPosOri.isFW)];
         refHits.emplace_back(memItr, refPosOri.pos, refPosOri.isFW);
         auto nh = refHits.size();
-        maxNonDecoyHits = (tid < firstDecoyIndex) ? std::max(nh, maxNonDecoyHits) : maxNonDecoyHits;
+        maxHits = std::max(nh, maxHits);
       //}
       }
     }
   }
-  return maxNonDecoyHits;
+  (void)firstDecoyIndex; // no longer used to gate hit counting (see maxHits above)
+  return maxHits;
 }
 
 bool MemClusterer::findOptChain(std::vector<std::pair<int, pufferfish::util::ProjectedHits>> &hits,