Penalize far apart pairs not more than as if they were two single ends

See #321

CHANGES.md

@@ -5,6 +5,9 @@
 * #293: Fix: When mapping single-end reads, many multimappers were previously
   assigned a high mapping quality. They now get assigned mapping quality zero
   as intended.
+* #321: Fix: For paired-end reads that cannot be placed as proper pairs, we now
+  prefer placing them onto the same chrosome instead of on different ones if
+  there is a choice.
 * #318: Added a `--details` option mainly intended for debugging. When used,
   some strobealign-specific tags are added to the SAM output that inform about
   things like no. of seeds found, whether mate rescue was performed etc.

src/aln.cpp

@@ -910,7 +910,7 @@ inline void align_PE(
         if (r1_r2 || r2_r1) {
             // Treat a1/a2 as a pair
             float x = std::abs(a1.ref_start - a2.ref_start);
-            combined_score = (double)a1.score + (double)a2.score + log(normal_pdf(x, mu, sigma));
+            combined_score = (double)a1.score + (double)a2.score + std::max(-20.0f + 0.001f, log(normal_pdf(x, mu, sigma)));
             //* (1 - s2 / s1) * min_matches * log(s1);
         } else {
             // Treat a1/a2 as two single-end reads