From 847f4c23bc80ce9a1d35eacc8cfd1a7c3b47349c Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Fri, 7 Aug 2026 16:03:30 -0700
Subject: [PATCH 1/3] src/simreads.cpp: the condition on require-value, which
 requires all sampled reads have all bases non-N, was inverted

---
 src/simreads.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/simreads.cpp b/src/simreads.cpp
index 592e91e..2e67769 100644
--- a/src/simreads.cpp
+++ b/src/simreads.cpp
@@ -283,7 +283,7 @@ sim_frag_position(const std::string &genome, const std::size_t frag_len,
   // NOLINTBEGIN(*-narrowing-conversions)
   the_frag = std::string(g_beg + the_posn, g_beg + the_posn + frag_len);
   while (require_valid &&
-         std::all_of(std::cbegin(the_frag), std::cend(the_frag), is_valid)) {
+         !std::all_of(std::cbegin(the_frag), std::cend(the_frag), is_valid)) {
     the_posn = simreads_random::rand() % lim;
     the_frag = std::string(g_beg + the_posn, g_beg + the_posn + frag_len);
   }

From baa8f75291497c2b015b4d9aae8964af99e815c3 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Fri, 7 Aug 2026 17:51:56 -0700
Subject: [PATCH 2/3] src/simreads.cpp: setting default quality scores to be
 good qualty

---
 src/simreads.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/simreads.cpp b/src/simreads.cpp
index 2e67769..d00fd67 100644
--- a/src/simreads.cpp
+++ b/src/simreads.cpp
@@ -81,6 +81,7 @@ rand_double() -> double {  // ADS: in the interval [0, 1]
 static inline auto
 format_fastq_record(const std::string &name,
                     const std::string &read) -> std::string {
+  static constexpr auto assumed_quality_score = 63;
   assert(!name.empty());
   std::string s;
   s += '@';
@@ -88,7 +89,7 @@ format_fastq_record(const std::string &name,
   s += '\n';
   s += read;
   s += "\n+\n";
-  s += std::string(std::size(read), 'B');
+  s += std::string(std::size(read), assumed_quality_score);
   return s;
 }
 

From 14b7c2ec006fa5552dd11ed9a092e0ca1411b60c Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Fri, 7 Aug 2026 18:02:32 -0700
Subject: [PATCH 3/3] src/abismal.cpp: removing extra semicolon caught by
 compiler

---
 src/abismal.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/abismal.cpp b/src/abismal.cpp
index d87c92f..c0cb01b 100644
--- a/src/abismal.cpp
+++ b/src/abismal.cpp
@@ -1067,7 +1067,7 @@ struct paired_end_mapping_statistics {
     return oss.str();
   }
   NLOHMANN_DEFINE_TYPE_INTRUSIVE(paired_end_mapping_statistics, read_pair_stats,
-                                 end1_stats, end2_stats);
+                                 end1_stats, end2_stats)
 };
 
 static void