From 503a06f1ce709b6377d670f07b282f2520aed9a9 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Mon, 8 Jan 2024 14:46:16 -0800
Subject: [PATCH 1/2] xcounts.cpp and counts_header.hpp and cpp: fixing a typo
 in a function name

---
 src/common/counts_header.cpp | 6 +++---
 src/common/counts_header.hpp | 6 +++---
 src/utils/xcounts.cpp        | 5 ++---
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/common/counts_header.cpp b/src/common/counts_header.cpp
index e6a814b0..051eb89e 100644
--- a/src/common/counts_header.cpp
+++ b/src/common/counts_header.cpp
@@ -38,9 +38,9 @@ using std::to_string;
 using bamxx::bgzf_file;
 
 void
-write_counts_header_from_chom_sizes(const vector<string> &chrom_names,
-                                    const vector<uint64_t> &chrom_sizes,
-                                    bgzf_file &out) {
+write_counts_header_from_chrom_sizes(const vector<string> &chrom_names,
+                                     const vector<uint64_t> &chrom_sizes,
+                                     bgzf_file &out) {
   const auto version = "#DNMTOOLS " + string(VERSION) + "\n";
   out.write(version.c_str());
   for (auto i = 0u; i < size(chrom_sizes); ++i) {
diff --git a/src/common/counts_header.hpp b/src/common/counts_header.hpp
index 171eff28..bb3f851b 100644
--- a/src/common/counts_header.hpp
+++ b/src/common/counts_header.hpp
@@ -26,9 +26,9 @@
 #include "bamxx.hpp"
 
 void
-write_counts_header_from_chom_sizes(const std::vector<std::string> &chrom_names,
-                                    const std::vector<uint64_t> &chrom_sizes,
-                                    bamxx::bgzf_file &out);
+write_counts_header_from_chrom_sizes(const std::vector<std::string> &chrom_names,
+                                     const std::vector<uint64_t> &chrom_sizes,
+                                     bamxx::bgzf_file &out);
 
 // returns -1 on failure, 0 on success
 int
diff --git a/src/utils/xcounts.cpp b/src/utils/xcounts.cpp
index ab271e6b..372f970e 100644
--- a/src/utils/xcounts.cpp
+++ b/src/utils/xcounts.cpp
@@ -1,5 +1,5 @@
 /* xcounts: reformat counts so they only give the m and u counts in a
- * wig format
+ * dynamic step wig format
  *
  * Copyright (C) 2023 Andrew D. Smith
  *
@@ -145,14 +145,13 @@ main_xcounts(int argc, const char **argv) {
     if (!out) throw dnmt_error("error opening output file: " + outfile);
 
     if (n_threads > 1) {
-      // ADS: something breaks when we use the thread for the input
       if (in.is_bgzf())
         tpool.set_io(in);
       tpool.set_io(out);
     }
 
     if (!genome_file.empty())
-      write_counts_header_from_chom_sizes(chrom_names, chrom_sizes, out);
+      write_counts_header_from_chrom_sizes(chrom_names, chrom_sizes, out);
 
     // use the kstring_t type to more directly use the BGZF file
     kstring_t line{0, 0, nullptr};

From d100541fa7be08e31cfeb4045d093f32b2b4ee6d Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Mon, 8 Jan 2024 14:58:28 -0800
Subject: [PATCH 2/2] pmd.cpp: if the fraction of bins passing after finding a
 bin size by the dynamic method is still not high enough, the bin size is set
 to numeric limits max

---
 src/analysis/pmd.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/analysis/pmd.cpp b/src/analysis/pmd.cpp
index 07c3e3b1..f8e3b047 100644
--- a/src/analysis/pmd.cpp
+++ b/src/analysis/pmd.cpp
@@ -1064,8 +1064,7 @@ binsize_selection(const size_t resolution, const size_t min_bin_sz,
     if (frac_passed < min_frac_passed)
       bin_size += resolution;
   }
-  return frac_passed <= num_lim<double>::min() ?
-    num_lim<size_t>::max() : bin_size;
+  return frac_passed < min_frac_passed ? num_lim<size_t>::max() : bin_size;
 }