From 935486c72589910b311d4cfdbff10dc2d3cda03f Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sat, 2 Dec 2023 20:23:56 -0800
Subject: [PATCH 1/3] updating submodule bamxx

---
 src/bamxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bamxx b/src/bamxx
index a9bf1878..09cfe360 160000
--- a/src/bamxx
+++ b/src/bamxx
@@ -1 +1 @@
-Subproject commit a9bf1878022235cdb331880957eff55889845315
+Subproject commit 09cfe360be875271014b2824fecd8b732e640630

From 06a032867e72e11f2f3479621ac7042ef36f5615 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sat, 2 Dec 2023 20:24:18 -0800
Subject: [PATCH 2/3] covered: using input file compression mode to determine
 output file compression mode

---
 src/utils/covered.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/utils/covered.cpp b/src/utils/covered.cpp
index 9f9f5927..0147bc88 100644
--- a/src/utils/covered.cpp
+++ b/src/utils/covered.cpp
@@ -118,12 +118,15 @@ main_covered(int argc, const char **argv) {
     bgzf_file in(filename, "r");
     if (!in) throw runtime_error("could not open file: " + filename);
 
-    bgzf_file out(outfile, "w");
+
+    const auto outfile_mode = in.compression() ? "w" : "wu";
+
+    bgzf_file out(outfile, outfile_mode);
     if (!out) throw runtime_error("error opening output file: " + outfile);
 
     if (n_threads > 1) {
       // ADS: something breaks when we use the thread for the input
-      // tpool.set_io(in);
+      tpool.set_io(in);
       tpool.set_io(out);
     }
 

From b5f987c123fad4c5ddfd4208e21c84f1640a56fd Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sat, 2 Dec 2023 20:31:00 -0800
Subject: [PATCH 3/3] covered.cpp: formatting

---
 src/utils/covered.cpp | 32 +++++++++++++-------------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/src/utils/covered.cpp b/src/utils/covered.cpp
index 0147bc88..0ce1c916 100644
--- a/src/utils/covered.cpp
+++ b/src/utils/covered.cpp
@@ -15,26 +15,26 @@
  * General Public License for more details.
  */
 
-#include <string>
-#include <vector>
+#include <bamxx.hpp>
+
 #include <iostream>
 #include <stdexcept>
-#include <bamxx.hpp>
+#include <string>
+#include <vector>
 
 // from smithlab_cpp
 #include "OptionParser.hpp"
-#include "smithlab_utils.hpp"
 #include "smithlab_os.hpp"
+#include "smithlab_utils.hpp"
 
-using std::string;
-using std::cout;
 using std::cerr;
+using std::cout;
 using std::endl;
 using std::runtime_error;
+using std::string;
 
 using bamxx::bgzf_file;
 
-
 inline auto
 getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
   if (file.f == nullptr) return file;
@@ -54,30 +54,25 @@ getline(bgzf_file &file, kstring_t &line) -> bgzf_file & {
   return file;
 }
 
-
-static inline
-bool get_is_mutated(const kstring_t &line) {
+static inline bool
+get_is_mutated(const kstring_t &line) {
   const auto end_itr = line.s + line.l;
   return std::find(line.s, end_itr, 'x') != end_itr;
 }
 
-
-static inline
-uint32_t get_n_reads(const kstring_t &line) {
+static inline uint32_t
+get_n_reads(const kstring_t &line) {
   const auto end_itr = std::make_reverse_iterator(line.s + line.l);
   const auto beg_itr = std::make_reverse_iterator(line.s);
-  auto n_reads_pos = std::find_if(end_itr, beg_itr, [](const char c) {
-    return c == ' ' || c == '\t';
-  });
+  auto n_reads_pos = std::find_if(
+    end_itr, beg_itr, [](const char c) { return c == ' ' || c == '\t'; });
   ++n_reads_pos;
   return atoi(n_reads_pos.base());
 }
 
-
 int
 main_covered(int argc, const char **argv) {
   try {
-
     size_t n_threads = 1;
 
     string outfile{"-"};
@@ -118,7 +113,6 @@ main_covered(int argc, const char **argv) {
     bgzf_file in(filename, "r");
     if (!in) throw runtime_error("could not open file: " + filename);
 
-
     const auto outfile_mode = in.compression() ? "w" : "wu";
 
     bgzf_file out(outfile, outfile_mode);