From b1dae36165f1839ad0c64376fc7c5ba7dd3b077b Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Tue, 24 Oct 2023 19:15:42 +1300
Subject: [PATCH] Fix various GCC 13 warnings and errors

Due to improvements in system and/or compiler header cleanliness,
where previously ParseTools.{cpp,h}'s headers have included <cstdint>
as a byproduct, this no longer occurs. Hence:
 - Ordinary unsigned is appropriate for the int2str() variable anyway;
 - Get CHRPOS from BedtoolsTypes.h instead of typedeffing it ourselves;
 - ParseTools.cpp's isHeaderLine() does use uint32_t, so include <cstdint>
   from the .cpp file for good measure.

Assignment operators should not be virtual (avoids "Record::operator=
was hidden" warnings). List member initialisers in the same order in
which they are declared (avoids "_testLastQueryRec will be initialized
after _runToDbEnd" warnings).
---
 src/utils/FileRecordTools/Records/Record.h | 2 +-
 src/utils/NewChromsweep/NewChromsweep.cpp  | 4 ++--
 src/utils/NewChromsweep/NewChromsweep.h    | 3 +--
 src/utils/general/ParseTools.cpp           | 1 +
 src/utils/general/ParseTools.h             | 5 ++---
 5 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index d38f6d3f..c651ac8c 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -73,7 +73,7 @@ class Record {
 	virtual void printNull(string &) const {}
 	friend ostream &operator << (ostream &out, const Record &record);
 
-	virtual const Record & operator=(const Record &);
+	const Record & operator=(const Record &);
 
 	virtual bool isZeroBased() const {return true;};
 
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index f73266e0..bb3df612 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -26,11 +26,11 @@ NewChromSweep::NewChromSweep(ContextIntersect *context)
      _wasInitialized(false),
      _currQueryRec(NULL),
      _runToQueryEnd(_context->getRunToQueryEnd()),
+     _runToDbEnd(false),
      _lexicoDisproven(false),
      _lexicoAssumed(false),
      _lexicoAssumedFileIdx(-1),
-     _testLastQueryRec(false),
-     _runToDbEnd(false)
+     _testLastQueryRec(false)
 {
 	_filePrevChrom.resize(_numFiles);
 	_runToDbEnd = context->shouldRunToDbEnd();
diff --git a/src/utils/NewChromsweep/NewChromsweep.h b/src/utils/NewChromsweep/NewChromsweep.h
index 5a89a784..90392d6b 100644
--- a/src/utils/NewChromsweep/NewChromsweep.h
+++ b/src/utils/NewChromsweep/NewChromsweep.h
@@ -90,8 +90,7 @@ class NewChromSweep {
     string _currQueryChromName;
     string _prevQueryChromName;
     bool _runToQueryEnd;
-	bool _runToDbEnd;
-
+    bool _runToDbEnd;
 
     virtual void masterScan(RecordKeyVector &retList);
 
diff --git a/src/utils/general/ParseTools.cpp b/src/utils/general/ParseTools.cpp
index 7850a02a..ad43bcd9 100644
--- a/src/utils/general/ParseTools.cpp
+++ b/src/utils/general/ParseTools.cpp
@@ -2,6 +2,7 @@
 #include <climits>
 #include <cctype>
 #include <cstring>
+#include <cstdint>
 #include <cstdio>
 #include <cstdlib>
 #include <sstream>
diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
index e056c149..6b8fe76d 100644
--- a/src/utils/general/ParseTools.h
+++ b/src/utils/general/ParseTools.h
@@ -16,11 +16,10 @@
 #include "string.h"
 #include <cstdio>
 #include <cstdlib>
+#include "BedtoolsTypes.h"
 
 using namespace std;
 
-typedef int64_t CHRPOS;
-
 bool isNumeric(const string &str);
 bool isInteger(const string &str);
 
@@ -54,7 +53,7 @@ void int2str(U number, T& buffer, bool appendToBuf = false)
 
 	bool neg = number < 0;
 	if(neg) number = -number;
-	uint32_t n;
+	unsigned int n;
 	for(n = 0; number; number /= 10)
 		tmp[12 - ++n] = number % 10 + '0';
 	if(neg) tmp[12 - ++n] = '-';