Merge pull request #1067 from jmarshall/gcc-13

Fix various GCC 13 warnings and errors
arq5x · Oct 30, 2023 · 1bae92c · 1bae92c
2 parents 07533e9 + b1dae36
commit 1bae92c
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Showing 5 changed files with 7 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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] = '-';