https://github.com/arq5x/bedtools2/pull/1087

From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Thu, 25 Apr 2024 11:18:48 +0200
Subject: [PATCH] Add missing `stdint.h` includes

* Musl is a lot stricter with transitive includes:
  Bug: https://bugs.gentoo.org/907971
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -22,6 +22,7 @@ using namespace BamTools;
 #include <sstream>
 #include <fstream>
 #include <stdlib.h>
+#include <stdint.h>
 
 using namespace std;
 
--- a/src/clusterBed/clusterBed.cpp
+++ b/src/clusterBed/clusterBed.cpp
@@ -12,6 +12,8 @@
 #include "lineFileUtilities.h"
 #include "clusterBed.h"
 
+#include <stdint.h>
+
 // = Constructor =
 BedCluster::BedCluster(string &bedFile, 
                    int  maxDistance, 
--- a/src/pairToBed/pairToBed.h
+++ b/src/pairToBed/pairToBed.h
@@ -22,6 +22,7 @@ using namespace BamTools;
 #include <vector>
 #include <iostream>
 #include <fstream>
+#include <stdint.h>
 
 using namespace std;
 
--- a/src/randomBed/randomBed.h
+++ b/src/randomBed/randomBed.h
@@ -22,6 +22,7 @@
 #include <unistd.h>
 #include <sys/types.h>
 #include <algorithm>  // for binary search
+#include <stdint.h>
 using namespace std;
 
 const int MAX_TRIES = 1000000;
--- a/src/summaryFile/summaryFile.h
+++ b/src/summaryFile/summaryFile.h
@@ -12,6 +12,8 @@
 #include "ToolBase.h"
 #include "ContextSummary.h"
 
+#include <stdint.h>
+
 struct Interval {
   CHRPOS start;
   CHRPOS end;
--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp
+++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp
@@ -1,3 +1,4 @@
+#include <stdint.h>
 
 struct _RefID_t {
     operator int32_t() const {return (int32_t)(_ptr()->core.tid);}
--- a/src/utils/BamTools/include/api/BamAux.h
+++ b/src/utils/BamTools/include/api/BamAux.h
@@ -1,4 +1,5 @@
 #include <string>
+#include <stdint.h>
 
 #ifndef BAMAUX_H
 #define BAMAUX_H
--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
@@ -9,6 +9,7 @@
 #define SINGLELINETEXTFILEREADER_H_
 
 #include <algorithm>
+#include <stdint.h>
 #include "FileReader.h"
 #include "string.h"
 #include "lineFileUtilities.h"
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -10,6 +10,8 @@
 #include "BamFileReader.h"
 #include "RecordKeyVector.h"
 
+#include <stdint.h>
+
 BamRecord::BamRecord()
 : _bamChromId(-1)
 {
--- a/src/utils/GenomeFile/GenomeFile.h
+++ b/src/utils/GenomeFile/GenomeFile.h
@@ -19,6 +19,7 @@
 #include <fstream>
 #include <cstring>
 #include <cstdio>
+#include <stdint.h>
 #include <algorithm> // for bsearch lower_bound()
 #include "api/BamReader.h"
 #include "api/BamAux.h"
--- a/src/utils/GenomeFile/NewGenomeFile.h
+++ b/src/utils/GenomeFile/NewGenomeFile.h
@@ -14,6 +14,7 @@
 #define NEW_GENOMEFILE_H
 
 #include <algorithm> // for bsearch lower_bound()
+#include <stdint.h>
 
 #include "BedtoolsTypes.h"
 
--- a/src/utils/bedFilePE/bedFilePE.h
+++ b/src/utils/bedFilePE/bedFilePE.h
@@ -8,6 +8,7 @@
 #include <fstream>
 #include <sstream>
 #include <cstring>
+#include <stdint.h>
 #include <algorithm>
 #include "bedFile.h"
 #include "lineFileUtilities.h"
--- a/src/utils/general/ParseTools.cpp
+++ b/src/utils/general/ParseTools.cpp
@@ -2,7 +2,7 @@
 #include <climits>
 #include <cctype>
 #include <cstring>
-#include <cstdint>
+#include <stdint.h>
 #include <cstdio>
 #include <cstdlib>
 #include <sstream>
--- a/src/utils/lineFileUtilities/lineFileUtilities.h
+++ b/src/utils/lineFileUtilities/lineFileUtilities.h
@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include <cstring>
+#include <stdint.h>
 #include <cstdlib>
 #include <sstream>
 #include <iostream>
--- a/src/utils/sequenceUtilities/sequenceUtils.h
+++ b/src/utils/sequenceUtilities/sequenceUtils.h
@@ -4,6 +4,7 @@
 #include <string>
 #include <algorithm>
 #include <cctype>
+#include <stdint.h>
 
 using namespace std;
 
--- a/src/windowMaker/windowMaker.h
+++ b/src/windowMaker/windowMaker.h
@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
 #include "NewGenomeFile.h"
 #include "bedFile.h"
 
+#include <stdint.h>
+
 using namespace std;
 
 
--- a/src/windowMaker/windowMakerMain.cpp
+++ b/src/windowMaker/windowMakerMain.cpp
@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
 #include "windowMaker.h"
 #include "version.h"
 
+#include <stdint.h>
+
 using namespace std;
 
 // define our program name