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181 lines
4.4 KiB
181 lines
4.4 KiB
https://github.com/arq5x/bedtools2/pull/1087
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From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001
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From: David Seifert <soap@gentoo.org>
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Date: Thu, 25 Apr 2024 11:18:48 +0200
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Subject: [PATCH] Add missing `stdint.h` includes
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* Musl is a lot stricter with transitive includes:
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Bug: https://bugs.gentoo.org/907971
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--- a/src/bamToBed/bamToBed.cpp
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+++ b/src/bamToBed/bamToBed.cpp
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@@ -22,6 +22,7 @@ using namespace BamTools;
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#include <sstream>
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#include <fstream>
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#include <stdlib.h>
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+#include <stdint.h>
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using namespace std;
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--- a/src/clusterBed/clusterBed.cpp
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+++ b/src/clusterBed/clusterBed.cpp
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@@ -12,6 +12,8 @@
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#include "lineFileUtilities.h"
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#include "clusterBed.h"
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+#include <stdint.h>
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+
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// = Constructor =
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BedCluster::BedCluster(string &bedFile,
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int maxDistance,
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--- a/src/pairToBed/pairToBed.h
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+++ b/src/pairToBed/pairToBed.h
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@@ -22,6 +22,7 @@ using namespace BamTools;
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#include <vector>
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#include <iostream>
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#include <fstream>
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+#include <stdint.h>
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using namespace std;
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--- a/src/randomBed/randomBed.h
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+++ b/src/randomBed/randomBed.h
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@@ -22,6 +22,7 @@
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#include <unistd.h>
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#include <sys/types.h>
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#include <algorithm> // for binary search
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+#include <stdint.h>
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using namespace std;
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const int MAX_TRIES = 1000000;
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--- a/src/summaryFile/summaryFile.h
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+++ b/src/summaryFile/summaryFile.h
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@@ -12,6 +12,8 @@
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#include "ToolBase.h"
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#include "ContextSummary.h"
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+#include <stdint.h>
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+
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struct Interval {
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CHRPOS start;
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CHRPOS end;
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--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp
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+++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp
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@@ -1,3 +1,4 @@
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+#include <stdint.h>
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struct _RefID_t {
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operator int32_t() const {return (int32_t)(_ptr()->core.tid);}
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--- a/src/utils/BamTools/include/api/BamAux.h
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+++ b/src/utils/BamTools/include/api/BamAux.h
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@@ -1,4 +1,5 @@
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#include <string>
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+#include <stdint.h>
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#ifndef BAMAUX_H
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#define BAMAUX_H
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--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
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+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
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@@ -9,6 +9,7 @@
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#define SINGLELINETEXTFILEREADER_H_
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#include <algorithm>
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+#include <stdint.h>
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#include "FileReader.h"
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#include "string.h"
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#include "lineFileUtilities.h"
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--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
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+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
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@@ -10,6 +10,8 @@
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#include "BamFileReader.h"
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#include "RecordKeyVector.h"
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+#include <stdint.h>
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+
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BamRecord::BamRecord()
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: _bamChromId(-1)
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{
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--- a/src/utils/GenomeFile/GenomeFile.h
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+++ b/src/utils/GenomeFile/GenomeFile.h
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@@ -19,6 +19,7 @@
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#include <fstream>
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#include <cstring>
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#include <cstdio>
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+#include <stdint.h>
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#include <algorithm> // for bsearch lower_bound()
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#include "api/BamReader.h"
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#include "api/BamAux.h"
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--- a/src/utils/GenomeFile/NewGenomeFile.h
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+++ b/src/utils/GenomeFile/NewGenomeFile.h
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@@ -14,6 +14,7 @@
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#define NEW_GENOMEFILE_H
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#include <algorithm> // for bsearch lower_bound()
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+#include <stdint.h>
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#include "BedtoolsTypes.h"
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--- a/src/utils/bedFilePE/bedFilePE.h
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+++ b/src/utils/bedFilePE/bedFilePE.h
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@@ -8,6 +8,7 @@
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#include <fstream>
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#include <sstream>
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#include <cstring>
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+#include <stdint.h>
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#include <algorithm>
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#include "bedFile.h"
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#include "lineFileUtilities.h"
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--- a/src/utils/general/ParseTools.cpp
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+++ b/src/utils/general/ParseTools.cpp
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@@ -2,7 +2,7 @@
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#include <climits>
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#include <cctype>
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#include <cstring>
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-#include <cstdint>
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+#include <stdint.h>
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#include <cstdio>
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#include <cstdlib>
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#include <sstream>
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--- a/src/utils/lineFileUtilities/lineFileUtilities.h
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+++ b/src/utils/lineFileUtilities/lineFileUtilities.h
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@@ -4,6 +4,7 @@
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#include <vector>
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#include <string>
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#include <cstring>
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+#include <stdint.h>
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#include <cstdlib>
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#include <sstream>
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#include <iostream>
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--- a/src/utils/sequenceUtilities/sequenceUtils.h
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+++ b/src/utils/sequenceUtilities/sequenceUtils.h
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@@ -4,6 +4,7 @@
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#include <string>
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#include <algorithm>
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#include <cctype>
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+#include <stdint.h>
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using namespace std;
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--- a/src/windowMaker/windowMaker.h
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+++ b/src/windowMaker/windowMaker.h
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@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
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#include "NewGenomeFile.h"
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#include "bedFile.h"
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+#include <stdint.h>
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+
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using namespace std;
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--- a/src/windowMaker/windowMakerMain.cpp
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+++ b/src/windowMaker/windowMakerMain.cpp
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@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
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#include "windowMaker.h"
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#include "version.h"
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+#include <stdint.h>
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+
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using namespace std;
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// define our program name
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