diff options
Diffstat (limited to 'sci-biology/bedtools/files/bedtools-2.31.1-includes.patch')
-rw-r--r-- | sci-biology/bedtools/files/bedtools-2.31.1-includes.patch | 178 |
1 files changed, 178 insertions, 0 deletions
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch new file mode 100644 index 000000000000..1b0a9f0849ed --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch @@ -0,0 +1,178 @@ +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 |