allow python from environment and missing includes on musl

src/bamToBed/bamToBed.cpp

@@ -22,6 +22,7 @@ using namespace BamTools;
 #include <sstream>
 #include <fstream>
 #include <stdlib.h>
+#include <stdint.h>
 
 using namespace std;
 

src/clusterBed/clusterBed.cpp

@@ -12,6 +12,8 @@
 #include "lineFileUtilities.h"
 #include "clusterBed.h"
 
+#include <stdint.h>
+
 // = Constructor =
 BedCluster::BedCluster(string &bedFile, 
                    int  maxDistance, 

src/pairToBed/pairToBed.h

@@ -22,6 +22,7 @@ using namespace BamTools;
 #include <vector>
 #include <iostream>
 #include <fstream>
+#include <stdint.h>
 
 using namespace std;
 

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;

src/summaryFile/summaryFile.h

@@ -12,6 +12,8 @@
 #include "ToolBase.h"
 #include "ContextSummary.h"
 
+#include <stdint.h>
+
 struct Interval {
   CHRPOS start;
   CHRPOS end;

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);}

src/utils/BamTools/include/api/BamAux.h

@@ -1,4 +1,5 @@
 #include <string>
+#include <stdint.h>
 
 #ifndef BAMAUX_H
 #define BAMAUX_H

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"

src/utils/FileRecordTools/Records/BamRecord.cpp

@@ -10,6 +10,8 @@
 #include "BamFileReader.h"
 #include "RecordKeyVector.h"
 
+#include <stdint.h>
+
 BamRecord::BamRecord()
 : _bamChromId(-1)
 {

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"

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"
 

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"

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>

src/utils/lineFileUtilities/lineFileUtilities.h

@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include <cstring>
+#include <stdint.h>
 #include <cstdlib>
 #include <sstream>
 #include <iostream>

src/utils/sequenceUtilities/sequenceUtils.h

@@ -4,6 +4,7 @@
 #include <string>
 #include <algorithm>
 #include <cctype>
+#include <stdint.h>
 
 using namespace std;
 

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;
 
 

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

test/bigchroms/test-bigchroms.sh

@@ -28,7 +28,7 @@ check obs abig.bed
 rm obs
 
 if [[ "$BT_NO_BIG_FILES" != "" ]]; then
-python make-big-chrom.py
+${PYTHON:-python} make-big-chrom.py
 
 echo -e "    bigchroms.t03...big get fasta \c"
 $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs

test/fisher/cmp.sh

@@ -3,7 +3,7 @@ set -eo pipefail
 echo "fisher,shuffled"
 
 for i in $(seq 1000); do
-    fisher=$(python ./sim.py | tail -1 | cut -f 2)
+    fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2)
     shuffle=$(bash shuf.sh)
     echo "$fisher,$shuffle"
 done

test/genomecov/test-genomecov.sh

@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs
 check obs exp
 rm obs exp
 
-python mk-deep.py > deep.sam
+${PYTHON:-python} mk-deep.py > deep.sam
 echo -e "    genomecov.t18...\c"
 echo "c1	1	1000000" > exp
 $BT genomecov -d -ibam deep.sam | head -1 > obs