.travis.yml

@@ -15,5 +15,5 @@ install:
   - if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -qq g++-4.8; fi; fi
   - if [[ "$CXX" == "g++" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50; fi; fi
 script: 
-  - if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make all; fi; fi
-  - if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make all; fi; fi
\ No newline at end of file
+  - if [[ "$CC" == "gcc" ]]; then if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then make all; make install_all; fi; fi
+  - if [[ "$CC" == "clang" ]]; then if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make all; make install_all; fi; fi

Makefile

@@ -22,7 +22,7 @@ WRAPPERS               = $(wildcard ${APPDIR}/conversion/src/wrappers/*)
 CWD                   := $(shell pwd)
 BINDIR                 = bin
 BINDIR_MODULE          = modules
-
+export DESTBINDIR      = .
 
 default:
 ifeq ($(KERNEL), Darwin)
@@ -45,7 +45,7 @@ all:
 	$(MAKE) megarow -f ${SELF}
 	$(MAKE) float128 -f ${SELF}
 	$(MAKE) install_all -f ${SELF}
-	$(MAKE) symlink_typical -f ${SELF}
+	$(MAKE) symlink_post_install_all -f ${SELF}
 
 module_all:
 	$(MAKE) support -f ${SELF}
@@ -64,6 +64,9 @@ megarow:
 typical:
 	$(MAKE) BINARY_TYPE=$(TYPICAL) -f ${SELF}
 
+symlink_post_install_all:
+	cd ${BINDIR} && ./switch-BEDOPS-binary-type --typical . && cd ${CWD}
+
 symlink_typical:
 	$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
 	for SRCNAME in ${SRCNAMES}; do \
@@ -242,7 +245,7 @@ install_starch_scripts_all: prep_c
 install_conversion_scripts: prep_c
 	cp $(WRAPPERS) ${BINDIR}
 
-.PHONY: $(WRAPPERS)
+.PHONY: $(WRAPPERS) tests
 
 install_conversion_scripts_all: $(WRAPPERS)
 
@@ -396,6 +399,9 @@ else
 	find . -exec sed -i "s/"$$OLD_CPD"/"$$NEW_CPD"/g" {} \;
 endif
 
+#######################
+# packaging
+
 docker: packaging/docker/Dockerfile
 	docker build -t bedops -f packaging/docker/Dockerfile  .
 
@@ -404,3 +410,9 @@ rpm: packaging/rpm/Dockerfile
 
 deb: packaging/deb/Dockerfile
 	docker build -t bedops:deb -f packaging/deb/Dockerfile .
+
+#######################
+# tests
+
+tests:
+	$(MAKE) all -f tests/Makefile

README.md

-## BEDOPS v2.4.35: high-performance genomic feature operations ##
+## BEDOPS v2.4.36: high-performance genomic feature operations ##
 
 [![Build Status](https://travis-ci.org/bedops/bedops.svg?branch=master)](https://travis-ci.org/bedops/bedops) [![GitHub stars](https://img.shields.io/github/stars/bedops/bedops.svg)](https://github.com/bedops/bedops/stargazers) [![Project license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://github.com/bedops/bedops/blob/master/LICENSE) [![Documentation Status](https://readthedocs.org/projects/bedops/badge/?version=latest)](https://readthedocs.org/projects/bedops/?badge=latest)
 
@@ -6,9 +6,9 @@
 
 ### About ###
 
-**BEDOPS v2.4.35** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. 
+**BEDOPS v2.4.36** is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data. 
 
-The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.35** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
+The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overview">overview</a> section of the **BEDOPS v2.4.36** documentation summarizes the toolkit, functionality and performance enhancements. The <a href="https://bedops.readthedocs.io/en/latest/index.html#reference">reference</a> table offers documentation for all applications and scripts.
 
 
 ### Downloads ###
@@ -28,20 +28,20 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
 <tr>
 <td valign="top">
 <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
-<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2">x86-64 (64-bit)</a> binaries</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/bedops_linux_x86_64-v2.4.36.tar.bz2">x86-64 (64-bit)</a> binaries</li>
 <li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#linux">Installation instructions</a> for Linux hosts</li>
 </ul>
 </td>
 <td valign="top">
 <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
-<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.35/BEDOPS.2.4.35.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
+<li><a href="https://github.com/bedops/bedops/releases/download/v2.4.36/BEDOPS.2.4.36.pkg.zip">Intel (64-bit, 10.10-10.13)</a> installer package</li>
 <li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#mac-os-x">Installation instructions</a> for Mac OS X hosts</li>
 </ul>
 </td>
 <td valign="top">
 <ul style="list-style-type:square; font-size:smaller; margin-left:0; margin-right:0px; padding-right:0px; padding-left:20px;">
-<li><a href="https://github.com/bedops/bedops/archive/v2.4.35.tar.gz">Source code</a> (tar.gz)</li>
-<li><a href="https://github.com/bedops/bedops/archive/v2.4.35.zip">Source code</a> (zip)</li>
+<li><a href="https://github.com/bedops/bedops/archive/v2.4.36.tar.gz">Source code</a> (tar.gz)</li>
+<li><a href="https://github.com/bedops/bedops/archive/v2.4.36.zip">Source code</a> (zip)</li>
 <li><a href="http://bedops.readthedocs.io/en/latest/content/installation.html#installation-via-source-code">Compilation instructions</a></li>
 </ul>
 </td>
@@ -50,11 +50,11 @@ The <a href="https://bedops.readthedocs.io/en/latest/content/overview.html#overv
 
 ### Documentation ###
 
-Complete documentation for **BEDOPS v2.4.35** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
+Complete documentation for **BEDOPS v2.4.36** tools is available at: <a href="https://bedops.readthedocs.io/en/latest/index.html">https://bedops.readthedocs.io/</a>
 
 ### Citation ###
 
-If you use **BEDOPS v2.4.35** in your research, please cite the following manuscript:
+If you use **BEDOPS v2.4.36** in your research, please cite the following manuscript:
 
 > Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al.  
 > [**BEDOPS: high-performance genomic feature operations**  
@@ -62,7 +62,7 @@ If you use **BEDOPS v2.4.35** in your research, please cite the following manusc
 
 ### Copyright ###
 
-> Copyright (C) 2011-2018 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
+> Copyright (C) 2011-2019 Shane J. Neph, M. Scott Kuehn and Alex P. Reynolds
 >
 > Source code, documentation and media assets released under <a href="https://github.com/bedops/bedops/blob/master/LICENSE">GNU Public License Version 2</a> (GPL v2).
 

applications/bed/bedmap/src/Input.hpp

@@ -79,7 +79,7 @@ namespace BedMap {
         precision_(6), useScientific_(false), useMinMemory_(false), setPrec_(false), numFiles_(0),
         minRefFields_(0), minMapFields_(0), errorCheck_(false), sweepAll_(false),
         outDelim_("|"), multiDelim_(";"), fastMode_(false), rangeAlias_(false),
-        chrom_("all"), skipUnmappedRows_(false) {
+        chrom_("all"), skipUnmappedRows_(false), unmappedVal_("") {
 
       // Process user's operation options
       if ( argc <= 1 )
@@ -108,6 +108,12 @@ namespace BedMap {
           fastMode_ = true;
         } else if ( next == "sweep-all" ) { // --> sweep through all of second file
           sweepAll_ = true;
+        } else if ( next == "unmapped-val" ) {
+          Ext::Assert<ArgError>(unmappedVal_.empty(), "--unmapped-val specified multiple times");
+          Ext::Assert<ArgError>(argcntr < argc, "No value given for --unmapped-val");
+          unmappedVal_ = argv[argcntr++];
+          Ext::Assert<ArgError>(unmappedVal_.find("--") != 0,
+                                "Apparent option: " + std::string(argv[argcntr]) + " where <val> expected for --unmapped-val.");
         } else if ( next == "delim" ) {
           Ext::Assert<ArgError>(outDelim_ == "|", "--delim specified multiple times");
           Ext::Assert<ArgError>(argcntr < argc, "No output delimiter given");
@@ -399,6 +405,7 @@ namespace BedMap {
     bool rangeAlias_;
     std::string chrom_;
     bool skipUnmappedRows_;
+    std::string unmappedVal_;
 
   private:
     struct MapFields {
@@ -480,6 +487,8 @@ namespace BedMap {
     usage << "      --sci                 Use scientific notation for score outputs.                              \n";
     usage << "      --skip-unmapped       Print no output for a row with no mapped elements.                      \n";
     usage << "      --sweep-all           Ensure <map-file> is read completely (helps to prevent broken pipes).   \n";
+    usage << "      --unmapped-val <val>  Print <val> on unmapped --echo-map* and --min/max-element* operations.  \n";
+    usage << "                              The default is to print nothing.                                      \n";
     usage << "      --version             Print program information.                                              \n";
     usage << "                                                                                                    \n";
     usage << "                                                                                                    \n";

applications/bed/bedops/test/Regression.java

@@ -196,7 +196,7 @@ class Test implements Comparable {
   }
 
 private int order_         = -1;
-private String call_       = "../../bin/bedops --ec ";
+private String call_       = "../../bin/bedops-typical --ec ";
 private String inputFiles_ = "";
 private String answer_     = "";
 private String output_     = "";

applications/bed/conversion/src/convert2bed.h

@@ -53,7 +53,7 @@
 
 #include "suite/BEDOPS.Constants.hpp"
 
-#define C2B_VERSION "2.4.35"
+#define C2B_VERSION "2.4.36"
 
 typedef int boolean;
 extern const boolean kTrue;

applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py

@@ -32,7 +32,7 @@ import logging
 name = "update-sort-bed-migrate-candidates"
 citation = "  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
 authors = "  authors:  Alex Reynolds and Shane Neph"
-version = "  version:  2.4.35"
+version = "  version:  2.4.36"
 usage = """  $ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]
                                        [ --write-list |
                                          --resort-immediately |

applications/bed/sort-bed/src/update-sort-bed-slurm.py

@@ -33,7 +33,7 @@ import logging
 name = "update-sort-bed-slurm"
 citation = "  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
 authors = "  authors:  Alex Reynolds and Shane Neph"
-version = "  version:  2.4.35"
+version = "  version:  2.4.36"
 usage = """  $ update-sort-bed-slurm [ --slurm-memory <MB> ] 
                           [ --slurm-partition <SLURM partition> ] 
                           [ --slurm-workdir <working directory> ]

applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py

@@ -33,7 +33,7 @@ import logging
 name = "update-sort-bed-starch-slurm"
 citation = "  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
 authors = "  authors:  Alex Reynolds and Shane Neph"
-version = "  version:  2.4.35"
+version = "  version:  2.4.36"
 usage = """  $ update-sort-bed-starch-slurm [ --slurm-memory <MB> ] 
                                  [ --slurm-partition <SLURM partition> ] 
                                  [ --slurm-workdir <working directory> ]

applications/bed/starch/src/Makefile

@@ -49,9 +49,9 @@ STARCH_OBJECTS            = $(addprefix $(LOCALOBJDIR)/, $(addsuffix .o, $(STARC
 
 build: starch unstarch starchcat starchcluster starch-diff starchstrip
 	rm -rf ${LOCALOBJDIR}
-build_debug: $(BINDIR)/debug.starch $(BINDIR)/debug.unstarch $(BINDIR)/debug.starchcat $(BINDIR)/debug.starchstrip
+build_debug: $(BINDIR)/debug.starch $(BINDIR)/debug.unstarch $(BINDIR)/debug.starchcat $(BINDIR)/debug.starchstrip starchcluster starch-diff
 	rm -rf ${LOCALOBJDIR}
-build_gprof: $(BINDIR)/gprof.starch $(BINDIR)/gprof.unstarch $(BINDIR)/gprof.starchcat $(BINDIR)/gprof.starchstrip
+build_gprof: $(BINDIR)/gprof.starch $(BINDIR)/gprof.unstarch $(BINDIR)/gprof.starchcat $(BINDIR)/gprof.starchstrip starchcluster starch-diff
 	rm -rf ${LOCALOBJDIR}
 
 # Cancel implicit compilation rules

applications/bed/starch/src/Makefile.darwin

@@ -31,7 +31,7 @@ LIBRARIES                 = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
 BINDIR                    = ../bin
 WARNINGS                  = -Weverything -Wno-c++98-compat-pedantic -Wno-padded
 ARCH_VERSION              = v2.2
-BIN_VERSION               = v2.4.35
+BIN_VERSION               = v2.4.36
 TEST                      = ../test
 TEST_OSX_BINDIR           = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
 

applications/bed/starch/src/starch-diff.py

@@ -32,7 +32,7 @@ import logging
 name = "starch-diff"
 citation = "  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract"
 authors = "  authors:  Alex Reynolds and Shane Neph"
-version = "  version:  2.4.35"
+version = "  version:  2.4.36"
 usage = "  $ starch-diff [ --chr <chr> ] starch-file-1 starch-file-2 [ starch-file-3 ... ]"
 help = """
   The 'starch-diff' utility compares the signatures of two or more specified 

applications/bed/starch/src/starch.c

@@ -46,18 +46,27 @@ main(int argc, char **argv)
 #ifdef DEBUG
     fprintf (stderr, "\n--- starch main() - enter ---\n");
 #endif
-    int parseValue = 0;
-    CompressionType type;
+#ifdef __cplusplus
+    char *note = nullptr;
+    char *tag = nullptr;
+    char *bedFn = nullptr;
+    FILE *bedFnPtr = nullptr;
+    Metadata *metadata = nullptr;
+    unsigned char *starchHeader = nullptr;
+#else
     char *note = NULL;
     char *tag = NULL;
     char *bedFn = NULL;
     FILE *bedFnPtr = NULL;
     Metadata *metadata = NULL;
+    unsigned char *starchHeader = NULL;
+#endif
+    int parseValue = 0;
+    CompressionType type;
     Boolean bedGeneratePerChrSignatureFlag = kStarchFalse;
     Boolean bedReportProgressFlag = kStarchFalse;
     LineCountType bedReportProgressN = 0;
     Boolean bedHeaderFlag = kStarchFalse;
-    unsigned char *starchHeader = NULL;
 
     setlocale (LC_ALL, "POSIX");
 
@@ -93,7 +102,7 @@ main(int argc, char **argv)
             if ((bedHeaderFlag == kStarchTrue) &&
 #ifdef __cplusplus
                  (STARCH_transformInput(&metadata, 
-                                       NULL, 
+                                       nullptr, 
                                        static_cast<const CompressionType>( type ), 
                                        reinterpret_cast<const char *>( tag ), 
                                        reinterpret_cast<const char *>( note )) != 0))
@@ -108,7 +117,7 @@ main(int argc, char **argv)
             else if ((bedHeaderFlag == kStarchFalse) &&
 #ifdef __cplusplus
                 (STARCH_transformHeaderlessInput(&metadata, 
-                                                 NULL, 
+                                                 nullptr, 
                                                  static_cast<const CompressionType>( type ), 
                                                  reinterpret_cast<const char *>( tag ), 
                                                  static_cast<const Boolean>( kStarchFinalizeTransformTrue ), 
@@ -212,6 +221,22 @@ main(int argc, char **argv)
     }
 
     /* cleanup */
+#ifdef __cplusplus
+    if (bedFnPtr != nullptr) {
+        fclose (bedFnPtr);
+        bedFnPtr = nullptr;
+    }
+    if (metadata != nullptr)
+        STARCH_freeMetadata (&metadata);
+    if (starchHeader) {
+        free (starchHeader);
+        starchHeader = nullptr;
+    }
+    if (starch_client_global_args.uniqueTag) {
+        free (starch_client_global_args.uniqueTag);
+        starch_client_global_args.uniqueTag = nullptr;
+    }
+#else
     if (bedFnPtr != NULL) {
         fclose (bedFnPtr);
         bedFnPtr = NULL;
@@ -226,6 +251,7 @@ main(int argc, char **argv)
         free (starch_client_global_args.uniqueTag);
         starch_client_global_args.uniqueTag = NULL;
     }
+#endif
 
 #ifdef DEBUG
     fprintf (stderr, "\n--- starch main() - exit ---\n");
@@ -244,16 +270,23 @@ STARCH_initializeGlobals()
 #ifdef DEBUG
     fprintf (stderr, "\n--- STARCH_initializeGlobals() ---\n");
 #endif
+#ifdef __cplusplus
+    starch_client_global_args.note = nullptr;
+    starch_client_global_args.inputFile = nullptr;
+    starch_client_global_args.uniqueTag = nullptr;
+    starch_client_global_args.inputFiles = nullptr;
+#else
     starch_client_global_args.note = NULL;
+    starch_client_global_args.inputFile = NULL;
+    starch_client_global_args.uniqueTag = NULL;
+    starch_client_global_args.inputFiles = NULL;
+#endif
     starch_client_global_args.compressionType = STARCH_DEFAULT_COMPRESSION_TYPE;
     starch_client_global_args.generatePerChromosomeSignatureFlag = kStarchTrue;
     starch_client_global_args.reportProgressFlag = kStarchFalse;
     starch_client_global_args.reportProgressN = 0;
     starch_client_global_args.headerFlag = kStarchFalse;
-    starch_client_global_args.inputFile = NULL;
-    starch_client_global_args.uniqueTag = NULL;
     starch_client_global_args.numberInputFiles = 0;
-    starch_client_global_args.inputFiles = NULL;
 }
 
 int
@@ -294,7 +327,11 @@ STARCH_parseCommandLineOptions(int argc, char **argv)
         case 'r':
             starch_client_global_args.reportProgressFlag = kStarchTrue;
             errno = 0;
+#ifdef __cplusplus
+            starch_client_global_args.reportProgressN = strtoumax(optarg, nullptr, 10);
+#else
             starch_client_global_args.reportProgressN = strtoumax(optarg, NULL, 10);
+#endif
             if (errno == ERANGE) {
                 fprintf (stderr, "ERROR: Numerical value is outside of range.\n");
                 return STARCH_FATAL_ERROR;
@@ -353,13 +390,15 @@ STARCH_printUsage(int errorType)
 #ifdef DEBUG
     fprintf (stderr, "\n--- STARCH_printUsage() ---\n");
 #endif
-    char *avStr = NULL;
 #ifdef __cplusplus
+    char *avStr = nullptr;
     avStr = static_cast<char *>( malloc (STARCH_ARCHIVE_VERSION_STRING_LENGTH) );
+    if (avStr != nullptr) {
 #else
+    char *avStr = NULL;
     avStr = malloc (STARCH_ARCHIVE_VERSION_STRING_LENGTH);
-#endif
     if (avStr != NULL) {
+#endif
         int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
         if (result != -1) {
             switch (errorType) {
@@ -381,13 +420,15 @@ STARCH_printRevision()
 #ifdef DEBUG
     fprintf (stderr, "\n--- STARCH_printRevision() ---\n");
 #endif
-    char *avStr = NULL;
 #ifdef __cplusplus
+    char *avStr = nullptr;
     avStr = static_cast<char *>( malloc (STARCH_ARCHIVE_VERSION_STRING_LENGTH) );
+    if (avStr != nullptr) {
 #else
+    char *avStr = NULL;
     avStr = malloc (STARCH_ARCHIVE_VERSION_STRING_LENGTH);
-#endif
     if (avStr != NULL) {
+#endif
         int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
         if (result != -1)
             fprintf (stderr, "%s\n  binary version: %s (creates archive version: %s)\n", name, BEDOPS::version(), avStr);

applications/bed/starch/src/starch.h

@@ -83,6 +83,19 @@ static struct starch_client_global_args_t {
     size_t numberInputFiles;
 } starch_client_global_args;
 
+#ifdef __cplusplus
+static struct option starch_client_long_options[] = {    
+    {"note",            required_argument,    nullptr, 'n'},
+    {"bzip2",           no_argument,          nullptr, 'b'},
+    {"gzip",            no_argument,          nullptr, 'g'},
+    {"omit-signature",  no_argument,          nullptr, 'o'},
+    {"report-progress", required_argument,    nullptr, 'r'},
+    {"header",          no_argument,          nullptr, 'e'},
+    {"version",         no_argument,          nullptr, 'v'},
+    {"help",            no_argument,          nullptr, 'h'},
+    {nullptr,           no_argument,          nullptr,  0 }
+};
+#else
 static struct option starch_client_long_options[] = {    
     {"note",            required_argument,    NULL, 'n'},
     {"bzip2",           no_argument,          NULL, 'b'},
@@ -94,6 +107,7 @@ static struct option starch_client_long_options[] = {
     {"help",            no_argument,          NULL, 'h'},
     {NULL,              no_argument,          NULL,  0 }
 };
+#endif
 
 static const char *starch_client_opt_string = "n:bgorevh?";
 

applications/bed/starch/src/starchcat.h

@@ -57,8 +57,11 @@ namespace starch {
 #define STARCHCAT_RETRANSFORM_BUFFER_SIZE 1024*1024
 #define STARCHCAT_FIELD_BUFFER_MAX_LENGTH 16
 
-#define GCC_COMPILER (defined(__GNUC__) && !defined(__clang__))
-#define CLANG_COMPILER defined(__clang__)
+#if defined(__GNUC__) && !defined(__clang__)
+#define HAS_GNU 1
+#else
+#define HAS_GNU 0
+#endif
 
 /*
     This is simply a struct containing a starch file's
@@ -177,6 +180,18 @@ static struct starchcat_client_global_args_t {
     LineCountType reportProgressN;
 } starchcat_client_global_args;
 
+#ifdef __cplusplus
+static struct option starchcat_client_long_options[] = {    
+    {"note",            required_argument, nullptr, 'n'},
+    {"bzip2",           no_argument,       nullptr, 'b'},
+    {"gzip",            no_argument,       nullptr, 'g'},
+    {"omit-signature",  no_argument,       nullptr, 'o'},
+    {"report-progress", required_argument, nullptr, 'r'},
+    {"version",         no_argument,       nullptr, 'v'},
+    {"help",            no_argument,       nullptr, 'h'},
+    {nullptr,           no_argument,       nullptr,  0 }
+};
+#else
 static struct option starchcat_client_long_options[] = {    
     {"note",            required_argument, NULL, 'n'},
     {"bzip2",           no_argument,       NULL, 'b'},
@@ -187,6 +202,7 @@ static struct option starchcat_client_long_options[] = {
     {"help",            no_argument,       NULL, 'h'},
     {NULL,              no_argument,       NULL,  0 }
 };
+#endif
 
 static const char *starchcat_client_opt_string = "n:bgorvh?";
 

applications/bed/starch/src/starchcluster_gnuParallel.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : Feb 2012
-# version : v2.4.35
+# version : v2.4.36
 
 #
 #    BEDOPS

applications/bed/starch/src/starchcluster_sge.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : Feb 2012
-# version : v2.4.35
+# version : v2.4.36
 
 #
 #    BEDOPS

applications/bed/starch/src/starchcluster_slurm.tcsh

@@ -2,7 +2,7 @@
 
 # author  : sjn and apr
 # date    : 13 Sep 2016
-# version : v2.4.35
+# version : v2.4.36
 
 #
 #    BEDOPS