Silicon chip

README.md

@@ -62,17 +62,46 @@ make STAR CXXFLAGS_SIMD=sse
 Compile under Mac OS X
 ----------------------
 
+For Intel-based Macs:
 ```bash
 # 1. Install brew (http://brew.sh/)
 # 2. Install gcc with brew:
 $ brew install gcc
 # 3. Build STAR:
 # run 'make' in the source directory
 # note that the path to c++ executable has to be adjusted to its current version
-$cd source
-$make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
-# 4. Make it availible through the terminal
-$cp STAR /usr/local/bin
+$ cd source
+$ make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
+# 4. Make it available through the terminal
+$ cp STAR /usr/local/bin/
+```
+
+For Apple Silicon (M1/M2/M3) Macs:
+```bash
+# 1. Install brew (http://brew.sh/)
+# 2. Install gcc:
+brew install gcc
+
+# 3. Find the gcc compiler path:
+brew list gcc | grep c++-
+
+# 4. Clone STAR repository:
+git clone https://github.com/alexdobin/STAR.git
+cd STAR/source/
+
+# 5. Build STAR (adjust gcc version as needed):
+make STARforMacStatic CXX=/opt/homebrew/Cellar/gcc/14.2.0_1/bin/c++-14
+
+# 6. Verify compilation:
+./STAR --version
+./STAR --help
+
+# 7. Make it available through the terminal
+sudo cp STAR /usr/local/bin/
+
+# 8. Verify installation:
+which STAR
+STAR --version
 ```
 
 All platforms - non-standard gcc

source/Makefile

@@ -106,7 +106,7 @@ all: cleanCompileInfo STAR$(SFX)
 
 opal/opal.o : opal/opal.cpp opal/opal.h
 	cd opal && \
-	$(CXX) -c -I./ -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGSextra) $(CXXFLAGS_SIMD) opal.cpp
+	$(CXX) -c -I./ -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGSextra) opal.cpp
 
 .PHONY: clean
 clean:

source/Parameters_openReadsFiles.cpp

@@ -2,6 +2,9 @@
 #include "ErrorWarning.h"
 #include <fstream>
 #include <sys/stat.h>
+#include <spawn.h>    // Add this for posix_spawn
+#include <errno.h>
+
 void Parameters::openReadsFiles() 
 {
     if (readFilesCommandString=="") {//read from file
@@ -78,25 +81,49 @@ void Parameters::openReadsFiles()
             chmod(readsCommandFileName.at(imate).c_str(),S_IXUSR | S_IRUSR | S_IWUSR);
 
             readFilesCommandPID[imate]=0;
+
+            // Prepare spawn attributes and actions
+            posix_spawnattr_t attr;
+            posix_spawn_file_actions_t actions;
+
+            if (posix_spawnattr_init(&attr) != 0 ||
+                posix_spawn_file_actions_init(&actions) != 0) {
+                ostringstream errOut;
+                errOut << "EXITING: because of fatal EXECUTION error: Failed initializing spawn attributes\n";
+                errOut << errno << ": " << strerror(errno) << "\n";
+                exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+            }
 
-            ostringstream errOut;
-            pid_t PID=vfork();
-            switch (PID) {
-                case -1:
-                    errOut << "EXITING: because of fatal EXECUTION error: Failed vforking readFilesCommand\n";
-                    errOut << errno << ": " << strerror(errno) << "\n";
-                    exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
-                    break;
-
-                case 0:
-                    //this is the child
-                    execlp(readsCommandFileName.at(imate).c_str(), readsCommandFileName.at(imate).c_str(), (char*) NULL);
-                    exit(0);
-
-                default:
-                    //this is the father, record PID of the children
-                    readFilesCommandPID[imate]=PID;
+            // Prepare arguments
+            char* argv[] = {
+                const_cast<char*>(readsCommandFileName.at(imate).c_str()),
+                nullptr
             };
+
+            // Spawn the process
+            pid_t PID;
+            int status = posix_spawn(
+                &PID,
+                readsCommandFileName.at(imate).c_str(),
+                &actions,
+                &attr,
+                argv,
+                nullptr  // Use current environment
+            );
+
+            // Clean up spawn attributes and actions
+            posix_spawnattr_destroy(&attr);
+            posix_spawn_file_actions_destroy(&actions);
+
+            if (status != 0) {
+                ostringstream errOut;
+                errOut << "EXITING: because of fatal EXECUTION error: Failed spawning readFilesCommand\n";
+                errOut << errno << ": " << strerror(errno) << "\n";
+                exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+            }
+
+            // Record the PID
+            readFilesCommandPID[imate] = PID;
 
             inOut->readIn[imate].open(readFilesInTmp.at(imate).c_str());
         };