• zzzSleep (40/40) Sep 07 2024 Could I ask some questions on the pipeline, the following code
• zzzSleep (3/3) Sep 07 2024 Thanks go to Paul Backus, nside the foreach loop, this will cause

zzzSleep <classreader 163.com> writes:

Could I ask some questions on the pipeline, the following code 
always stops at the second cmds, cmds[1]. I tested the command 
under shell and found it can quickly end and get output.bam

```
import std.process;
import std.stdio;
import std.conv;
void executeCommandPipe(string[][] cmds) {

     // pipe init
     auto temp_pipe = pipe(); // save cmd1, cmd2, cmd3 ...

     // process first
     auto pid_first = spawnProcess(cmds[0], stdin, 
temp_pipe.writeEnd);
     scope(exit) wait(pid_first);

     // process cmd2 ~ cmdN-1
     for (int i = 1; i < cmds.length - 1; i++) {
         auto new_pipe = pipe(); // create next pipe

         auto pid = spawnProcess(cmds[i], temp_pipe.readEnd, 
new_pipe.writeEnd);
         scope(exit) wait(pid);

         temp_pipe = new_pipe; // update the pipe
     }

     // process final, output to stdout
     auto pid_final = spawnProcess(cmds[$-1], temp_pipe.readEnd, 
stdout);
     scope(exit) wait(pid_final);
}
void main() {
     string[][]cmds=[["samtools", "fixmate", "- ", "8", "-m", 
"-u", "input.bam", "-"], ["samtools", "sort", "- ", "8", "-u", 
"-",], ["samtools", "markdup", "- ", "8", "-u", "-", 
"output.bam"]];
     executeCommandPipe(cmds);
}

```
corresponding Linux command is
```
samtools fixmate -  8 -m -u input.bam - | samtools sort -  8 -u - 
| samtools markdup -u - output.bam
```

zzzSleep <classreader 163.com> writes:

Thanks go to Paul Backus, nside the foreach loop, this will cause 
your code to wait at the end of the current loop iteration, not 
at the end of the function.