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
```
