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Each | tells the shell to connect the standard output of the command on the left to the standard input of the command on the right by an inter-process communication mechanism called an (anonymous) pipe, implemented in the operating system. Pipes are unidirectional; data flows through the pipeline from left to right.
PIPE selects programs to run and chains them together in a pipeline to pump data through. Because CMS programs and utilities don't provide a device independent stdin and stdout interface, CMS Pipelines has a built-in library of programs that can be called in a pipeline specification.
Like many Unix commands, SAMtool commands follow a stream model, where data runs through each command as if carried on a conveyor belt. This allows combining multiple commands into a data processing pipeline. Although the final output can be very complex, only a limited number of simple commands are needed to produce it.
In other words, a read from an empty pipe will cause the calling thread to wait until at least one byte becomes available or an end-of-file is received as a result of the write handle of the pipe being closed. Likewise, a write to a full pipe will cause the calling thread to wait until space becomes available to store the data being written.
This pipe will be accessible with something like /dev/fd/63; you can see it with a command like echo <(true). Execute the substituted command in the background (sort file2 in this case), piping its output to the anonymous pipe. Execute the primary command, replacing the substituted command with the path of the anonymous pipe.
A named pipe can be accessed much like a file. Win32 SDK functions CreateFile, ReadFile, WriteFile and CloseHandle open, read from, write to, and close a pipe, respectively. Unlike Unix, there is no command line interface, except for PowerShell. Named pipes cannot be created as files within a normal filesystem, unlike in Unix.
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splice() works by using the pipe buffer. A pipe buffer is an in-kernel memory buffer that is opaque to the userspace process. A user process can splice the contents of a source file into this pipe buffer, then splice the pipe buffer into the destination file, all without moving any data through userspace.