-s flag is unclear

[bbushnell]

It's not obvious what the -s flag does. There are basically 4 use cases for a program that does a transform on some data:

1. program infile outfile
2. program stdin outfile
3. program infile stdout
4. program stdin stdout

The definition of "-s" leaves it vague as to which of the last 3 is intended - so it's not clear how you differentiate between case 2 and case 3, or if case 4 is even supported. Can you clarify how -s works in the compression and decompression modes?

[jvolkening]

I remember having this same thought when STDIN/STDOUT support was added, but you always need to give a filename for the file being read from or written to. This makes some sense conceptually, since it's difficult to imagine a situation where you'd want/need to pipe the compressed bytes to or from another program. Agree that the documentation could be clearer on this, however.

[lrog]

Good point. This feature could have been explained more clearly. The only possible use-cases of using this feature are for reading and writing FASTQ data only, as there would be no big point on streaming in/out DSRC binary data in binary form.
I've corrected the description, so hopefully now it should not make confusion:

-s: read FASTQ data from stdin (compression) or write FASTQ data to stdout (decompression)