Enable create to take input from stdin

[jdidion]

It looks like create relies on the file extension to determine the type of input, which precludes using /dev/stdin as the input file. Since create doesn't have many filtering options, it is often necessary to use samtools view to filter the file (e.g. remove duplicate reads) upstream of create.

You could be fancy and try to sniff the file type using the magic bytes, or you could just add an option for the user to specify the file type.

[arq5x]

We will look into this, but will likely be a while before this could be implemented.