#79 File Descriptor Input from Command Line

[Anonymous]

Right now (I'm referring to Bowtie 2) you can specify "-" as the input file on the command line and bowtie2 will read the data from stdin. This breaks down, however, with mate pairs because there is only one stdin, which is in fact file descriptor 0.

It would be a very nice feature to be able to specify other file descriptors that would be inherited from the calling shell for input so that multiple inputs can be piped in. This is incredibly useful in a pipeline situation where we want to distribute the computation without having to deal with the file sustem.