feature request: ubam input/output?

[eboyden]

Pretty self-explanatory. We are trying to eliminate the need to ever process data in fastq format in our pipeline. We probably wouldn't need the ability to convert fastq to ubam or vice-versa (although I wouldn't object), but having the ability to run ubam < ngmerge > ubam would be very appreciated.

[jsh58]

This can be accomplished via piping and samtools, though that is functionally equivalent to converting to/from fastq.