Selecting which types of reads [feature request]

[sjackman]

To allow more fine grained selection of which types of reads are selected, may I suggest the following options, intended primarily for use with writing to stdout, but could be used with files too.

--mp: Output mate-pair reads
--no-mp: Do not output mate-pair reads
--un: Output unknown reads
--no-un: Do not output unknown reads
--pe: Output paired-end reads
--no-pe: Do not output paired-end reads
--se: Output single-end reads
--no-se: Do not output single-end reads