Support adding index sequence to header

[Lance Parsons]

Illumina's bcl2fastq software places the index sequence into output read names. Since this is somewhat common, it might be helpful to some downstream tools to do the same.

Illumina's format for read id (as of bcl2fastq v 2.19) is:

@Instrument:RunID:FlowCellID:Lane:Tile:X:Y:UMI ReadNum:FilterFlag:0:IndexSequence or SampleNumber

I'm not sure the best way to specify options for this, but perhaps simply an optional separator character, option to append to end of header or end of read name (read name is up to the first space space in the header).