add IGNORE_INDEX to illumina2bam

[idot]

We mix indexed and non indexed lanes on one flowcell which runs with the index protocol. It would be nice if illumina2bam would have a flag to ignore the index read and simply not put it into the bam file. It does waste some space.

[gq1]

Currently we always store the indexing reads but I will add this option later.

[idot]

For me its not necessary anymore. I always store index reads now.