Modified samples with 0 index to get converted to fastq, Added WIP index stats for reads 2 or 3.
Using NumCycles from runinfo.xml to get index_size. This is problematic though
Added: Moving R2/R3 index files to Undetermined_indices, Rename second read if any to R2
Changed: Merged Undemultiplexed.metrics files will now be sorted to accomodate indices as reads