limit inclusion of fastq/bam files in input dirs

it's just a suggestion, so, it will be good to have feedback

moving forward, I wonder what's the best way to handle template creation for standard bcl2fastq output where fastq of each sample is kept in a single folder and the fastq files are split for every x number of reads

I think we can change the way pair fastq is identified to ignore the index barcode, lane, and the counter in the end. '1', and '2' should be extend to 'R1' and 'R2' (see example below)
Sample_NA12878_GAAACC_L002_R2_002.fastq.gz
subroutine to modify: https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/bam/fastq.py#L106