BAM fai order compare script improvements
Merge pull request #5 from fwip/master

Fix for '_' to '-' replacement in bcl2fastq2
Fix chrom buckets missing first chromosome

FAI files have no header, leading the buckets to be missing
the first chromosme
Fix windowing size; standardize filename format between starch and bw
Standardize nextseq Undetermined naming schema

Specifically, include the L001 bit, to bring in line with bcl2fastq v1.8
naming schema.