Same ID documentation for use and sanitization

[yashpatel6]

          suggestion (non-blocking): 

• I think it would be helpful to have something in the Inputs section of the Readme that notes which fields will be sanitized and what that involves.
• It would also be helpful to clarify...
  • For FASTQ input: the difference between sample and bam_header_sm
  • For BAM input: whether the output will use the input sample string or the sample ID from the input BAM readgroups.

Originally posted by @sorelfitzgibbon in #225 (review)