moving the exception throw from body_sub to inside a submission so that lack of a control sample would result in a submission failure rather than an indefinite number of exceptions
added options to enable bamtofastq to run with split option so input bam files are directly converted to fastq chunks
mapped_fastq files might not have the source_fastq metadata in which case we look for source_bam metadata
removing the split_fastq step as bamtofastq now produces its outputs in chunks