Command to recreate per lane bam from a merged bam

Refer to AT-658, this command tool is needed to recreate per lane bam from a merged bam. The steps involved are: extract read group bam, compare flagstat, revert markdup tag, reheader bam, create bam index, create bam md5, move outputs over.
Actually this will be used in the pipeline. I agree to you that optional samtools/picard versions are confusing and dangerous. I went ahead and made the change to make those versions not optional.