Rename BAM_INDEX to BAM_LIST, make the population column optional, and add validation that each BAM only has 1 sample and that the sample id matches the one in BAM_LIST (--ignoreSMcheck will turn this last validation off).  Also, by default, create the BAM_LIST file for the aligner.
Align - Use SAMPLE instead of MERGE_NAME if it is missing from the FASTQ list/info file.