Feat faster bam pipeline

[hdashnow]

• Allow identify_locus.py to take multiple bams from the same sample
• Update install to set ngs tools, include CRAM_REF option For bam pipeline:
• align_bwa_bam to default 1 concurrency
• use CRAM_REF instead of REF to for CRAM files
• set SLOP = 5, and only apply SLOP once (it was applied at both the bed generation stage and the read extraction stage)