Improve process paired BAM by turning more targets into changeable variables
Use the correct samtools fai option; this means older BAM files will need to be resorted
Short script to check BAM ref order status
Create picard hist file off INSERTMETRICS variable name
Make sure original BAM file is always indexed, continue improving variable usage
Sync spot-Rboth method with spot-R1 method
BAM fai order compare script improvements