Switching to work with bwa ont2d mode, not pacbio mode. This only affects the alignment when using the --bwa flag. 
Switching to work with bwa ont2d mode, not pacbio mode. This only
affects the alignment when using the --bwa flag. 
isovic/marginAlign,benedictpaten/marginAlign,benedictpaten/marginAlign,benedictpaten/marginAlign,isovic/marginAlign