This contains various scripts written by Copilot upon my request, to
post-process the CRAM files produced by the
nf-core/pairgenomealign pipeline.
The CRAM files represent pairwise whole-genome alignments of mutliple query genomes to a single target genome. The target genome takes the role of the reference sequence in the CRAM files. The query genomes are represented as read groups. Hard-clipped regions can be longer than the 268,435,455 length limit (28 bits) in the BAM and CRAM files; in CIGAR lines they are represented as adjascent clipping operations.
The mergeAdjascentAlns.sam is toy test data.