I have an alignment of an assembled contig with the reference genome. The contigs are very long (PacBio + HiC assembly), and one "query" will generate multiple alignments with the "reference", as a consequence of structural variation, which breaks up the alignments.
I want to figure out if those alignments are in the right order relative to the contig they originate from. Next step would be to check if any of these alignments have deletions - leading to gaps, or change direction (due to inversions). I can't find any pysam attributes which seem do to the trick, right now, and I'm not sure if it's encoded in some obscure tag of the bam?