Watchout for alignments with > 65535 CIGAR operations

[SHuang-Broad]

As the reads and assemblies gets longer, we will get there.
In fact we might already be there for some assemblies with NG50 > 10Mb.

See minimap2's comment about how to do that.

A tricky thing is how up-to-date downstream tools are, when it comes to adhering to the hts-specs.

[SHuang-Broad]

The alignment workflow now turns on -L by default.
We are unsure if the downstream tools are aware of the CG tag yet.

[kvg]

I may have broken this when the merge of the kvg_ont_fixes branch into master. We should update the AlignReads.Minimap2 task.

[kvg]

Done - by default we now supply the -L argument to minimap2, which writes long cigar strings to a special tag.