Minimap2-2.16 (r922)

This release is 50% faster for mapping ultra-long nanopore reads at comparable
accuracy. For short-read mapping, long-read overlapping and ordinary long-read
mapping, the performance and accuracy remain similar. This speedup is achieved
with a new heuristic to limit the number of chaining iterations (#324). Users
can disable the heuristic by increasing a new option --max-chain-iter to a
huge number.

Other changes to minimap2:

• Implemented option --paf-no-hit to output unmapped query sequences in PAF.
  The strand and reference name columns are both * at an unmapped line. The
  hidden option is available in earlier minimap2 but had a different 2-column
  output format instead of PAF.

• Fixed a bug that leads to wrongly calculated de tags when ambiguous bases
  are involved (#309). This bug only affects v2.15.

• Fixed a bug when parsing command-line option --splice (#344). This bug was
  introduced in v2.13.

• Fixed two division-by-zero cases (#326). They don't affect final alignments
  because the results of the divisions are not used in both case.

• Added an option -o to output alignments to a specified file. It is still
  recommended to use UNIX pipes for on-the-fly conversion or compression.

• Output a new rl tag to give the length of query regions harboring
  repetitive seeds.

Changes to paftool.js:

• Added a new option to convert the MD tag to the long form of the cs tag.

Changes to mappy:

• Added the mappy.Aligner.seq_names method to return sequence names (#312).

For NA12878 ultra-long reads, this release changes the alignments of <0.1% of
reads in comparison to v2.15. All these reads have highly fragmented alignments
and are likely to be problematic anyway. For shorter or well aligned reads,
this release should produce mostly identical alignments to v2.15.

(2.16: 28 February 2019, r922)