Minimap2-2.11 (r797)

Changes to minimap2:

• Improved alignment accuracy in low-complexity regions for SV calling. Thank
  @armintoepfer for multiple offline examples.

• Added option --eqx to encode sequence match/mismatch with the =/X CIGAR
  operators (#156, #157 and #175).

• When compiled with VC++, minimap2 generated wrong alignments due to a
  comparison between a signed integer and an unsigned integer (#184). Also
  fixed warnings reported by "clang -Wextra".

• Fixed incorrect anchor filtering due to a missing 64- to 32-bit cast.

• Fixed incorrect mapping quality for inversions (#148).

• Fixed incorrect alignment involving ambiguous bases (#155).

• Fixed incorrect presets: option -r 2000 is intended to be used with
  ava-ont, not ava-pb. The bug was introduced in 2.10.

• Fixed a bug when --for-only/--rev-only is used together with --sr or
  --heap-sort=yes (#166).

• Fixed option -Y that was not working in the previous releases.

• Added option --lj-min-ratio to fine control the alignment of long gaps
  found by the "long-join" heuristic (#128).

• Exposed mm_idx_is_idx, mm_idx_load and mm_idx_dump C APIs (#177).
  Also fixed a bug when indexing without reference names (this feature is not
  exposed to the command line).

Changes to mappy:

• Added __version__ (#165).

• Exposed the maximum fragment length parameter to mappy (#174).

Changes to paftools:

• Don't crash when there is no "cg" tag (#153).

• Fixed wrong coverage report by "paftools.js call" (#145).

This version may produce slightly different base-level alignment. The overall
alignment statistics should remain similar.

(2.11: 20 June 2018, r797)