Minigraph-0.21 (r606)

Notable changes:

• New feature: added mgutils-es6.js for converting merged BED to VCF. This
  replaces the older BED-to-VCF converter. This script requires k8 v1.0.

• New feature: output a new ds:Z tag. ds is similar to cs but it
  additionally indicates microhomology around INDELs.

• New experimental feature: added gafcall.js for calling structural
  variants. This script will be moved a separate repo in future.

(21 April 2024, r606)

Minigraph-0.20 (r559)

This release fixes several assertion failures (#78, #79 and #80) caused by
recent changes in graph chaining. It also fixes an integer overflow that may
happen to chromosomes longer than 256 Mb (#76). Results remain the same.

(20 November 2022, r559)

Minigraph-0.19 (r551)

This release fixes a segmental fault if minigraph is compiled with certain
compiler-libc combinations. This is apparently caused by memcpy(0,0,0).
Minigraph is otherwise identical v0.18.

(12 June 2022, r551)

Minigraph-0.18 (r538)

This release uses heuristics to speed up base alignment in long divergent
regions. The heuristics does not guarantee optimal alignment but it reliably
produces alignment close to the optimal except in centromeres where the
algorithmically optimal alignment may not represent true evolution in biology.
The new version is 10-700% faster than v0.17 depending on input data and
parameters in use.

(9 May 2022, r538)

Minigraph-0.17 (r524)

This release adds base alignment to minigraph. It represents the first major
improvement to minigraph. Specifically, this release attempts to connect linear
chains with the graph wavefront alignemnt algorithm (GWFA) and produces the
final alignment with miniwfa under the 2-piece gap penalty. Graph generation
also considers base alignment. This gives more accurate graph alignment and
generally simpler graph topology. Note that minigraph still focuses on
structural variations and does not generate base-level graphs. To endusers,
minigraph remains similar feature wise.

Notable changes:

• New feature: option -c for base alignment and graph generation. In the
  alignment mode, the option adds the cg:Z CIGAR tag like minimap2. Graph
  generation still works without -c but applying this option is generally
  recommended now.

It should be noted that the base alignment is currently slow for species of
high diversity. This will be addressed in the next couple of releases.

(29 April 2022, r524)

Minigraph-0.16 (r436)

Notable changes:

• Improvement: 2-level chaining. This is a feature backported from minimap2.
  It speeds up graph generation for human graphs.

• Improvement: break a chain at poorly aligned regions, another recent
  minimap2 feature.

• Added the script for generating figures in the minigraph paper.

(21 February 2022, r436)

Minigraph-0.15 (r426)

Fixed a bug in bubble identification around inversions. This version should be
used together with the latest gfatools for consistency. Only --call is affected.

Minigraph-0.14 (r415)

Notable changes:

• Added the --call option to find the allele/walk in each bubble.

• Reduced the default minimum variant length (option -L) from 100 to 50 for
  the consistency with the SV community.

(19 December 2020, r415)

Minigraph-0.13 (r397)

Notable change:

• Fixed incorrect anchors in linear chains. In older versions, a linear chain
  may contain two anchors with identical reference or query coordinates.

(3 December 2020, r397)

Minigraph-0.12 (r389)

Notable changes:

• Improve alignments towards ends of graph segments. If there is an SV close to
  the ends but not at the ends, older versions may produce an excessively
  large bubble including high-identity matches.

• Heuristically accelerates alignment in complex subgraphs by skipping
  many unnecessary sequence-aware graph traversals. This speeds up graph
  generation for CHM13 by three folds without obviously affecting accuracy.

• Added option --inv to optionally disable inversions. Graph traversal is hard
  with inversions.

• Fixed the bug that prevents large -K.

• Apply option -K4g to the asm preset.

• Added option --write-mz to output the positions of minimizer anchors.

(26 October 2020, r389)