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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 scr...
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)
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)
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....
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...