v1.2.2

• Fixed including documentation in binary releases.

v1.2.1

• The input sample set can now be empty.
• Improved reporting subprocess errors.
• REF column mismatches can now be set to cause a warning to be logged instead of resulting in a fatal error.

v1.2

• Added an option to include only the given samples.

v1.1.1

• Fixed parsing floating point values in VCF’s QUAL field.

v1.1

• Trivial segmentations are now handled when producing founder sequences.

v1.0.1

• Fixed a bug which caused building a variant graph (and any subsequent operations) to fail if overlap output path was not specified in command line options.

v1.0

• Variant graph building, optimisation, and sequence generation are again done in a single executable.
• The variant graph building and the sequence output algorithms have been rewritten and are now much faster than before.
• Founder sequence building algorithms have also been rewritten to use the binary pBWT instead of the extended version that utilises the sequence alphabet. Consequently they are now faster as well.
• A2M output of sequences has been added.
• Less relevant matching algorithms for generating founder sequences have been removed.

v0.6.1

• Updated the VCF parser.

v0.6

• Added separate tools for preprocessing, creating a variant graph and outputting the corresponding sequences.
• Added support for generating founder sequences.
• Added a tool for generating a variant file from two aligned sequences and variants relative to the second sequence.

v0.5

• Added command line options for specifying the reference sequence and chromosome identifiers.
• Removed --structural-variant-handling command line option as keeping them was always the most useful option.
• Added an experimental preprocessing tool for combining overlapping variants.