v1.10.0

Added

• Support for building a genome graph from multiple MSAs and/or genome sub-graphs built by make_prg.
  Addresses #130.
• CONTRIBUTING.md document

Changed

• Dependencies: added make_prg and pybedtools, updated biopython version.

v1.9.0

Added

• Changelog
• Static executable statically-linked against glibc/libgcc/libstd++ [#101,#163]
• Script to build the gramtools backend (build.sh). Simplifies CI (docker image building), removes
  hacking into setup.py, and simplifies compiling on user machine.

Changed

• Switched from setup.py to pyproject.toml and setup.cfg [#164], following PEP517

Removed

• Retired variant-aware kmer indexing code [#159]
• No longer install py-cortex-api by default. If gramtools discover is used,
  its installation is requested

Fixed

• Variant rebasing in discover was incompletely tested- simplified algorithm and added tests
• Infinite loop when no reads mapped to genome graph

v1.8.0

Added

• Use Conan dependency manager for available dependencies (boost, gtest, json). Fixes #158
• Region-based (chr:start-stop) subgraph visualisation (libgramtools/submods/visualise_prg)

Changed

• Bump CMake requirements to 3.1.2
• Bump boost libraries to 1.69.0

v1.7.0

• genome graphs (PRGs) can be nested (sites inside sites)
• introduce genotype command: runs both read mapping and genotyping, with genotyping model now implemented in C++
• concurrent querying of alleles: faster mapping
• genotype produces both a VCF and a jVCF

v1.6.0

• Build and serialise a coverage graph to support nested PRGs
• It records nesting-related information in the graph and per base coverage of mapped reads
• Full backward-compatibility with non-nested PRGs