0.7.3

• bugfix in graph building: a particular edge-case would cause minor inconsistencies in the block alignment when merging graphs, see issue #62 and PR #63.

0.7.2

• minor fix in tree midpoint rooting during panX export, see #59.

0.7.1

• minor fix for multi-threaded marginalize, see #58.

0.7.0

• fasta input files are checked for duplicated records, and white lines between records are tolerated, see #55.
• PanGraph execution is now deterministic, and same input files always produce the same output, see #57. For the build command, a random seed can be set with the -r flag.
• introduced the -t flag in the build and merge command. This activates consistency checks to verify that the input genomes can be exactly reconstructed. See #57.
• Fixed #56

0.6.3

• fixed an issue with PanX export by upgrading TreeTools version, see #52 by @mmolari and @PierreBarrat
• minor upgrades to the analysis scripts following PanGraph's paper reviews, see #51.

0.6.2

• removed the dependency on conda/PyCall and substituted it with TreeTools, by @PierreBarrat and @mmolari, see #45. This reduces the size of the docker image.
• added script/config/accnums.json file with list of accession number for GenBank sequences used for pangraph algorithm validation.
• added procps to docker image. This is needed for compatibility of the docker image with nextflow. By @plaquette, see #48.
• minor improvements in the analysis pipeline, see #49.

v0.6.1

What's Changed

• added pangraph version command that prints PanGraph's version on stderr, by @mmolari and @ivan-aksamentov, see #40.
• fix: wrong PanGraph's package version tag in Project.toml.
• added tools/release.sh script to automate the release process, by @mmolari and @ivan-aksamentov, see #41.

v0.6.0

What's Changed

• added mmseqs2 as an alternative alignment kernel that guarantees higher sensitivity at the expense of longer computational time, see #33, by @mmolari and @nnoll.
• updated Docker file to include mmseqs2 in the container, by @ivan-aksamentov.
• updated the documentation, including discussion of alignment kernel sensitivities and examples of application of PanGraph to plasmids by @liampshaw .
• errors that occur in worker threads are now emitted on the main thread, see #25.
• fixed bug when using mash option see this commit
• fixed a bug in detransitive, see this commit
• added snakemake pipeline in the script folder to perform the analysis published in our paper.
• added -K option to the build command to control kmer length for mmseqs aligner, see this commit.
• added fasttree to docker container and PanX export to docker tests, see #37 .

New Contributors

• @liampshaw made their first contribution

v0.5.0

What's Changed

• fix: error with gfa export of fully duplicated paths by @mmolari in #19
• GFA export bug fixes by @nnoll in #28
• chore: add docker container by @ivan-aksamentov in #27
• fix: deal with zero length blocks getting added to segment by @nnoll in #20

New Contributors

• @mmolari made their first contribution in #19
• @ivan-aksamentov made their first contribution in #27

Full Changelog: v0.4.1...0.5.0

v0.4.1

Smaller binaries: Artifacts now pulled in as needed.