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PanGraph Changelog

v0.7.3

  • 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.

v0.7.2

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

v0.7.1

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

v0.7.0

  • 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

v0.6.3

  • 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.

v0.6.2

  • 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

  • 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

  • added mmseqs2 as an alternative alignment kernel that guarantees higher sensitivity at the expense of longer computational time, see #33.
  • updated Docker file to include mmseqs2 in the container.
  • 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.

v0.5.0

  • 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

Full changelog

v0.4.1

  • Smaller binaries: Artifacts now pulled in as needed.

v0.4.0

  • Marginalize command now (optionally) takes list of strains to project onto.
  • Command line arguments and flags can now be mixed in order.
  • Export can filter out any duplications.

v0.3.0

Added command line options:

  • Build: -u => force sequences to uppercase letters
  • Polish: -c => preserve case (uses MAFFT command line flag) Additionally, removed bug associated with sequences mapping as empty intervals to blocks.

Lastly, large improvement to the algorithm's multicore usage by balancing the initial guide tree.

v0.2.1

Modified CLI to accept input on standard input for all subcommands. This allows for a nicer chaining of pangraph functions from the shell. Additionally, there were many small bugs that are fixed.

v0.1-alpha

Source code bundled as a relocatable application. Currently only for Linux-based operating systems but intend to release for MacOSX as well.