mGEMS-v1.3.3 (20 August 2024)

What's Changed

• Get rid of the telescope dependency by rewriting the input reading code around it.
• Autodetect csv or tsv format for --probs.
• Update prebuilt binaries workflow.
• Add an undocumented -t option for using more threads on linux.

Full Changelog: v1.3.2...v1.3.3

mGEMS-v1.3.2 (4 June 2024)

What's Changed

• Add installation instructions for conda installation by @tmaklin in #20
• Add GitHub actions workflow for building the precompiled binaries by @tmaklin in #22
• Update build pipeline and dependencies. by @tmaklin in #23
• Add precompiled macOS arm64 binaries by @tmaklin in #24

Full Changelog: v1.3.1...v1.3.2

mGEMS-v1.3.1 (24 April 2023)

Update dependency seamat to v0.2.1. This fixes a bug with very large inputs that could arise in some build configurations.

mGEMS-v1.3.0 (1 February 2023)

Mostly internal changes to accommodate future plans.

Changelog

New features

• Allow reading pseudoalignment files that have been compacted with alignment-writer library. The format is detected automatically.

Build pipeline

• Require c++17.
• Build using relative paths.
• Add alignment-writer and seamat as dependencies.
• Update other dependencies versions.

Internal changes

• Implement BinFromMatrix to bin directly from the probability matrix (allows calling binning in other projects through the mGEMS headers).
• Refactor the code to allow the above.

mGEMS-v1.2.0 (20 November 2021)

Added compatibility with the changes to Themisto's command line interface and new index file structure in Themisto v2.0.0.

New feature

Added the -i argument for inputting the mSWEEP group indicators file to mGEMS so that the number of the reference sequences in the pseudoalignment can be determined.

• If mGEMS can't find the Themisto <=v1.2.0 files in the --themisto-index directory and the -i argument is not supplied, the program will throw an error instructing the user to supply the -i argument.
• If the files are found, the -i argument is ignored and the program functions as it did previously.

Documentation

• Updated documentation with usage instructions for both Themisto <=v1.2..0 and >=v2.0.0.

mGEMS-v1.1.0 (20 October 2021)

Submitted & accepted edition:

New features

--unique-only option to write out only the reads that are assigned to a single lineage.

--write-unassigned option to write the reads that are not assigned to any lineage at all.

• Writes the unassigned_reads_*.fastq files in the output directory when running in combined mode with call mGEMS --write-unassigned.
• Writes the unassigned_reads.bin file to the output directory when called with mGEMS bin --write-unassigned.
• The unassigned_reads.bin file can be passed to mGEMS extract --bins unassigned_reads.bin as argument.

--write-assignment-table option to write the raw read to group assignments as a table.

• Writes the reads_to_groups.tsv tab separated table to the output directory if called with mGEMS --write-assignment-table or mGEMS bin --write-assignment-table.
• The first column of the table contains the read ids (line numbers in .fastq files divided by 4). The column, and by extension the table, are unsorted. Use sort -gk1 reads_to_groups.tsv if you need the table in a sorted format.
• The first row contains the names of the reference groups.
• The table is written in compressed format by default. This can be toggled off with --compress.

Code restructuring

• Removed many unused functions, variables, and parameters.
• Restructuring of the source code files to enable implementing the new features.
• Cleaned up the headers.
• Moved some functions and function calls to more appropriate places.
• Added documentation for the functions in bin_reads.h and extract_bin.h and some functions in bin_reads.cpp.

Build pipeline & dependencies

• The external library handling input/output file validations is now available on GitHub. Download the code when building instead of shipping with mGEMS.
• Bump telescope version to 0.2.1 and reuse common dependencies.

mGEMS-v1.0.0 (2 April 2020)

Public release edition.

What's new

• Add a tutorial for reproducing the E. coli, E. faecalis, and S. aureus experiments from the mGEMS paper.
• Add the '--min-abundance' option for filtering the target bins by some minimum abundance threshold.

mGEMS-v0.2.0 (8 March 2020)

mGEMS-v0.2.0 (8 March 2020)

Single executable edition.

• Install dependencies with cmake rather than with git submodules.
• Sanify the codebase.
• Create the single mGEMS executable; shorthand for running mGEMS bin (bin the reads) and mGEMS extract (extract bins from a mixed sample).
• Support working with Themisto files natively.
• Error checking for input files and directories.
• Validate number of pseudoalignment targets by requiring the Themisto pseudoalignment index as input instead of --n-refs.
• Use the functions from telescope natively.
• Incorporate the rest of the shell commands in the mGEMS codebase.

v0.1.1

- Better documentation (usage instructions).
- Supply telescope with the installation
- Fix issues with parsing arguments by updating the library.

v0.1.0

Basic functionality in a relatively easy-to-use form + usage instructions.