mSWEEP-v2.2.1 (16 October 2024)

What's Changed

• Initialize pointers (fixes issue #37 with --read-likelihood) by @jnalanko in #38

New Contributors

• @jnalanko made their first contribution in #38

Full Changelog: v2.2.0...v2.2.1

mSWEEP-v2.2.0 (11 September 2024)

What's Changed

• Add GPU accelerated abundance estimation by @Piketulus and @tmaklin in #34
• Remove remaining MPI code by @tmaklin in #35
• Bump actions/download-artifact from 2 to 4.1.7 by @tmaklin in #33

Full Changelog: v2.1.2...v2.2.0

mSWEEP-v2.1.2 (20 August 2024)

What's Changed

• Refactor input reading by @tmaklin in #31

Details

• Can now scale to inputs that are ~ 100 million queries x 50 000 targets in size.
• Remove dependency on telescope.
• More fixes related to parallelism in the input reading and likelihood construction phase.

Full Changelog: v2.1.1...v2.1.2

mSWEEP-v2.1.1 (15 August 2024)

What's Changed

• Parallelism & CI fixes by @tmaklin in #30

Full Changelog: v2.1.0...v2.1.1

mSWEEP-v2.1.0 (30 May 2024)

New features

• Allow adjusting zero inflation in the model with the --zero-inflation parameter. The default value is 0.01 which was used in the previous versions.

New experimental features:

• Implement the quality scores that were planned for v2.0.0. These can be enabled with the --run-rate toggle. (added in https://github.com/PROBIC/mSWEEP/tree/add-dirichlet-KLD-calculation)
• Implement option to ignore reference clusters that have 0 (or a higher number) alignments in the input using the --min-hits flag (saves memory on sparse inputs) (added in https://github.com/PROBIC/mSWEEP/tree/ignore-empty-groups)

Experimental feature implies that the user interface is not stable and is subject to change.

Enhancements

• Adjust --tol automatically to avoid convergence issues (resolves #25 and https://github.com/PROBIC/mSWEEP/tree/v2.0.1-dev)

Bugfixes

• Enable compression when reading plaintext alignment (#24)

Build changes:

• Update build pipeline to no longer require config files. (added in https://github.com/PROBIC/mSWEEP/tree/remove-config-files)

Continuous integration

• Compile binaries for macOS x86_64 and arm64 (#26 https://github.com/PROBIC/mSWEEP/tree/cross-compilation-compatibility)
• Github actions to compile binaries automatically. (added in https://github.com/PROBIC/mSWEEP/tree/add-prebuilt-binaries-CI-workflow)

Full Changelog: v2.0.0...v2.1.0

mSWEEP-v2.0.0 (4 July 2023)

First major version increment of mSWEEP (breaks backwards-compatibility).

Output format changes:

• Add the total number of reads to the abundances file (resolves #21)
• Renamed total_hits to num_aligned in the abundances file (#21)
• Status messages are now silenced by default but can be enabled with the --verbose toggle.

New features

• Added an option to evaluate the mGEMS binning algorithm from the mSWEEP call with the --bin-reads toggle. (54004d8)
• Support reading alignments compressed with alignment-writer. (f169fcc)
• Read alignments from cin. (9878f8e)

Removed features:

• Matching a fasta file to groups indicators is no longer supported (deprecated options --fasta, --groups-list, --groups-delimiter).

Pseudoaligner support

• Removed kallisto support (remove-kallisto-support)
• Removed support for Themisto v1.2.0 and older. (remove-kallisto-support)

Installation

• Added a conda recipe and instructions on installing mSWEEP from bioconda. (#22)

Build pipeline changes

• Require C++17 to build from source.
• Removed support for building zlib from source (5c94591)
• Added the CMAKE_BUILD_WITH_FLTO flag for building with link-time optimization (ee1db01)

Internal changes

• Bump C++ standard to C++17.
• Rewrote most of the codebase.
• Fixed dependency versions to avoid conflicts.

mSWEEP-v2.0.0-prerelease3 (29 March 2023)

Prerelease version of mSWEEP v2.0.0, pending some further testing.

mSWEEP-v1.6.3 (1 February 2023)

Fix build issues caused by an update in one of the dependencies.

mSWEEP-v1.6.2 (12 August 2022)

Updated dependencies and bug hunting.

Bug fixes

• Fix interaction of --no-fit-model with WriteResults.
• Skip erroneously trying to write the probability matrix if --no-fit-model was toggled.

Updated dependencies

Use telescope v0.4.0

• About 10x speedup in reading pseudoalignments.
• May reduce the memory footprint on large input.

Use rcgpar v1.0.2

• Fixes MPI estimation when the input data dimensions exceed the capacity of 32 bit signed integers.
• Enables compilation without MPI support even when MPI headers are present on the system.

Internal changes

• Rename log.hpp -> msweep_log.hpp and correct the header guard to avoid some conflicts with dependencies.

Build pipeline

• Use the CMAKE_ENABLE_MPI_SUPPORT flag to compile with or without support for MPI.

mSWEEP-v1.6.1 (5 May 2022)

Changes:

• Updated dependency bxzstr to v1.1.0.
• Disabled zstd support from bxzstr by default.
• • Support can be enabled when compiling by changing -D ZSTD_FOUND=0 to -D ZSTD_FOUND=1 in config/CMakeLists-bxzstr.txt.in but requires also handling linking in the main CMakeLists.txt file.