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.