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.