v1.3.2

Bug Fixes:

• Resolved an issue where the build command failed to process MSA (Multiple Sequence Alignment) files when the --align flag was not specified. The tool now handles MSA inputs correctly in default mode.

• Addressed edge case failures in the sensitivity command.

v1.3.1

Improvements & Bug Fixes:

• The --align option is now supported in the sensitivity sub-command, enabling alignment of input sequences before sensitivity analysis.
• When the --align option is used in both build and sensitivity sub-commands, the aligned MSA file is saved in the specified output path for reference.
• A new --min-var option has been added for MSA input in the build sub-command. This option sets the minimum frequency threshold (default=0.01) for sequence variations generated from the MSA.
• The tiling sub-command now includes a --iterMul option (default=1), allowing users to specify a multiplier for the default number of iterations during PDR optimization.

v1.3.0

• Build an Olivar reference file (.olvr) with a multiple sequence alignment (MSA), or a group of unaligned sequences.
  • A concensus sequence is generated from the MSA and used as the reference.
  • A list of sequence variations is also called from the MSA.
  • mafft is used to make the MSA if input sequences are not already aligned, by adding the --align option.
• Check the sensitivity of existing primers against an MSA, with the new sensitivity sub-command.
  • Outputs primer alignments and sensitivity scores of each primer, as well as an interactive plot to view the primers and the MSA.
  • The previous validate sub-command is renamed as specificity.

v1.2.1

• FASTA header ID is used as the reference name by default, instead of the name of the FASTA file.
  The header ID is everything before a space character in the FASTA header ("EPI_ISL_402124" for EPI_ISL_402124.fasta). This will change the names and content of several output files, including

  1. Default name of the .olvr file
  2. Output file names of olivar tiling (e.g., EPI_ISL_402124.html)
  3. Columns in olivar-design.csv and olivar-design.primer.bed, as well as outputs of olivar validate (e.g., olivar-val_pool-1.csv)

• Fixed BED/ARTIC output format (see issue #17)

v1.2.0

• Support for multiple tiling targets (e.g., designing tiled amplicons for each Influenza A segment)
  • olivar tiling can also take multiple .olvr files in the same directory as input, and amplicons under each target will now have their names determined by the file name of the corresponding .olvr file (e.g., olivar-ref.olvr)
  • design title (olivar tiling --title) will not affect amplicon names, and will only determine output files names for the whole design (e.g., olivar-design.csv and olivar-design.scheme.bed)
  • output files are also generated for each target, including the html plot showing primers and risk scores (see the updated example_output/)
• Fixed incorrect coordinates in .scheme.bed files (issue #14)

v1.1.5

• Change license to GPL v3.0

v1.1.4

• Updated Loss function for short genomes (Loss is multiplied by 1/coverage^2).
• Added error messages for ambiguous bases (non 'A', 'T', 'C', 'G' bases).
• Fixed compatibility issues with Biopython (Bio.Blast.Applications.NcbiblastnCommandline have been deprecated).

v1.1.3

• Improved backward compatibility

v1.1.2

• Sanity check for input reference genome and variant list, with error messages for ambiguous bases and invalid values.
• Additional output file in ARTIC/PrimalScheme format.
• Bug fixed: when multiple variants with the same genome position is provided, the sum of frequencies of each variant should be calculated first, then the square root.
• Amplicon name is now the same as user provided title.