- implements the option to set custom taxon cutoffs allowing to extends default gene divergence cutoffs for any gene
- rename the default kraken files
- fix the output file writing after the consensus generation
- fix error during creation of the blutils output file if it not exists
- create-kraken2-db: allow deletion of files and dirs on check the path for the ouput of kraken database
- jsonl-output: include line breaks on write jsonl file
- implements the kraken database custom source files generator from a blast database
- renament blutils database generator use-case
- write-to-stdout: fix cli methods related to read and write data from stdin and stdout
- main
- allow stdin and stdout redirects
- replace all positional arguments of the cli by nominal arguments with exception of the query sequences
- tabular-result: fix the tabular columns order
- implements a cli command to convert the default blutils json result into a tabular result
- fix the consensus generation to replace the sequence hash by the original id during the blutils database generation
- improve the write or append to file auxiliary function to allow write to file with it oppened
- gh:issue4: include exceptions to enable the validation of chunked blast databases
- gh:issue3: The qiime default header was included into the generated qiime database
- implements a converter to build the qiime database from the blutils one
- fix the consensus generation to include additional information from the blast results
- wip - fix the database generation to allow low memory machines to generate databases
- refacrore blat command to split commands from execution parts
- build-db: fix bug on generate reference database which missing names data on load inicial taxdump database
- consensus-generation-use-case: fix the consensus generation issue that leads our algorithm to select a clade below the maximum expexted lca ideitity
- fix the multi-taxa filtration process
- fix the lca filtration process
- consensus-generation: fix the generation of the consensus identities that stop the search for subjects early without evaluate the full results
- finish the implementation of the consensus generator for the blast command
- replace the taxid by identifier in taxonomy parsing to allow input non taxid values
- set the non-linnaean rank other as untagged
- move the blast build use-cases to a dedicated module
- refactors building database related use-cases and dtos related to blast results generation
- refacores the blast run with consensus use-case to allow search for the code at the file level
- fix the database generation to includ eoptions to remove non-linnaean ranks to kept the database more consistene
- include the taxid when taxnames are not available allowing users to check identities
- include the main workspace package in cz tracked files
- fix the workspace dependency from local packages
- fix dependencies to local package to allow publish in crate
- fix the database building command
- wip - implements the database builder to create the initial database for blast runst
- replace the default log from tracing and refactores the workspace to share dependencies
- wip - start implementation of the database generator parts
- comment ref-database functionalities from the project temporary
- move the blast run to a dedicated submodule
- include kingdom as valida taxonomic rank
- include in debug message when an error is found on parse taxonomy
- upgrade cli port to include blast arguments as parameters
- main
- include a print function to output the user arguments on cli execution
- include taxonomy in results and review the taxid and rank information delivered to the output object
- include options to control the word-size during blast executions
- filter_rank_by_identity: remove unwanted print from filter_rank_by_identity use-case
- main
- fix bug on filter taxonomies by rank
- remove the min_consensus argument which is not used
- rename blastn execution entity and adapter to match the target of the execution which is the blastn
- remove unused dependencies from packages crates
- split the project into sub-crates to better manage dependencies
- main
- passthrough all blast builder arguments to the adapter executor
- implements the system check and upgrade logs to turn it better for human users
- implements the consensus check for multiple query results
- implements the identity based filtration of the taxon rank
- upgrade the cli port that execute the blast with consensus
- update consensus results to include a more informative results object
- split the parallel blast execution from the main use-case
- wip - start implemetation of the consensus check for the blast results
- create a method to parse taxonomy literals as a internal object
- wip - create the project base
- initial-commit
- change type of bit-score from int64 to float64
- fix image paths on readme file
- fix the sort order of imports of the identity based filtration
- remove old rustfmt file
- review the access control modifiers of the application