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* updating muts of int to include nucletoide differences in addition to aa differences with help from @samcwiley * add missing aa logic back in * updating to obtain partial codon info as well * Some refactoring ideas * updating seq same length logic to match seqs aligned logic * adding amino acid "X" handling * created a hamming distance package that measures hamm dist of all of the seqs within a fasta * creating a package that compares all of the seqs within a fasta file and give the positions and nucleotide diffs btw them all * updating documentation * adding in tail handlilng logic * updating docs * start containerization * improving Dockerfile * update docker compose * init GitHub Actions workflow for building binaries across multiple targets * refactor GitHub Actions workflow to use OS matrix for builds and rust nightly * bug * bug * Update GitHub Actions workflow to trigger on all branches except main * bug * Strip images to keep them small * Use multi-stage build with latest nightly alpine image * Add check_chemistry for Illumina and ONT to replace python scripts in MIRA-NF (#13) Adds module for argument parsing/handling and selecting proper configuration filepaths and IRMA modules. --------- Co-authored-by: Sam Wiley <dzw2@cdp-client-02.biotech.cdc.gov> * add check_chemistry * tweaking files for docker * updating output * changed package name * adding documentation for adding a package to the workspace * Updating docs * updating docs * restructing readme situation * fix picture * fixing link and finishing up * fix link * link test * fix link * fix typo * fix pic * fix format * arguments and subplots per segment * subplots and variant data * Add consistent color generation for segment names in plots * read flow Sankey diagram * Refactor subplot layout and enhance annotations for segment names in coverage plots * Update .gitignore to exclude lock files * Fix typo in README and update package addition steps for clarity * adding mutation_of_interest package * compress logic and sest up structs for Serde * Reading in info with serde and structs * Remove some clones * removing lock file and adding to .gitignore * Updating docs * updating docs * restructing readme situation * fix pic * fix format * update documentation * typo fixes and adding output structure * fix header size * created a hamming distance package that measures hamm dist of all of the seqs within a fasta * creating a package that compares all of the seqs within a fasta file and give the positions and nucleotide diffs btw them all * updating documentation * Some refactoring ideas * updating seq same length logic to match seqs aligned logic * adding in tail handlilng logic * updating docs * init GitHub Actions workflow for building binaries across multiple targets * refactor GitHub Actions workflow to use OS matrix for builds and rust nightly * bug * bug * Update GitHub Actions workflow to trigger on all branches except main * bug * Update .gitignore to exclude all lock files recursively * Refactor plot coverage segment function to remove unused variable and simplify fallback formulas * mira-oxide logo * smaller logo * Update Cargo.toml and main.rs: comment out file count increment and enhance filename formatting for Sankey plot * Enhance Sankey plot: add hover templates and update title for clarity * Update Cargo.toml and main.rs: switch plotly dependency to Git; enhance argument help descriptions; explicit node x,y * Remove unused Label import from plotly common * Update plotly dependency to use Git repository * Remove mutations_of_interest_table package and update workspace members * merge cleanup -- plots working * update docs * tweaking package to include subtype as a filter when filtering variants of interest (#24) --------- Co-authored-by: Samuel Shepard <vfn4@cdc.gov> Co-authored-by: Ben Rambo-Martin <nbx0@cdc.gov> Co-authored-by: Ben Rambo-Martin <39743838+nbx0@users.noreply.github.com> Co-authored-by: Samuel Wiley <26017589+samcwiley@users.noreply.github.com> Co-authored-by: Sam Wiley <dzw2@cdp-client-02.biotech.cdc.gov>
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