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Dev#22

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tmaklin merged 103 commits intomaintmaklin/kbo:mainfrom devtmaklin/kbo:devCopy head branch name to clipboardSep 25, 2024

+1,451-380

Commits

Commits on Sep 21, 2024

• Need rust >= v1.77.0 to build sbwt

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• Add integration test for sablast::map.

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Commits on Sep 22, 2024

• Remove overlapping cases from ms_to_run, write documentation.

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• Add docs to random_match_threshold

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• Add bounds checking

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• Characters -> bases in documentation.

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• Add k-bounded.

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• Clarify documentation

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• Merge run_to_aln and translate_runs.

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• Update test values.

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• Rewrite translate_runs and re-enable its test.

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• Use slice arguments in translate_runs

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• More documentation.

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• Create new module format for formatting results and move run_lengths.

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• Update integration test map_clbs.rs

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• Remove use of TranslateParams, replace with access to k, threshold.

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• Rename map.rs -> translate.rs

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• Split translate.rs into translate.rs and derandomize.rs

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Commits on Sep 23, 2024

• Docs formatting.

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• Better variable names.

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• Remove passing the noisy MS vec to translate_ms_vec (not needed).

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• Add asserts ti translate_ms_val

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• Update parameter names in documentation.

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• Fix compiler warnings.

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• Fix initialising derandomized ms vec when last MS is noise.

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• Update test

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• Add tests for translate_ms_val.

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• Add a more comprehensives test for translate_ms_vec that fails.

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• Take &[u8] in query_sbwt instead of the file name.

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• Rewrite and document load_sbwt

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• Document query_sbwt

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• Rewrote serialize_sbwt

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• Rewrite build_index

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• Rename build_sbwt to build_sbwt_from_file

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• Add build_sbwt_from_vecs to build from sequences in memory.

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• Always use sbwt::IndexVariant outside of index.rs.

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• Unwrap the lcs array when returning.

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• Update calls to index::

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• Document index.rs with examples.

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• Add tests.

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• Fix calling fns that take Some(BuildOpts) with None.

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• Fix failing test for translate_ms_vec.

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• Clear todo in translate_ms_vec test.

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• Add documentation examples to tests.

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• Add input checks to build_sbwt_from_vecs and query_sbwt.

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• Add examples to translate.rs documentation.

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• Always run all tests.

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• Add more documentation and examples.

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• Fix race condition in documentation tests.

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• Add test cases for derandomize_ms_val.

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• Documentation and examples for derandomize.rs

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• Fix comparison in build_serialize_load_sbwt.

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• Patch needletail to respect compression features; disable xz,bzip2.

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• Remove patch.crates-io (use build.rs script).

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• Revert "Remove patch.crates-io (use build.rs script)."

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• Revert "Patch needletail to respect compression features; disable xz,bzip2."

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• Fix clippy suggestions.

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• Add examples and tests with recombination.

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Commits on Sep 24, 2024

• Handle multiple files in seq_files by indexing them all at once.

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• Remove --input list from build and index everything to same file.

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• Move sablast build implementation to lib.rs.

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• Add documentation to build.

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• Minor fixes.

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• Implement multiple queries in map and parallelise over input files.

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• Move implementation of sablast map to find() in lib.rs.

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• Rename sablast map to sablast find.

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• Take &str instead of &String.

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• Add documentation to find.

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• Rename map to matches.

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• Document matches.

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• Fix typos.

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• Use matches in the test instead of map.

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• Revert "Use matches in the test instead of map."

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• Call map via the new find syntax.

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Commits on Sep 25, 2024

• Take &[u8] in find, matches and handle input reading elsewhere.

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• Update test

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• Handle fragmented queries in sablast find.

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• Don't add strand in find.

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• Add back reverse complements to sablast find.

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  f2a69b2

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• Update documentation

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• Update test.

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• Update examples

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• Take seq data instead of file names in build

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• Read input files in main.

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• Move input format detection docs to main.rs

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• Remove build_sbwt_from_file and the needletail wrapper.

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• Update

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• Add todo to fix a bug

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• Implement sablast map to map a query to a reference.

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• Only a single file at a time to sablast map.

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• Move formatting to format.rs

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• Read all data from query in sablast map, only take 1 query at a time

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• Move implementation of most file reads to read_fastx_file.

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• Document map

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• Map doesn't use rayon so remove it.

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• Fix derandomizing the first matching statistic.

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• Add hidden asserts to documentation tests.

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• Add hidden asserts to documentation tests.

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• Add hidden asserts where possible.

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• Add hidden asserts.

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• Disable compression in needletail.

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• Comment out the test.

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• Add reminder to implement refine_translation.

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