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feat: porting ngsderive#35

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a-frantz wants to merge 91 commits intomainstjude-rust-labs/ngs:mainfrom a-frantz/ngsderivestjude-rust-labs/ngs:a-frantz/ngsderiveCopy head branch name to clipboard

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Commits on Dec 3, 2023

• feat(derive): new readlen subcommand

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Commits on Dec 4, 2023

• fix(derive/command/readlen): proper error message

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• [WIP] protoype for endedness and skeleton of encoding

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Commits on Dec 5, 2023

• [WIP]: doesn't compile. Begin implementing RPT calculations

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• revise: applies Clay's edits

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Commits on Dec 6, 2023

• [WIP]: Broken, not compiling. starting to calc RPT.

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• [WIP]

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Commits on Dec 7, 2023

• feat: working derive endedness subcommand

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Commits on Dec 8, 2023

• chore: better comments/test name/log message

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Commits on Dec 9, 2023

• fix: apply some of Clay's performance suggestions

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• fix(derive/endedness/compute.rs): test updates

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• chore(derive/readlen/compute): cleanup

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Commits on Dec 10, 2023

• fix(derive/command/endedness): try using HashMap instead of Trie

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Commits on Dec 11, 2023

• feat(derive/command/endedness): lazy record reading

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Commits on Dec 14, 2023

• Revert "feat(derive/command/endedness): lazy record reading"

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• tests(derive/endedness/comput): reimplement tests

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• [WIP] suggestions from @zaeleus. Compiler error

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Commits on Dec 15, 2023

• tests(derive/command/endedness): rewrite tests with latest changes

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• chore(endedness): handle error where RG tag can't be parsed as_str()

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• fix(endedness): remove all Arcs and lazy_statics

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• refactor(derive/readlen): move num_samples counting to outer func

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• perf(derive/readlen): don't iterate through all read_lengths

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• feat(derive/endedness): add validate_read_group_info() call

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• fix: typos

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• revert

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• revert

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• fix: corrections made after previous reverts

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• tests(derive/endedness): reimplement tests

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Commits on Dec 16, 2023

• chore(derive): disable index checking when not needed

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• chore:(derive/readlen): return an anyhow::Ok instead of plain Ok

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• docs(derive/readlen): correction in module name

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• docs(derive/endedness): fix docs referring to wrong subcommand

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Commits on Dec 18, 2023

• fix: cap QNAME warnings to 100 QNAMES

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Commits on Dec 20, 2023

• feat(src/derive): use NumberOfRecords and RecordCounter structs

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• style: make arg_in_range() nicer everywhere its used

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Commits on Dec 22, 2023

• [WIP]: junction annotation

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Commits on Dec 26, 2023

• feat(derive): junction-annotation subcommand

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• chore: remove radix_trie dep

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• feat(derive/junction-annotation): better results reporting

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Commits on Dec 27, 2023

• docs(derive/junction_annotation): be more clear in results docs

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Commits on Dec 28, 2023

• feat(derive/junction_annotation): add short options to params

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• chore: return anyhow::Ok where appropriate

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• tests: add a test for process() and summarize()

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• chore: typos

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Commits on Jan 10, 2024

• feat: remove fuzzy searching ability. Boosts performance as well.

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Commits on Feb 6, 2024

• feat: first pass implementation of encoding

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Commits on Feb 8, 2024

• [WIP] to share code. Partial strandedness implementation

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• fix(derive/endedness): add logic for 0x1 bit

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• [WIP] pushing to share. Partial strandedness implementation

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• style: rename ignored_flags to filtered_by_flags

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• feat: derive strandedness (prototype)

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Commits on Feb 9, 2024

• style: much prettier code. One broken test.

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• refactor: make read_groups util nicer

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• refactor(derive/strandedness): separate out results from compute

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• fix(strandedness): break when successful

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• docs: junction_annotation to junction-annotation

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• [WIP]: switch min_mapq to a proper MappingQuality

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Commits on Feb 10, 2024

• fix: rework MappingQuality argument to work

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• style: f32 -> f64 and code cleanup

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• feat: add a log_every param to RecordCounter

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• style: code clean up

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• style: use custom Strand enum more

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• fix: junction-annotation works again

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Commits on Feb 11, 2024

• feat(derive/instrument): behave more like other derive commands

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• fix(derive): print!(output) -> println!(output)

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• fix(derive/strandedness): move RG validation out of compute

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• tests(derive/endedness): fix the broken tests

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• style(derive/junction-annotation): group reported junctions by contig

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• fix: lots of code cleanup

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• tests(derive): all derive commands have tests

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Commits on Feb 12, 2024

• fix: consistently return Options for String results

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• style: prettify imports

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• style: wrap optional variable in Option

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• docs: fix intra links

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• tests: fix broken gene test

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• feat(derive/instrument): more debug statements

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Commits on Feb 13, 2024

• feat(derive/instrument): in output, report found unique names

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• feat: more info in JSON report. Not complete yet. Open TODOs

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• style(derive/instrument): a bit of code clean up

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• docs: filling in TODOs

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Commits on Feb 14, 2024

• chore: delete dead code

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• tests(derive/junction-annotation): rewrite tests more modular

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Commits on Feb 22, 2024

• stlye: Michael M. feedback

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Commits on Mar 22, 2024

• Apply suggestions from code review

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• fix(derive/endedness): complete rename from last commit

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• feat: use NonZeroUsize for Number of Records

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Commits on Mar 23, 2024

• feat(utils/args): improved behavior for NumberOfRecords CL utility

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• feat(derive): report by read group where appropriate and feasible

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Commits on Mar 25, 2024

• chore: removing dead code

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• tests(derive/instrument): assert that read groups succeed

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Commits on Aug 26, 2024

• fix(instrument): properly init flowcell entries

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