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feat: porting ngsderive #35

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feat: porting ngsderive #35

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Commits on Dec 3, 2023

  1. feat(derive): new readlen subcommand

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    a-frantz committed Dec 3, 2023
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Commits on Dec 4, 2023

  1. fix(derive/command/readlen): proper error message

    @a-frantz
    a-frantz committed Dec 4, 2023
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  2. [WIP] protoype for endedness and skeleton of encoding

    @a-frantz
    a-frantz committed Dec 4, 2023
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Commits on Dec 5, 2023

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

    @a-frantz
    a-frantz committed Dec 5, 2023
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  2. revise: applies Clay's edits

    @claymcleod
    claymcleod committed Dec 5, 2023
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Commits on Dec 6, 2023

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

    @a-frantz
    a-frantz committed Dec 6, 2023
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  2. [WIP]

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    a-frantz committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. feat: working derive endedness subcommand

    @a-frantz
    a-frantz committed Dec 7, 2023
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Commits on Dec 8, 2023

  1. chore: better comments/test name/log message

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    a-frantz committed Dec 8, 2023
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Commits on Dec 9, 2023

  1. fix: apply some of Clay's performance suggestions

    @a-frantz
    a-frantz committed Dec 9, 2023
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  2. fix(derive/endedness/compute.rs): test updates

    @a-frantz
    a-frantz committed Dec 9, 2023
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  3. chore(derive/readlen/compute): cleanup

    @a-frantz
    a-frantz committed Dec 9, 2023
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Commits on Dec 10, 2023

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

    @a-frantz
    a-frantz committed Dec 10, 2023
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Commits on Dec 11, 2023

  1. feat(derive/command/endedness): lazy record reading

    @a-frantz
    a-frantz committed Dec 11, 2023
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Commits on Dec 14, 2023

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

    This reverts commit 553fd68.
    @a-frantz
    a-frantz committed Dec 14, 2023
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  2. tests(derive/endedness/comput): reimplement tests

    @a-frantz
    a-frantz committed Dec 14, 2023
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  3. [WIP] suggestions from @zaeleus. Compiler error

    @a-frantz
    a-frantz committed Dec 14, 2023
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Commits on Dec 15, 2023

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

    @a-frantz
    a-frantz committed Dec 15, 2023
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  2. chore(endedness): handle error where RG tag can't be parsed as_str()

    @a-frantz
    a-frantz committed Dec 15, 2023
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  3. fix(endedness): remove all Arcs and lazy_statics

    @a-frantz
    a-frantz committed Dec 15, 2023
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  4. refactor(derive/readlen): move num_samples counting to outer func

    @a-frantz
    a-frantz committed Dec 15, 2023
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  5. perf(derive/readlen): don't iterate through all read_lengths

    @a-frantz
    a-frantz committed Dec 15, 2023
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  6. feat(derive/endedness): add validate_read_group_info() call

    @a-frantz
    a-frantz committed Dec 15, 2023
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  7. fix: typos

    @a-frantz
    a-frantz committed Dec 15, 2023
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  8. revert

    @a-frantz
    a-frantz committed Dec 15, 2023
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  9. revert

    @a-frantz
    a-frantz committed Dec 15, 2023
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  10. fix: corrections made after previous reverts

    @a-frantz
    a-frantz committed Dec 15, 2023
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  11. tests(derive/endedness): reimplement tests

    @a-frantz
    a-frantz committed Dec 15, 2023
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Commits on Dec 16, 2023

  1. chore(derive): disable index checking when not needed

    @a-frantz
    a-frantz committed Dec 16, 2023
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  2. chore:(derive/readlen): return an anyhow::Ok instead of plain Ok

    @a-frantz
    a-frantz committed Dec 16, 2023
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  3. docs(derive/readlen): correction in module name

    @a-frantz
    a-frantz committed Dec 16, 2023
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  4. docs(derive/endedness): fix docs referring to wrong subcommand

    @a-frantz
    a-frantz committed Dec 16, 2023
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Commits on Dec 18, 2023

  1. fix: cap QNAME warnings to 100 QNAMES

    @a-frantz
    a-frantz committed Dec 18, 2023
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Commits on Dec 20, 2023

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

    @a-frantz
    a-frantz committed Dec 20, 2023
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  2. style: make arg_in_range() nicer everywhere its used

    @a-frantz
    a-frantz committed Dec 20, 2023
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Commits on Dec 22, 2023

  1. [WIP]: junction annotation

    @a-frantz
    a-frantz committed Dec 22, 2023
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Commits on Dec 26, 2023

  1. feat(derive): junction-annotation subcommand

    @a-frantz
    a-frantz committed Dec 26, 2023
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  2. chore: remove radix_trie dep

    @a-frantz
    a-frantz committed Dec 26, 2023
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  3. feat(derive/junction-annotation): better results reporting

    @a-frantz
    a-frantz committed Dec 26, 2023
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Commits on Dec 27, 2023

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

    @a-frantz
    a-frantz committed Dec 27, 2023
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Commits on Dec 28, 2023

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

    @a-frantz
    a-frantz committed Dec 28, 2023
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  2. chore: return anyhow::Ok where appropriate

    @a-frantz
    a-frantz committed Dec 28, 2023
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  3. tests: add a test for process() and summarize()

    @a-frantz
    a-frantz committed Dec 28, 2023
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  4. chore: typos

    @a-frantz
    a-frantz committed Dec 28, 2023
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Commits on Jan 10, 2024

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

    @a-frantz
    a-frantz committed Jan 10, 2024
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Commits on Feb 6, 2024

  1. feat: first pass implementation of encoding

    @a-frantz
    a-frantz committed Feb 6, 2024
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Commits on Feb 8, 2024

  1. [WIP] to share code. Partial strandedness implementation

    @a-frantz
    a-frantz committed Feb 8, 2024
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  2. fix(derive/endedness): add logic for 0x1 bit

    @a-frantz
    a-frantz committed Feb 8, 2024
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  3. [WIP] pushing to share. Partial strandedness implementation

    @a-frantz
    a-frantz committed Feb 8, 2024
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  4. style: rename ignored_flags to filtered_by_flags

    @a-frantz
    a-frantz committed Feb 8, 2024
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  5. feat: derive strandedness (prototype)

    @a-frantz
    a-frantz committed Feb 8, 2024
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Commits on Feb 9, 2024

  1. style: much prettier code. One broken test.

    @a-frantz
    a-frantz committed Feb 9, 2024
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  2. refactor: make read_groups util nicer

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    a-frantz committed Feb 9, 2024
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  3. refactor(derive/strandedness): separate out results from compute

    @a-frantz
    a-frantz committed Feb 9, 2024
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  4. fix(strandedness): break when successful

    @a-frantz
    a-frantz committed Feb 9, 2024
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  5. docs: junction_annotation to junction-annotation

    @a-frantz
    a-frantz committed Feb 9, 2024
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  6. [WIP]: switch min_mapq to a proper MappingQuality

    @a-frantz
    a-frantz committed Feb 9, 2024
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Commits on Feb 10, 2024

  1. fix: rework MappingQuality argument to work

    @a-frantz
    a-frantz committed Feb 10, 2024
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  2. style: f32 -> f64 and code cleanup

    @a-frantz
    a-frantz committed Feb 10, 2024
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  3. feat: add a log_every param to RecordCounter

    @a-frantz
    a-frantz committed Feb 10, 2024
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  4. style: code clean up

    @a-frantz
    a-frantz committed Feb 10, 2024
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  5. style: use custom Strand enum more

    @a-frantz
    a-frantz committed Feb 10, 2024
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  6. fix: junction-annotation works again

    @a-frantz
    a-frantz committed Feb 10, 2024
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Commits on Feb 11, 2024

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

    @a-frantz
    a-frantz committed Feb 11, 2024
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  2. fix(derive): print!(output) -> println!(output)

    @a-frantz
    a-frantz committed Feb 11, 2024
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  3. fix(derive/strandedness): move RG validation out of compute

    @a-frantz
    a-frantz committed Feb 11, 2024
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  4. tests(derive/endedness): fix the broken tests

    @a-frantz
    a-frantz committed Feb 11, 2024
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  5. style(derive/junction-annotation): group reported junctions by contig

    @a-frantz
    a-frantz committed Feb 11, 2024
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  6. fix: lots of code cleanup

    @a-frantz
    a-frantz committed Feb 11, 2024
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  7. tests(derive): all derive commands have tests

    @a-frantz
    a-frantz committed Feb 11, 2024
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Commits on Feb 12, 2024

  1. fix: consistently return Options for String results

    @a-frantz
    a-frantz committed Feb 12, 2024
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  2. style: prettify imports

    @a-frantz
    a-frantz committed Feb 12, 2024
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  3. style: wrap optional variable in Option

    @a-frantz
    a-frantz committed Feb 12, 2024
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  4. docs: fix intra links

    @a-frantz
    a-frantz committed Feb 12, 2024
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  5. tests: fix broken gene test

    @a-frantz
    a-frantz committed Feb 12, 2024
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  6. feat(derive/instrument): more debug statements

    @a-frantz
    a-frantz committed Feb 12, 2024
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Commits on Feb 13, 2024

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

    @a-frantz
    a-frantz committed Feb 13, 2024
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  2. feat: more info in JSON report. Not complete yet. Open TODOs

    @a-frantz
    a-frantz committed Feb 13, 2024
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  3. style(derive/instrument): a bit of code clean up

    @a-frantz
    a-frantz committed Feb 13, 2024
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  4. docs: filling in TODOs

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    a-frantz committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. chore: delete dead code

    @a-frantz
    a-frantz committed Feb 14, 2024
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  2. tests(derive/junction-annotation): rewrite tests more modular

    @a-frantz
    a-frantz committed Feb 14, 2024
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Commits on Feb 22, 2024

  1. stlye: Michael M. feedback

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    a-frantz committed Feb 22, 2024
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Commits on Mar 22, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Clay McLeod <[email protected]>
    @a-frantz @claymcleod
    a-frantz and claymcleod authored Mar 22, 2024
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  2. fix(derive/endedness): complete rename from last commit

    @a-frantz
    a-frantz committed Mar 22, 2024
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  3. feat: use NonZeroUsize for Number of Records

    @a-frantz
    a-frantz committed Mar 22, 2024
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Commits on Mar 23, 2024

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

    @a-frantz
    a-frantz committed Mar 23, 2024
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  2. feat(derive): report by read group where appropriate and feasible

    @a-frantz
    a-frantz committed Mar 23, 2024
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Commits on Mar 25, 2024

  1. chore: removing dead code

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    a-frantz committed Mar 25, 2024
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  2. tests(derive/instrument): assert that read groups succeed

    @a-frantz
    a-frantz committed Mar 25, 2024
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Commits on Aug 26, 2024

  1. fix(instrument): properly init flowcell entries

    @a-frantz
    a-frantz committed Aug 26, 2024
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