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Dev #3573

Merged
merged 185 commits into from
Aug 22, 2023
Merged

Dev #3573

merged 185 commits into from
Aug 22, 2023

Commits on Jul 27, 2023

  1. add gt configs

    @hanars
    hanars committed Jul 27, 2023
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  2. inheritance search

    @hanars
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  3. custom genotype inheritance

    @hanars
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  4. clean up

    @hanars
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  5. codacy cleanup

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Commits on Jul 28, 2023

  1. quality filter

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  2. add tests

    @hanars
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  3. codacy cleanup

    @hanars
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  4. update export parsing for hail backend;

    @hanars
    hanars committed Jul 28, 2023
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  5. add freq filter

    @hanars
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  6. unit tests

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Commits on Jul 31, 2023

  1. add loactioan filtering

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  2. update fixtures

    @hanars
    hanars committed Jul 31, 2023
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  3. shared location search constant

    @hanars
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  4. Merge branch 'hail-backend-projects-response' of https://github.com/b… 

    …roadinstitute/seqr into hail-backend-filter-inheritance
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  5. Merge branch 'hail-backend-projects-response' of https://github.com/b… 

    …roadinstitute/seqr into hail-backend-frequency-filter
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  6. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-location
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  7. unit tests

    @hanars
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  8. clean up

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  9. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-location
    @hanars
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  10. remove unused test code

    @hanars
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  11. fix new fixture ids

    @hanars
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  12. add in silico filtering

    @hanars
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  13. unit tests

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Commits on Aug 1, 2023

  1. Bump aiohttp from 3.8.4 to 3.8.5 in /hail_search 

    Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.8.4 to 3.8.5.
- [Release notes](https://github.com/aio-libs/aiohttp/releases)
- [Changelog](https://github.com/aio-libs/aiohttp/blob/v3.8.5/CHANGES.rst)
- [Commits](aio-libs/aiohttp@v3.8.4...v3.8.5)

---
updated-dependencies:
- dependency-name: aiohttp
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
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  2. Merge pull request #3533 from broadinstitute/dependabot/pip/hail_sear… 

    …ch/aiohttp-3.8.5

Bump aiohttp from 3.8.4 to 3.8.5 in /hail_search
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Commits on Aug 2, 2023

  1. Bump cryptography from 41.0.2 to 41.0.3 

    Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.2 to 41.0.3.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@41.0.2...41.0.3)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
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  2. Merge pull request #3534 from broadinstitute/dependabot/pip/cryptogra… 

    …phy-41.0.3

Bump cryptography from 41.0.2 to 41.0.3
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  3. Merge pull request #3521 from broadinstitute/hail-backend-export-fix 

    update export parsing for hail backend
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  4. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-filter-inheritance
    @hanars
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  5. add missing newline

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  6. Merge branch 'hail-backend-filter-inheritance' of https://github.com/… 

    …broadinstitute/seqr into hail-backend-filter-quality
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  7. Merge pull request #3519 from broadinstitute/hail-backend-filter-inhe… 

    …ritance

Hail backend filter inheritance
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  8. pr feedback

    @hanars
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  9. fix test

    @hanars
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  10. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-frequency-filter
    @hanars
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  11. handle empty fre filters

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  12. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-location
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  13. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-in-silico-filter
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  14. Merge pull request #3520 from broadinstitute/hail-backend-filter-quality 

    Hail backend filter quality
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  15. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-frequency-filter
    @hanars
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  16. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-location
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  17. Merge branch 'hail-backend-frequency-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-in-silico-filter
    @hanars
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  18. use cached property

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  19. clean up add chr prefix logic

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  20. Merge pull request #3522 from broadinstitute/hail-backend-frequency-f… 

    …ilter

Hail backend frequency filter
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  21. save table globals to class instance

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  22. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-in-silico-filter
    @hanars
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  23. Merge branch 'hail-backend-enum-setting' of https://github.com/broadi… 

    …nstitute/seqr into hail-backend-in-silico-filter
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  24. codacy fix

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  25. first pass annotation filter

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  26. first pass annotation filter

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  27. pr feedback

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  28. Merge branch 'hail-backend-in-silico-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-annotations
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  29. Merge branch 'hail-backend-enum-setting' of https://github.com/broadi… 

    …nstitute/seqr into hail-backend-in-silico-filter
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  30. Merge branch 'hail-backend-in-silico-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-annotations
    @hanars
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  31. shared in silico filters

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Commits on Aug 3, 2023

  1. add range enum filter

    @hanars
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  2. clean up or filter

    @hanars
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  3. annotate which consequences pass

    @hanars
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  4. cleaner annotations

    @hanars
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  5. class specific consequences

    @hanars
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  6. clean up override consequence annotation

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  7. do not modify override ilters

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  8. Merge pull request #3528 from broadinstitute/hail-backend-filter-loca… 

    …tion

Hail backend filter location
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  9. Merge pull request #3536 from broadinstitute/hail-backend-enum-setting 

    save table globals to class instance
    @hanars
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  10. add unit tests

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  11. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-in-silico-filter
    @hanars
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  12. fix merge

    @hanars
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  13. Merge branch 'hail-backend-in-silico-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-annotations
    @hanars
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Commits on Aug 4, 2023

  1. codacy clean up

    @hanars
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  2. seelcted main transcript field

    @hanars
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  3. add selected transcript and tests

    @hanars
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  4. pr feedback

    @hanars
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  5. use hl.any

    @hanars
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  6. use hl.all

    @hanars
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  7. Merge branch 'hail-backend-in-silico-filter' of https://github.com/br… 

    …oadinstitute/seqr into hail-backend-filter-annotations
    @hanars
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  8. clean up _or_filter

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  9. Merge pull request #3530 from broadinstitute/hail-backend-in-silico-f… 

    …ilter

Hail backend - In-silico filter
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  10. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-filter-annotations
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  11. Merge branch 'hail-backend-filter-annotations' of https://github.com/… 

    …broadinstitute/seqr into hail-backend-selected-transcript
    @hanars
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  12. abstract logic for filter table loading

    @hanars
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  13. path quality override

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Commits on Aug 7, 2023

  1. add freq path override

    @hanars
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  2. pdate freq override tests

    @hanars
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  3. fix unit tests

    @hanars
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  4. pr feedback

    @hanars
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  5. initial comp het implementation

    @hanars
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  6. format results

    @hanars
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  7. clean up annotation recompute

    @hanars
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  8. clean up genotype logic

    @hanars
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  9. fix all inheritance filter

    @hanars
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  10. merge project fields

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Commits on Aug 8, 2023

  1. secondary csq

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  2. cleaner comp het filter logic

    @hanars
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  3. fix comp het search

    @hanars
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  4. test secondary annotations

    @hanars
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  5. codacy clean up

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  6. pr feedback

    @hanars
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  7. fix decipher link

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  8. Merge pull request #3537 from broadinstitute/hail-backend-filter-anno… 

    …tations

Hail backend - filter annotations
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Commits on Aug 9, 2023

  1. fix: requirements.txt to reduce vulnerabilities 

    The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-5813745
- https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-5813746
- https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-5813750
    @snyk-bot
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  2. clean up super usage

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  3. Merge pull request #3538 from broadinstitute/hail-backend-selected-tr… 

    …anscript

Hail backend selected transcript
    @hanars
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  4. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-comp-het
    @hanars
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  5. only run cram check weekly

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  6. Merge pull request #3540 from broadinstitute/hail-backend-clinvar-ove… 

    …rrides

Hail backend - clinvar overrides
    @hanars
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  7. optimize tpm query

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  8. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-comp-het
    @hanars
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  9. clean p merge

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Commits on Aug 10, 2023

  1. use db index for query

    @hanars
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  2. cache globals for hail backend

    @hanars
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  3. add comp het only annotation secondary test

    @hanars
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  4. codacy tweaks

    @hanars
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  5. pr feedback

    @hanars
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  6. add sorts

    @hanars
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  7. add sort tests

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Commits on Aug 11, 2023

  1. Merge pull request #3544 from broadinstitute/snyk-fix-66471e31a5924ad… 

    …0e9e790348506528b

[Snyk] Security upgrade cryptography from 41.0.2 to 41.0.3
    @hanars
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  2. Merge pull request #3543 from broadinstitute/decipher-link-update 

    fix decipher link
    @hanars
    hanars authored Aug 11, 2023
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  3. update changelog

    @hanars
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  4. test remaining sorts

    @hanars
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  5. codacy fixes

    @hanars
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  6. Merge pull request #3546 from broadinstitute/saved-variant-timeout-fix 

    Saved variant timeout fix
    @hanars
    hanars authored Aug 11, 2023
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  7. use correc message field for error

    @hanars
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  8. add af prefilter

    @hanars
    hanars committed Aug 11, 2023
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  9. updat etests

    @hanars
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  10. clean up

    @hanars
    hanars committed Aug 11, 2023
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  11. fix tests

    @hanars
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  12. add gene counts endpoint

    @hanars
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  13. Merge branch 'hail-backend-sort' of https://github.com/broadinstitute… 

    …/seqr into hail-backend-gene-counts
    @hanars
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  14. use geen_ids helper

    @hanars
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  15. tes gene counts

    @hanars
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Commits on Aug 14, 2023

  1. use data type specific gregor metadata

    @hanars
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  2. update test to pass

    @hanars
    hanars committed Aug 14, 2023
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  3. update test to pass

    @hanars
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  4. test wrond data in airtable case

    @hanars
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Commits on Aug 15, 2023

  1. update test fixtures

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  2. add mock airtable data

    @hanars
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  3. abstract gregor checks

    @hanars
    hanars committed Aug 15, 2023
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  4. test multiple data types

    @hanars
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  5. clean up

    @hanars
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  6. handle dup individual ids for sample metadata

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  7. Merge branch 'sample-metadata-handle-dup-ids' of https://github.com/b… 

    …roadinstitute/seqr into gregor-metadata-airtable-update
    @hanars
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  8. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-comp-het
    @hanars
    hanars committed Aug 15, 2023
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  9. pr feedback

    @hanars
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  10. Merge branch 'hail-backend-comp-het' of https://github.com/broadinsti… 

    …tute/seqr into hail-backend-sort
    @hanars
    hanars committed Aug 15, 2023
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  11. shared population sort config

    @hanars
    hanars committed Aug 15, 2023
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  12. add conditional validation

    @hanars
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  13. add rna columns

    @hanars
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  14. add rna airtable data

    @hanars
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  15. clean up column order

    @hanars
    hanars committed Aug 15, 2023
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  16. get tests passing

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Commits on Aug 16, 2023

  1. Merge pull request #3551 from broadinstitute/hail-backend-error-fix 

    use correct message field for error
    @hanars
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  2. fix: requirements.txt to reduce vulnerabilities 

    The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-5813746
    @snyk-bot
    snyk-bot committed Aug 16, 2023
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  3. clean up gregor file config

    @hanars
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  4. add experiment lookup file

    @hanars
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  5. test empty rna data

    @hanars
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  6. test rna data

    @hanars
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  7. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-af-prefilter
    @hanars
    hanars committed Aug 16, 2023
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  8. pr feedback

    @hanars
    hanars committed Aug 16, 2023
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  9. better validation

    @hanars
    hanars committed Aug 16, 2023
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  10. add tests

    @hanars
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  11. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-comp-het
    @hanars
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  12. pr feedback

    @hanars
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  13. Merge pull request #3552 from broadinstitute/hail-backend-af-prefilter 

    Hail backend - AF prefilter
    @hanars
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  14. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-comp-het
    @hanars
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  15. Merge branch 'hail-backend-comp-het' of https://github.com/broadinsti… 

    …tute/seqr into hail-backend-sort
    @hanars
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Commits on Aug 17, 2023

  1. Merge pull request #3542 from broadinstitute/hail-backend-comp-het 

    Hail backend - compound het/ recessive search
    @hanars
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  2. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-cache-globals
    @hanars
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  3. Merge pull request #3547 from broadinstitute/hail-backend-cache-globals 

    cache globals for hail backend
    @hanars
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  4. Merge pull request #3555 from broadinstitute/sample-metadata-handle-d… 

    …up-ids

handle dup individual ids for sample metadata
    @hanars
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  5. Merge pull request #3557 from broadinstitute/snyk-fix-e1d38c9fd3ae19b… 

    …4ea498acda2c3bb33

[Snyk] Security upgrade cryptography from 41.0.2 to 41.0.3
    @hanars
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  6. Merge branch 'dev' of https://github.com/broadinstitute/seqr into hai… 

    …l-backend-sort
    @hanars
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  7. pr feedback

    @hanars
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  8. Merge branch 'hail-backend-sort' of https://github.com/broadinstitute… 

    …/seqr into hail-backend-gene-counts
    @hanars
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  9. pr feedback

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  10. Merge pull request #3556 from broadinstitute/gregor-metadata-airtable… 

    …-update

Gregor metadata airtable update
    @hanars
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  11. Merge pull request #3550 from broadinstitute/hail-backend-sort 

    Hail backend sort
    @hanars
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Commits on Aug 18, 2023

  1. update called variant file filter missing

    @hanars
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  2. better flot and int validation and testing

    @hanars
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  3. Add "wait_for_routes" helper script for CronJobs. (#3565) 

    * add wait_for_routes script

* add wait

* wait for routes

* Add wait_for_routes helper script

* Flush out description

* Update wait_for_routes
    @bpblanken
    bpblanken authored Aug 18, 2023
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Commits on Aug 21, 2023

  1. Merge pull request #3553 from broadinstitute/hail-backend-gene-counts 

    Hail backend gene counts
    @hanars
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  2. Merge pull request #3559 from broadinstitute/gregor-metadata-validati… 

    …on-update

Gregor metadata validation update
    @hanars
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  3. Merge pull request #3564 from broadinstitute/gregor-metdata-called-va… 

    …riant-file-filtering

Gregor metadata called variant file filtering
    @hanars
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Commits on Aug 22, 2023

  1. bump changelog

    @hanars
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