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IN-500 eggd_generate_variant_workbook v2.9.0 #196

Merged
merged 112 commits into from
Oct 18, 2024
Merged

IN-500 eggd_generate_variant_workbook v2.9.0 #196

merged 112 commits into from
Oct 18, 2024

Commits on Mar 18, 2024

  1. IN-501 add report text

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  2. IN-501 rm details json

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Commits on Mar 19, 2024

  1. IN-501 add arg to dx app

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  2. IN-501 add arg to dx app json

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  3. IN-501 reorder commands

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  4. IN-501 remove redudant variables

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  5. IN-501 rm space

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  6. IN-501 rm letter

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  7. IN-501 update readme

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  8. IN-501 namespace fix

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  9. IN-501 pytest action fix

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  10. IN-501 add AF to text

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  11. IN-501 increase height

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  12. IN-501 rm blank lines

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  13. IN-501 only add exon if not intronic with .

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  14. IN-501 rm caps

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  15. IN-502 add arg option for uranus

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  16. IN-502 add summary sheet for uranus

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  17. IN-501 include intron

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  18. IN-502 get header

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  19. IN-501 dont drop report text

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  20. IN-501 increase height

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  21. IN-502 get vcf header onto the summary page

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Commits on Mar 20, 2024

  1. IN-503 amend AF column to percent if arg is set

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  2. IN-503 add AF arg to set as decimal or percent

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  3. IN-503 fix typo

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  4. IN-503 update dxapp json

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  5. IN-503 update READme

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  6. IN-501 try to make pytest work

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  7. IN-501 try to make pytest work2

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  8. IN-501 undo changes

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  9. IN-501 try to make pytest work3

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  10. Merge pull request #179 from eastgenomics/IN-501-add-a-report-text 

    IN-501 add report text
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  11. Merge branch 'IN-500-eggd-generate-variant-workbook-v-2-9-0' of https… 

    …://github.com/eastgenomics/eggd_generate_variant_workbook into IN-502-make-a-uranus-summary-sheet
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  12. IN-502 set witdth for summary

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  13. Merge pull request #181 from eastgenomics/IN-502-make-a-uranus-summar… 

    …y-sheet

IN-502 make a uranus summary sheet
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  14. IN-503 accept incoming changes from IN-500

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  15. IN-503 add parse arg

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  16. IN-503 add dxapp json arg

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  17. IN-503 accept incoming changes from IN-500

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  18. IN-503 remove af percentage change

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  19. IN-503 ad af percentage change

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  20. IN-503 fix pytest fail

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  21. IN-503 1dp as percent

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  22. IN-503 indentation

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  23. IN-503 indentation2

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  24. IN-503 indentation3

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  25. IN-503 change AF to af_format

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  26. IN-503 change AF to af_format

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  27. IN-503 change AF to af_format

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  28. IN-503 include af)format to source code

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  29. IN-503 skip if AF not in VCF

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  30. IN-503 pep8

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  31. IN-503 pytest fix

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  32. IN-503 add ws

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  33. Merge pull request #183 from eastgenomics/IN-503-option-to-have-af-pr… 

    …esented-as-a-decimal-or-percentage

IN-503 Option to have AF presented as a decimal or percentage (#183)
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  34. IN-500 update version

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  35. handle vcf as an additional file

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  36. fix indentation in vcf.make_report_text()

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  37. refactor vcf.make_report_text to separate function

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  38. better format report text

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  39. formatting

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  40. Merge pull request #184 from eastgenomics/IN-500-update-version 

    IN-500 update version of app
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  41. fix borked tests from changes to vcf.add_hyperlinks

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  42. fix formatting of report text

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  43. once again fixing the borked tests

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  44. Merge branch 'IN-500-eggd-generate-variant-workbook-v-2-9-0' into IN-… 

    …511-handle_vcfs_in_additional_files
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  45. fixed broken report text formatting

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  46. Merge branch 'IN-511-handle_vcfs_in_additional_files' of https://gith… 

    …ub.com/eastgenomics/eggd_generate_variant_workbook into IN-511-handle_vcfs_in_additional_files
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  47. set row height proportional to no. lines in report text

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Commits on Mar 21, 2024

  1. Update Readme.md

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  2. Merge pull request #185 from eastgenomics/IN-511-handle_vcfs_in_addit… 

    …ional_files

IN-511 handle vcfs as additional files (#185)
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Commits on Apr 17, 2024

  1. IN-534 update pecan link

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  2. Merge branch 'IN-500-eggd-generate-variant-workbook-v-2-9-0' of https… 

    …://github.com/eastgenomics/eggd_generate_variant_workbook into IN-534-bug-fix-pecan-link-needs-updating
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  3. IN-534 update readme

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  4. Merge pull request #191 from eastgenomics/IN-534-bug-fix-pecan-link-n… 

    …eeds-updating

IN-534 pecan link needs updating (#191)
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  5. IN-510 test_percent_af

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  6. IN-510 fix report text & make tests

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Commits on Apr 23, 2024

  1. IN-510 restructure

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  2. IN-510 add haemonc test vcf

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  3. IN-510 small bugfix

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  4. IN-510 rm dup code

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  5. IN-510 subtest

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  6. IN-510 fix subtest

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  7. IN-510 rm package

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  8. Merge pull request #192 from eastgenomics/IN-510-unit-test-new-features 

    IN-510 unit test new features
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Commits on Apr 24, 2024

  1. rm samplename + populate samplename for additional files

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  2. rm ws

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  3. add samplename when reading in file

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  4. Merge pull request #193 from eastgenomics/IN-500-samplecolumn-duplicated 

    Sample Column duplicated
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Commits on Apr 25, 2024

  1. URA-679 add include/exclude

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  2. URA-679 strip csq after dropping columns

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  3. URA-679 add parameter

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  4. URA-679 match lines

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  5. Merge pull request #194 from eastgenomics/URA-679-bug-fix-additional-… 

    …files-doesnt-include-exclude

URA-679 add include/exclude functionality to additional VCF files (#194)
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Commits on Apr 26, 2024

  1. syntax fix

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  2. add space

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  3. Merge pull request #195 from eastgenomics/IN-500-syntax-fix 

    IN-500 syntax fix (#195)
    @Jay-Miles
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Commits on May 1, 2024

  1. merge conflicts

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  2. include v2.8.1 and v2.8.2

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Commits on May 2, 2024

  1. rm split test vcf

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Commits on Aug 30, 2024

  1. add space to recognise if statement

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  2. Merge pull request #197 from eastgenomics/IN-500-space-syntax 

    Add space to recognise arg (#197)
    @cnascim1
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Commits on Oct 17, 2024

  1. IN-500 use dna or protein change if provided

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  2. IN-500 typo

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  3. Merge pull request #199 from eastgenomics/IN-500-update-report-text 

    IN-500 use dna or protein change if provided
    @jethror1
    jethror1 authored Oct 17, 2024
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  4. IN-500 make AF percent and order columns

    @Aisha-D
    Aisha-D committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. IN-500 correct AF and order

    @Aisha-D
    Aisha-D committed Oct 18, 2024
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  2. update function tests

    @Aisha-D
    Aisha-D committed Oct 18, 2024
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  3. allow split of HGVS properly for additional sheets

    @Aisha-D
    Aisha-D committed Oct 18, 2024
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  4. IN-500 better readability

    @Aisha-D
    Aisha-D committed Oct 18, 2024
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  5. Merge pull request #200 from eastgenomics/IN-500-make-additional-shee… 

    …t-consistent-with-main-vcf

In 500 make additional sheet consistent with main vcf (#200)
    @jethror1
    jethror1 authored Oct 18, 2024
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