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chore: dev to master #443

Merged
merged 56 commits into from
Apr 26, 2024
Merged

chore: dev to master #443

merged 56 commits into from
Apr 26, 2024

Commits on Feb 15, 2024

  1. feat: hg38 config and reference file setup

    @Smeds
    Smeds committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. minor fixes

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    Smeds committed Feb 16, 2024
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  2. set file version

    @Smeds
    Smeds committed Feb 16, 2024
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  3. fix checksum

    @Smeds
    Smeds committed Feb 16, 2024
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Commits on Feb 21, 2024

  1. Update references.hg19.yaml

    @Smeds
    Smeds authored Feb 21, 2024
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  2. Update requirements.txt

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    Smeds authored Feb 21, 2024
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Commits on Mar 21, 2024

  1. Merge branch 'develop' into update-hg38-ref-files

    @Smeds
    Smeds authored Mar 21, 2024
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  2. Merge pull request #412 from genomic-medicine-sweden/update-hg38-ref-… 

    …files

feat: hg38 config and reference file setup
    @Smeds
    Smeds authored Mar 21, 2024
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Commits on Mar 22, 2024

  1. fix: add implied msi configuration from module to config

    @jonca79
    jonca79 authored Mar 22, 2024
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Commits on Apr 9, 2024

  1. feat: do not merge regions that are not identical 

    Some GATK CNV results are missing from the table as they where merged with CNVkit results. This will mitigate this.
    @jonca79
    jonca79 authored Apr 9, 2024
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Commits on Apr 10, 2024

  1. fix: add "_" to regexp so that indels are reported correctly

    @jonca79
    jonca79 authored Apr 10, 2024
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Commits on Apr 15, 2024

  1. feat: added chromosome arm support to rule

    @jonca79
    jonca79 committed Apr 15, 2024
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  2. feat: added calculation of cnv in chrom arms

    @jonca79
    jonca79 committed Apr 15, 2024
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  3. docs: added schema

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    jonca79 committed Apr 15, 2024
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Commits on Apr 16, 2024

  1. feat: added warnings for baseline and polyploidy

    @jonca79
    jonca79 committed Apr 16, 2024
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  2. fix: bugfix

    @jonca79
    jonca79 committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. feat: added more config variables

    @jonca79
    jonca79 committed Apr 17, 2024
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  2. fix: handle CNVs bridging the chromosome arms

    @jonca79
    jonca79 committed Apr 17, 2024
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  3. fix: variable baf bugfix

    @jonca79
    jonca79 committed Apr 17, 2024
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  4. feat: decreased chr arm fraction

    @jonca79
    jonca79 committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. feat: added table to cnv_html_report

    @jonca79
    jonca79 committed Apr 18, 2024
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  2. docs: added config schemas for new params

    @jonca79
    jonca79 committed Apr 18, 2024
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  3. test: added params to test config

    @jonca79
    jonca79 committed Apr 18, 2024
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  4. feat: added configuration of polyploidy and baseline limits

    @jonca79
    jonca79 committed Apr 18, 2024
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  5. test: added unit tests

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    jonca79 committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. Merge pull request #442 from genomic-medicine-sweden/cnv_report_chr 

    feat: calling chromosome arm CNVs
    @Smeds
    Smeds authored Apr 19, 2024
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  2. Merge pull request #441 from genomic-medicine-sweden/fix_coverage_and… 

    …_mutations

fix: add "_" to regexp so that indels are reported correctly
    @Smeds
    Smeds authored Apr 19, 2024
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  3. Merge pull request #440 from genomic-medicine-sweden/svdb_skip_merging 

    feat: do not merge regions that are not identical
    @Smeds
    Smeds authored Apr 19, 2024
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  4. Merge pull request #439 from genomic-medicine-sweden/msi_config 

    fix: add implied msi configuration from module to config
    @Smeds
    Smeds authored Apr 19, 2024
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  5. feat: two new amplification genes reported

    @jonca79
    jonca79 authored Apr 19, 2024
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  6. feat: new amp genes for hg38

    @jonca79
    jonca79 authored Apr 19, 2024
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  7. fix: spelling error

    @jonca79
    jonca79 authored Apr 19, 2024
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  8. feat: updated with new reference files

    @jonca79
    jonca79 authored Apr 19, 2024
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  9. feat: update ref files for hg38

    @jonca79
    jonca79 authored Apr 19, 2024
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  10. Merge pull request #445 from genomic-medicine-sweden/new_ref_files 

    feat: updated with new reference files
    @jonca79
    jonca79 authored Apr 19, 2024
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  11. Merge pull request #444 from genomic-medicine-sweden/new_amp_genes-1 

    feat: two new amplification genes reported
    @Smeds
    Smeds authored Apr 19, 2024
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  12. refactor: move chrom arm file

    @Smeds
    Smeds authored Apr 19, 2024
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  13. Update config.data.hg19.yaml

    @Smeds
    Smeds authored Apr 19, 2024
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  14. Update config.data.hg38.yaml

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    Smeds authored Apr 19, 2024
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  15. Merge pull request #446 from genomic-medicine-sweden/Smeds-patch-1 

    refactor: move chrom arm file
    @jonca79
    jonca79 authored Apr 19, 2024
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  16. fix: correct missing part of vep ref file path

    @Smeds
    Smeds authored Apr 19, 2024
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  17. Merge pull request #447 from genomic-medicine-sweden/Smeds-patch-1 

    fix: correct missing part of vep ref file path
    @Smeds
    Smeds authored Apr 19, 2024
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  18. fix: rm duplicate entries of cnv in report

    @jonca79
    jonca79 authored Apr 19, 2024
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  19. fix: update hg38 ref files, point to correct release

    @Smeds
    Smeds authored Apr 19, 2024
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  20. chore: pycodestyle

    @jonca79
    jonca79 authored Apr 19, 2024
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  21. chore: pycodestyle

    @jonca79
    jonca79 authored Apr 19, 2024
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  22. Merge pull request #449 from genomic-medicine-sweden/Smeds-patch-1 

    fix: update hg38 ref files, point to correct release
    @jonca79
    jonca79 authored Apr 19, 2024
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  23. Merge pull request #448 from genomic-medicine-sweden/fix_tsv_report 

    fix: rm duplicate entries of cnv in report
    @jonca79
    jonca79 authored Apr 19, 2024
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Commits on Apr 22, 2024

  1. fix: update config, merge_cnv_json, to use latest amp gene bed file

    @Smeds
    Smeds authored Apr 22, 2024
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  2. Merge pull request #450 from genomic-medicine-sweden/Smeds-patch-1 

    fix: update config, merge_cnv_json, to use latest amp gene bed file
    @jonca79
    jonca79 authored Apr 22, 2024
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Commits on Apr 24, 2024

  1. feat: update test file for develop

    @Smeds
    Smeds authored Apr 24, 2024
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  2. Merge pull request #451 from genomic-medicine-sweden/Smeds-patch-1 

    feat: update test file for develop
    @Smeds
    Smeds authored Apr 24, 2024
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Commits on Apr 25, 2024

  1. ci: update test file

    @Smeds
    Smeds authored Apr 25, 2024
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  2. Merge pull request #453 from genomic-medicine-sweden/Smeds-patch-2 

    ci: update test file
    @Smeds
    Smeds authored Apr 25, 2024
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Commits on Apr 26, 2024

  1. ci: update main test file

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    Smeds authored Apr 26, 2024
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  2. Merge pull request #454 from genomic-medicine-sweden/Smeds-patch-2 

    ci: update main test file
    @Smeds
    Smeds authored Apr 26, 2024
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