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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

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Smeds
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@Smeds Smeds commented Apr 19, 2024

This PR:

(If this is a release PR, no need to add following. Leave this part empty)
(Use the following lines to create a PR text body. Make sure to remove all non-relevant one after you're done)
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Added: for new features.
Changed: for changes in existing functionality.
Deprecated: for soon-to-be removed features.
Removed: for now removed features.
Fixed: for any bug fixes.
Security: in case of vulnerabilities.

Review and tests:

  • Tests pass
  • If you've fixed a bug or added code that should be tested, add tests!
  • Code review
  • CHANGELOG.md is updated
  • New code is executed and covered by tests, and test approve

Smeds and others added 29 commits February 15, 2024 16:51
@Smeds
feat: hg38 config and reference file setup
6f41281
@Smeds
minor fixes
d3e6ea3
@Smeds
set file version
608d2bc
@Smeds
fix checksum
d704c7f
@Smeds
Update references.hg19.yaml
1fddcad
@Smeds
Update requirements.txt
fabe8ae
@Smeds
Merge branch 'develop' into update-hg38-ref-files
738aa33
@Smeds
Merge pull request #412 from genomic-medicine-sweden/update-hg38-ref-…
d6914f5 
…files

feat: hg38 config and reference file setup
@jonca79
fix: add implied msi configuration from module to config
a9dea4e
@jonca79
feat: do not merge regions that are not identical
1d9a027 
Some GATK CNV results are missing from the table as they where merged with CNVkit results. This will mitigate this.
@jonca79
fix: add "_" to regexp so that indels are reported correctly
7549036
@jonca79
feat: added chromosome arm support to rule
ccbe735
@jonca79
feat: added calculation of cnv in chrom arms
667d53f
@jonca79
docs: added schema
b1c9bfe
@jonca79
feat: added warnings for baseline and polyploidy
9a25cdc
@jonca79
fix: bugfix
e681fee
@jonca79
feat: added more config variables
9a92bf2
@jonca79
fix: handle CNVs bridging the chromosome arms
8a508ad
@jonca79
fix: variable baf bugfix
d460172
@jonca79
feat: decreased chr arm fraction
b1ce417
@jonca79
feat: added table to cnv_html_report
e577cdd
@jonca79
docs: added config schemas for new params
62c832d
@jonca79
test: added params to test config
2d4eb4c
@jonca79
feat: added configuration of polyploidy and baseline limits
8f91b42
@jonca79
test: added unit tests
4f62f57
@Smeds
Merge pull request #442 from genomic-medicine-sweden/cnv_report_chr
cee1f59 
feat: calling chromosome arm CNVs
@Smeds
Merge pull request #441 from genomic-medicine-sweden/fix_coverage_and…
59a7e89 
…_mutations

fix: add "_" to regexp so that indels are reported correctly
@Smeds
Merge pull request #440 from genomic-medicine-sweden/svdb_skip_merging
1a3bdca 
feat: do not merge regions that are not identical
@Smeds
Merge pull request #439 from genomic-medicine-sweden/msi_config
482c5d4 
fix: add implied msi configuration from module to config
@Smeds Smeds requested a review from jonca79 as a code owner April 19, 2024 06:39
jonca79 and others added 21 commits April 19, 2024 08:49
@jonca79
feat: two new amplification genes reported
c8264b2
@jonca79
feat: new amp genes for hg38
c6f7b5e
@jonca79
fix: spelling error
46aef96
@jonca79
feat: updated with new reference files
5e057e7
@jonca79
feat: update ref files for hg38
0ad022c
@jonca79
Merge pull request #445 from genomic-medicine-sweden/new_ref_files
3e83b49 
feat: updated with new reference files
@Smeds
Merge pull request #444 from genomic-medicine-sweden/new_amp_genes-1
73a9450 
feat: two new amplification genes reported
@Smeds
refactor: move chrom arm file
f8d69e7
@Smeds
Update config.data.hg19.yaml
4dd24f2
@Smeds
Update config.data.hg38.yaml
acf3871
@jonca79
Merge pull request #446 from genomic-medicine-sweden/Smeds-patch-1
b39f438 
refactor: move chrom arm file
@Smeds
fix: correct missing part of vep ref file path
36b3b0a
@Smeds
Merge pull request #447 from genomic-medicine-sweden/Smeds-patch-1
510dcce 
fix: correct missing part of vep ref file path
@jonca79
fix: rm duplicate entries of cnv in report
3a2cae4
@Smeds
fix: update hg38 ref files, point to correct release
e8efb8c
@jonca79
chore: pycodestyle
6dc14a9
@jonca79
chore: pycodestyle
e616490
@jonca79
Merge pull request #449 from genomic-medicine-sweden/Smeds-patch-1
682d605 
fix: update hg38 ref files, point to correct release
@jonca79
Merge pull request #448 from genomic-medicine-sweden/fix_tsv_report
0fe8c17 
fix: rm duplicate entries of cnv in report
@Smeds
fix: update config, merge_cnv_json, to use latest amp gene bed file
be98e22
@jonca79
Merge pull request #450 from genomic-medicine-sweden/Smeds-patch-1
bcbadf7 
fix: update config, merge_cnv_json, to use latest amp gene bed file
@Smeds Smeds merged commit f95bb41 into master Apr 26, 2024
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