TASK-5278 - Add haploid calls treatment parameter to family-qc and relatedness #2466
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…K/IBD in the analyses family-qc and relatedness, #TASK-5282, #TASK-5278
…s, #TASK-5282, #TASK-5278
…K-5282, #TASK-5278
Resolve conflicts by generation clients: opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java opencga-client/src/main/R/R/Admin-methods.R opencga-client/src/main/R/R/Alignment-methods.R opencga-client/src/main/R/R/AllGenerics.R opencga-client/src/main/R/R/Clinical-methods.R opencga-client/src/main/R/R/Cohort-methods.R opencga-client/src/main/R/R/Family-methods.R opencga-client/src/main/R/R/File-methods.R opencga-client/src/main/R/R/GA4GH-methods.R opencga-client/src/main/R/R/Individual-methods.R opencga-client/src/main/R/R/Job-methods.R opencga-client/src/main/R/R/Meta-methods.R opencga-client/src/main/R/R/Operation-methods.R opencga-client/src/main/R/R/Panel-methods.R opencga-client/src/main/R/R/Project-methods.R opencga-client/src/main/R/R/Sample-methods.R opencga-client/src/main/R/R/Study-methods.R opencga-client/src/main/R/R/User-methods.R opencga-client/src/main/R/R/Variant-methods.R opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java opencga-client/src/main/javascript/Admin.js opencga-client/src/main/javascript/Alignment.js opencga-client/src/main/javascript/ClinicalAnalysis.js opencga-client/src/main/javascript/Cohort.js opencga-client/src/main/javascript/DiseasePanel.js opencga-client/src/main/javascript/Family.js opencga-client/src/main/javascript/File.js opencga-client/src/main/javascript/GA4GH.js opencga-client/src/main/javascript/Individual.js opencga-client/src/main/javascript/Job.js opencga-client/src/main/javascript/Meta.js opencga-client/src/main/javascript/Project.js opencga-client/src/main/javascript/Sample.js opencga-client/src/main/javascript/Study.js opencga-client/src/main/javascript/User.js opencga-client/src/main/javascript/Variant.js opencga-client/src/main/javascript/VariantOperation.js opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py opencga-client/src/main/python/pyopencga/rest_clients/family_client.py opencga-client/src/main/python/pyopencga/rest_clients/file_client.py opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py opencga-client/src/main/python/pyopencga/rest_clients/job_client.py opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py opencga-client/src/main/python/pyopencga/rest_clients/project_client.py opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py opencga-client/src/main/python/pyopencga/rest_clients/study_client.py opencga-client/src/main/python/pyopencga/rest_clients/user_client.py opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
…SK-5282, #TASK-5278 On branch TASK-5278 Changes to be committed: modified: opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java
On branch TASK-5278 Changes to be committed: modified: opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java
…TASK-5282 On branch TASK-5278 Changes to be committed: modified: opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java modified: opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java modified: opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java modified: opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java modified: opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java
jtarraga
changed the title
pfurio
previously approved these changes
Jun 17, 2024
j-coll
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
TASK-5278 Add haploid calls treatment parameter to family-qc and relatedness