TASK-5278 - Add haploid calls treatment parameter to family-qc and relatedness #2466
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…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
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TASK-5278 Add haploid calls treatment parameter to family-qc and relatedness