From cb44d9101c3fe4798b4611a455f9d313392df2de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 27 Mar 2024 11:05:17 +0100 Subject: [PATCH] client: generate client, #TASK-5795, #TASK-5343 --- .../roh/RohWrapperAnalysisExecutor.java | 12 ++- .../app/cli/main/OpenCgaCompleter.java | 4 +- .../app/cli/main/OpencgaCliOptionsParser.java | 3 +- .../AnalysisVariantCommandExecutor.java | 54 +++++++++++++ .../AnalysisVariantCommandOptions.java | 76 +++++++++++++++++++ opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 20 ++--- .../src/main/R/R/Clinical-methods.R | 4 +- opencga-client/src/main/R/R/Cohort-methods.R | 4 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 4 +- .../src/main/R/R/Individual-methods.R | 4 +- opencga-client/src/main/R/R/Job-methods.R | 4 +- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- .../src/main/R/R/Organization-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 2 +- opencga-client/src/main/R/R/Project-methods.R | 4 +- opencga-client/src/main/R/R/Sample-methods.R | 2 +- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 4 +- opencga-client/src/main/R/R/Variant-methods.R | 14 +++- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../rest/clients/OrganizationClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 21 ++++- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- .../src/main/javascript/Organization.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 17 ++++- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../rest_clients/organization_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 21 ++++- .../rest_clients/variant_operation_client.py | 2 +- .../opencga/core/api/FieldConstants.java | 2 +- .../models/alignment/RohWrapperParams.java | 10 +-- 80 files changed, 305 insertions(+), 105 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/roh/RohWrapperAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/roh/RohWrapperAnalysisExecutor.java index b54fb02f3e7..b223bcb0b0b 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/roh/RohWrapperAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/roh/RohWrapperAnalysisExecutor.java @@ -34,7 +34,7 @@ public class RohWrapperAnalysisExecutor extends DockerWrapperAnalysisExecutor { private Integer homozygWindowSnp; private Integer homozygWindowHet; private Integer homozygWindowMissing; - private Float homozygWindowThreshold; + private Double homozygWindowThreshold; private Integer homozygKb; private Integer homozygSnp; private Integer homozygHet; @@ -110,7 +110,11 @@ public void run() throws ToolException { cli.append(" --homozyg-snp ").append(getHomozygWindowSnp()); } if (getHomozygHet() != null) { - cli.append(" --homozyg-het ").append(getHomozygHet()); + if (getHomozygHet() == -1) { + cli.append(" --homozyg-het unlimited"); + } else { + cli.append(" --homozyg-het ").append(getHomozygHet()); + } } if (getHomozygDensity() != null) { cli.append(" --homozyg-density ").append(getHomozygDensity()); @@ -224,11 +228,11 @@ public RohWrapperAnalysisExecutor setHomozygWindowMissing(Integer homozygWindowM return this; } - public Float getHomozygWindowThreshold() { + public Double getHomozygWindowThreshold() { return homozygWindowThreshold; } - public RohWrapperAnalysisExecutor setHomozygWindowThreshold(Float homozygWindowThreshold) { + public RohWrapperAnalysisExecutor setHomozygWindowThreshold(Double homozygWindowThreshold) { this.homozygWindowThreshold = homozygWindowThreshold; return this; } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 140e5c0f8c2..ac193b446ae 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-03-12 OpenCB +* Copyright 2015-2024-03-27 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -45,7 +45,7 @@ public abstract class OpenCgaCompleter implements Completer { .map(Candidate::new) .collect(toList()); - private List variantList = asList( "aggregationstats","annotation-metadata","annotation-query","circos-run","cohort-stats-delete","cohort-stats-info","cohort-stats-run","exomiser-run","export-run","family-genotypes","family-qc-run","file-delete","gatk-run","genome-plot-run","gwas-run","hr-detect-run","index-run","individual-qc-run","inferred-sex-run","knockout-gene-query","knockout-individual-query","knockout-run","mendelian-error-run","metadata","mutational-signature-query","mutational-signature-run","plink-run","query","relatedness-run","rvtests-run","sample-aggregation-stats","sample-eligibility-run","sample-qc-run","sample-query","sample-run","sample-stats-query","sample-stats-run","stats-export-run","stats-run") + private List variantList = asList( "aggregationstats","annotation-metadata","annotation-query","circos-run","cohort-stats-delete","cohort-stats-info","cohort-stats-run","exomiser-run","export-run","family-genotypes","family-qc-run","file-delete","gatk-run","genome-plot-run","gwas-run","hr-detect-run","index-run","individual-qc-run","inferred-sex-run","knockout-gene-query","knockout-individual-query","knockout-run","mendelian-error-run","metadata","mutational-signature-query","mutational-signature-run","plink-run","query","relatedness-run","roh-run","rvtests-run","sample-aggregation-stats","sample-eligibility-run","sample-qc-run","sample-query","sample-run","sample-stats-query","sample-stats-run","stats-export-run","stats-run") .stream() .map(Candidate::new) .collect(toList()); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index 02e2876bf2e..f143f7da2c1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-03-12 OpenCB +* Copyright 2015-2024-03-27 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -90,6 +90,7 @@ public OpencgaCliOptionsParser() { analysisVariantSubCommands.addCommand("plink-run", analysisVariantCommandOptions.runPlinkCommandOptions); analysisVariantSubCommands.addCommand("query", analysisVariantCommandOptions.queryCommandOptions); analysisVariantSubCommands.addCommand("relatedness-run", analysisVariantCommandOptions.runRelatednessCommandOptions); + analysisVariantSubCommands.addCommand("roh-run", analysisVariantCommandOptions.runRohCommandOptions); analysisVariantSubCommands.addCommand("rvtests-run", analysisVariantCommandOptions.runRvtestsCommandOptions); analysisVariantSubCommands.addCommand("sample-aggregation-stats", analysisVariantCommandOptions.aggregationStatsSampleCommandOptions); analysisVariantSubCommands.addCommand("sample-eligibility-run", analysisVariantCommandOptions.runSampleEligibilityCommandOptions); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java index 33dfbc54a41..cd2bb86b49d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java @@ -24,6 +24,7 @@ import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException; import org.opencb.opencga.client.exceptions.ClientException; import org.opencb.opencga.core.common.JacksonUtils; +import org.opencb.opencga.core.models.alignment.RohWrapperParams; import org.opencb.opencga.core.models.analysis.knockout.KnockoutByGene; import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividual; import org.opencb.opencga.core.models.clinical.ExomiserWrapperParams; @@ -177,6 +178,9 @@ public void execute() throws Exception { case "relatedness-run": queryResponse = runRelatedness(); break; + case "roh-run": + queryResponse = runRoh(); + break; case "rvtests-run": queryResponse = runRvtests(); break; @@ -1342,6 +1346,56 @@ private RestResponse runRelatedness() throws Exception { return openCGAClient.getVariantClient().runRelatedness(relatednessAnalysisParams, queryParams); } + private RestResponse runRoh() throws Exception { + logger.debug("Executing runRoh in Analysis - Variant command line"); + + AnalysisVariantCommandOptions.RunRohCommandOptions commandOptions = analysisVariantCommandOptions.runRohCommandOptions; + + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("study", commandOptions.study); + queryParams.putIfNotEmpty("jobId", commandOptions.jobId); + queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription); + queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn); + queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags); + if (queryParams.get("study") == null && OpencgaMain.isShellMode()) { + queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy()); + } + + + RohWrapperParams rohWrapperParams = null; + if (commandOptions.jsonDataModel) { + RestResponse res = new RestResponse<>(); + res.setType(QueryType.VOID); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/roh/run")); + return res; + } else if (commandOptions.jsonFile != null) { + rohWrapperParams = JacksonUtils.getDefaultObjectMapper() + .readValue(new java.io.File(commandOptions.jsonFile), RohWrapperParams.class); + } else { + ObjectMap beanParams = new ObjectMap(); + putNestedIfNotEmpty(beanParams, "sampleId",commandOptions.sampleId, true); + putNestedIfNotEmpty(beanParams, "chromosome",commandOptions.chromosome, true); + putNestedIfNotEmpty(beanParams, "filter",commandOptions.filter, true); + putNestedIfNotNull(beanParams, "genotypeQuality",commandOptions.genotypeQuality, true); + putNestedIfNotNull(beanParams, "skipGenotypeQuality",commandOptions.skipGenotypeQuality, true); + putNestedIfNotNull(beanParams, "homozygWindowSnp",commandOptions.homozygWindowSnp, true); + putNestedIfNotNull(beanParams, "homozygWindowHet",commandOptions.homozygWindowHet, true); + putNestedIfNotNull(beanParams, "homozygWindowMissing",commandOptions.homozygWindowMissing, true); + putNestedIfNotNull(beanParams, "homozygWindowThreshold",commandOptions.homozygWindowThreshold, true); + putNestedIfNotNull(beanParams, "homozygKb",commandOptions.homozygKb, true); + putNestedIfNotNull(beanParams, "homozygSnp",commandOptions.homozygSnp, true); + putNestedIfNotNull(beanParams, "homozygHet",commandOptions.homozygHet, true); + putNestedIfNotEmpty(beanParams, "homozygDensity",commandOptions.homozygDensity, true); + putNestedIfNotEmpty(beanParams, "homozygGap",commandOptions.homozygGap, true); + putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true); + + rohWrapperParams = JacksonUtils.getDefaultObjectMapper().copy() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true) + .readValue(beanParams.toJson(), RohWrapperParams.class); + } + return openCGAClient.getVariantClient().runRoh(rohWrapperParams, queryParams); + } + private RestResponse runRvtests() throws Exception { logger.debug("Executing runRvtests in Analysis - Variant command line"); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java index 82b9edc17a4..1413d3c39d2 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java @@ -62,6 +62,7 @@ public class AnalysisVariantCommandOptions { public RunPlinkCommandOptions runPlinkCommandOptions; public QueryCommandOptions queryCommandOptions; public RunRelatednessCommandOptions runRelatednessCommandOptions; + public RunRohCommandOptions runRohCommandOptions; public RunRvtestsCommandOptions runRvtestsCommandOptions; public AggregationStatsSampleCommandOptions aggregationStatsSampleCommandOptions; public RunSampleEligibilityCommandOptions runSampleEligibilityCommandOptions; @@ -107,6 +108,7 @@ public AnalysisVariantCommandOptions(CommonCommandOptions commonCommandOptions, this.runPlinkCommandOptions = new RunPlinkCommandOptions(); this.queryCommandOptions = new QueryCommandOptions(); this.runRelatednessCommandOptions = new RunRelatednessCommandOptions(); + this.runRohCommandOptions = new RunRohCommandOptions(); this.runRvtestsCommandOptions = new RunRvtestsCommandOptions(); this.aggregationStatsSampleCommandOptions = new AggregationStatsSampleCommandOptions(); this.runSampleEligibilityCommandOptions = new RunSampleEligibilityCommandOptions(); @@ -1858,6 +1860,80 @@ public class RunRelatednessCommandOptions { } + @Parameters(commandNames = {"roh-run"}, commandDescription ="Analysis to calculate and visualise regions of homozygosity (ROHs) for a given sample") + public class RunRohCommandOptions { + + @ParametersDelegate + public CommonCommandOptions commonOptions = commonCommandOptions; + + @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1) + public String jsonFile; + + @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0) + public Boolean jsonDataModel = false; + + @Parameter(names = {"--study", "-s"}, description = "Study [[organization@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) + public String study; + + @Parameter(names = {"--job-id"}, description = "Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.", required = false, arity = 1) + public String jobId; + + @Parameter(names = {"--job-description"}, description = "Job description", required = false, arity = 1) + public String jobDescription; + + @Parameter(names = {"--job-depends-on"}, description = "Comma separated list of existing job IDs the job will depend on.", required = false, arity = 1) + public String jobDependsOn; + + @Parameter(names = {"--job-tags"}, description = "Job tags", required = false, arity = 1) + public String jobTags; + + @Parameter(names = {"--sample-id"}, description = "Sample to analyse", required = false, arity = 1) + public String sampleId; + + @Parameter(names = {"--chromosome"}, description = "Chromosome to analyse", required = false, arity = 1) + public String chromosome; + + @Parameter(names = {"--filter"}, description = "FILTER (VCF FILTER annotation field) category to filter in variants in the ROH analysis. Default: PASS.", required = false, arity = 1) + public String filter = "PASS"; + + @Parameter(names = {"--genotype-quality"}, description = "GQ (VCF genotype quality annotation field) threshold to filter in variants in the ROH analysis. Default: 40 (GQ>40).", required = false, arity = 1) + public Integer genotypeQuality = 40; + + @Parameter(names = {"--skip-genotype-quality"}, description = "Flag to not use the GQ (VCF genotype quality annotation field) to filter in variants in the ROH analysis. Default: false", required = false, arity = 1) + public Boolean skipGenotypeQuality; + + @Parameter(names = {"--homozyg-window-snp"}, description = "Plink's parameter to set the scanning window size to look for ROHs. Default: 50", required = false, arity = 1) + public Integer homozygWindowSnp = 50; + + @Parameter(names = {"--homozyg-window-het"}, description = "Plink's parameter to set the maximum number of heterozygous calls in a scanning window hit. Default: 1", required = false, arity = 1) + public Integer homozygWindowHet = 1; + + @Parameter(names = {"--homozyg-window-missing"}, description = "Plink's parameter to set the maximum number of missing calls in a scanning window hit. Default: 5", required = false, arity = 1) + public Integer homozygWindowMissing = 5; + + @Parameter(names = {"--homozyg-window-threshold"}, description = "Plink's parameter to set the minimum scanning window rate. Default: 0.05", required = false, arity = 1) + public Double homozygWindowThreshold = 0.05; + + @Parameter(names = {"--homozyg-kb"}, description = "Plink's parameter to set the minimum ROH length in kilobases (kb). Default: 1000", required = false, arity = 1) + public Integer homozygKb = 1000; + + @Parameter(names = {"--homozyg-snp"}, description = "Plink's parameter to set the minimum number of snps in a ROH. Default: 100", required = false, arity = 1) + public Integer homozygSnp = 100; + + @Parameter(names = {"--homozyg-het"}, description = "Plink's parameter to set the maximum number of heterozygous calls in a ROH. Default: -1 that means 'unlimited'.", required = false, arity = 1) + public Integer homozygHet = -1; + + @Parameter(names = {"--homozyg-density"}, description = "Plink's parameter to set the maximum inverse ROH density (kb/SNP). Minimum ROH density: 1 SNP per X kb. Default: 50", required = false, arity = 1) + public String homozygDensity = "50"; + + @Parameter(names = {"--homozyg-gap"}, description = "Plink's parameter to set the maximum gap length in kb between two consecutive SNPs to be considered part of the same ROH. Default: 1000", required = false, arity = 1) + public String homozygGap = "1000"; + + @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1) + public String outdir; + + } + @Parameters(commandNames = {"rvtests-run"}, commandDescription ="Rvtests is a flexible software package for genetic association studies. Supported RvTests commands: rvtest, vcf2kinship") public class RunRvtestsCommandOptions { diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 6bf61415c9b..640a765d6f4 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 69c82c573a3..ae8b40c7577 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 1b566838bf7..026bb2d835c 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -5,27 +5,27 @@ setGeneric("organizationClient", function(OpencgaR, organization, endpointName, # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, studies, variableSet, members, templateId, group, study, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, studies, study, group, templateId, variableSet, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, folder, files, members, annotationSet, file, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, file, members, annotationSet, files, folder, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## @@ -35,17 +35,17 @@ setGeneric("sampleClient", function(OpencgaR, samples, annotationSet, sample, me # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, annotationSet, individuals, members, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, annotationSet, family, members, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, family, annotationSet, families, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohort, annotationSet, cohorts, members, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohorts, cohort, members, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -65,7 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, annotationSet, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, annotationSet, clinicalAnalyses, interpretation, interpretations, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -80,7 +80,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index f807bde4301..80249c58d62 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -62,7 +62,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, annotationSet, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, annotationSet, clinicalAnalyses, interpretation, interpretations, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 99482a604c9..f1587203693 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, annotationSet, cohorts, members, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohorts, cohort, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index f41421db5a1..8e60364d545 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, family, members, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, family, annotationSet, families, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 8b8e60cf054..36455430350 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -53,7 +53,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, files, members, annotationSet, file, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, file, members, annotationSet, files, folder, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index a176ca0951d..c428cf6a4c5 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +31,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 3a9e4d0710d..f2936887f9c 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individuals, members, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index 1d033cbc80a..cbe0c8f0523 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 975200c2b12..f5d2569f4da 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index bd6884c6906..6527a4bf3a6 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Organization-methods.R b/opencga-client/src/main/R/R/Organization-methods.R index 0260f97f9df..d34741600c4 100644 --- a/opencga-client/src/main/R/R/Organization-methods.R +++ b/opencga-client/src/main/R/R/Organization-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index 887ec48d5b0..7e8b35829e0 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 3a136539be5..dcac835ab30 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -33,7 +33,7 @@ #' [*]: Required parameter #' @export -setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/projects/create: diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 39ceaba71d4..73b2e0fbe7d 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 5ff6deccb29..b9e518f9759 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, studies, variableSet, members, templateId, group, study, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, studies, study, group, templateId, variableSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 921e466d5e4..403137883c6 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/anonymous: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index f03c5b00d9d..5a895acd541 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-03-12 +# Autogenerated on: 2024-03-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -49,6 +49,7 @@ #' | runPlink | /{apiVersion}/analysis/variant/plink/run | study, jobId, jobDescription, jobDependsOn, jobTags, body[*] | #' | query | /{apiVersion}/analysis/variant/query | include, exclude, limit, skip, count, sort, summary, approximateCount, approximateCountSamplingSize, savedFilter, id, region, type, reference, alternate, project, study, file, filter, qual, fileData, sample, genotype, sampleData, sampleAnnotation, sampleMetadata, unknownGenotype, sampleLimit, sampleSkip, cohort, cohortStatsRef, cohortStatsAlt, cohortStatsMaf, cohortStatsMgf, cohortStatsPass, missingAlleles, missingGenotypes, score, family, familyDisorder, familySegregation, familyMembers, familyProband, includeStudy, includeFile, includeSample, includeSampleData, includeGenotype, includeSampleId, annotationExists, gene, ct, xref, biotype, proteinSubstitution, conservation, populationFrequencyAlt, populationFrequencyRef, populationFrequencyMaf, transcriptFlag, geneTraitId, go, expression, proteinKeyword, drug, functionalScore, clinical, clinicalSignificance, clinicalConfirmedStatus, customAnnotation, panel, panelModeOfInheritance, panelConfidence, panelRoleInCancer, panelFeatureType, panelIntersection, trait | #' | runRelatedness | /{apiVersion}/analysis/variant/relatedness/run | study, jobId, jobDescription, jobDependsOn, jobTags, body[*] | +#' | runRoh | /{apiVersion}/analysis/variant/roh/run | study, jobId, jobDescription, jobDependsOn, jobTags, body[*] | #' | runRvtests | /{apiVersion}/analysis/variant/rvtests/run | study, jobId, jobDescription, jobDependsOn, jobTags, body[*] | #' | aggregationStatsSample | /{apiVersion}/analysis/variant/sample/aggregationStats | savedFilter, region, type, project, study, file, filter, sample, genotype, sampleAnnotation, family, familyDisorder, familySegregation, familyMembers, familyProband, ct, biotype, populationFrequencyAlt, clinical, clinicalSignificance, clinicalConfirmedStatus, field | #' | runSampleEligibility | /{apiVersion}/analysis/variant/sample/eligibility/run | study, jobId, jobDescription, jobDependsOn, jobTags, body[*] | @@ -507,6 +508,17 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N subcategory="variant/relatedness", subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), + #' @section Endpoint /{apiVersion}/analysis/variant/roh/run: + #' Analysis to calculate and visualise regions of homozygosity (ROHs) for a given sample. + #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID. + #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. + #' @param jobDescription Job description. + #' @param jobDependsOn Comma separated list of existing job IDs the job will depend on. + #' @param jobTags Job tags. + #' @param data ROH parameters. + runRoh=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="variant/roh", + subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), + #' @section Endpoint /{apiVersion}/analysis/variant/rvtests/run: #' Rvtests is a flexible software package for genetic association studies. Supported RvTests commands: rvtest, vcf2kinship. #' @param study study. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index dd0251bd427..f8dca939d99 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 3efdbd23bb1..1f9fdb6e04b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 050f9e9ca68..e730ae8fff5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -55,7 +55,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 4dd5000180b..5092f93a5c3 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index b9967e99b99..ef558b7f772 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 11c95587092..f8ac9ee0a98 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 537d9f525c5..951d5d8a77f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -42,7 +42,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 1a94000c0a8..d8c82d0d4f0 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 261eb7b7659..103d1625334 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 69536b9f108..0a36f85d1da 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index cec88c6b456..565f9bd7ff7 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java index 5caccab45d2..e7f248eadb9 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java @@ -30,7 +30,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 10e1ad23a81..16705dc1e6f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -31,7 +31,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index 9e557189f2d..7a9abc5214e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 5afd9ea399e..74c0f3f806b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -44,7 +44,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index ab798ce82f0..41cb84b78f5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 1a528519366..2f973cb6da1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -28,6 +28,7 @@ import org.opencb.opencga.client.config.ClientConfiguration; import org.opencb.opencga.client.exceptions.ClientException; import org.opencb.opencga.client.rest.*; +import org.opencb.opencga.core.models.alignment.RohWrapperParams; import org.opencb.opencga.core.models.analysis.knockout.KnockoutByGene; import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividual; import org.opencb.opencga.core.models.clinical.ExomiserWrapperParams; @@ -62,7 +63,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -770,6 +771,24 @@ public RestResponse runRelatedness(RelatednessAnalysisParams data, ObjectMa return execute("analysis", null, "variant/relatedness", null, "run", params, POST, Job.class); } + /** + * Analysis to calculate and visualise regions of homozygosity (ROHs) for a given sample. + * @param data ROH parameters. + * @param params Map containing any of the following optional parameters. + * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. + * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. + * jobDescription: Job description. + * jobDependsOn: Comma separated list of existing job IDs the job will depend on. + * jobTags: Job tags. + * @return a RestResponse object. + * @throws ClientException ClientException if there is any server error. + */ + public RestResponse runRoh(RohWrapperParams data, ObjectMap params) throws ClientException { + params = params != null ? params : new ObjectMap(); + params.put("body", data); + return execute("analysis", null, "variant/roh", null, "run", params, POST, Job.class); + } + /** * Rvtests is a flexible software package for genetic association studies. Supported RvTests commands: rvtest, vcf2kinship. * @param data RvTests parameters. Supported RvTests commands: rvtest, vcf2kinship. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 1aae70260a3..6007711d1df 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-03-12 +* Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 3ab8837cfde..a27f7b18eee 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 550e528c9d0..1306e8c0ca6 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 0a4a554b1e7..32e52cb8ce2 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index a8beab20022..7b60e02487f 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index e109c595a4e..ec87f1e1917 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index f9dc5c48dac..c9a785aeb94 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 68a977dc9a3..46cdc6078fd 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 1c8bc3aec74..864c00a1e41 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 893ad686998..83f85dbc606 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 6b59792e2be..e29bc5501da 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 20aa39d36d3..6107a9fdd2a 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Organization.js b/opencga-client/src/main/javascript/Organization.js index 848305cb541..f18a736eb00 100644 --- a/opencga-client/src/main/javascript/Organization.js +++ b/opencga-client/src/main/javascript/Organization.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index 96fd5d76d5b..db01ff9dd4b 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 2bff7c6c805..45661a9eab6 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 9cba17724a2..a1824643e97 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index ca89e9c6cd8..2f6aadfd024 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index b2b717f2733..b09040f5b82 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -654,6 +654,21 @@ export default class Variant extends OpenCGAParentClass { return this._post("analysis", null, "variant/relatedness", null, "run", data, params); } + /** Analysis to calculate and visualise regions of homozygosity (ROHs) for a given sample + * @param {Object} data - ROH parameters. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.study] - Study [[organization@]project:]study where study and project can be either the ID or UUID. + * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not + * provided. + * @param {String} [params.jobDescription] - Job description. + * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. + * @param {String} [params.jobTags] - Job tags. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + runRoh(data, params) { + return this._post("analysis", null, "variant/roh", null, "run", data, params); + } + /** Rvtests is a flexible software package for genetic association studies. Supported RvTests commands: rvtest, vcf2kinship * @param {Object} data - RvTests parameters. Supported RvTests commands: rvtest, vcf2kinship. * @param {Object} [params] - The Object containing the following optional parameters: diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index 9bc29ecfedd..5d524256ec8 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-03-12 + * Autogenerated on: 2024-03-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 5c7acf23a1b..46695cd2315 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 3f88bb0d464..c7d67f3db1d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index 5ad28af0295..9bb4201eb57 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index ac75391b6ab..a3258ff9359 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 0392ebc1ff7..27938a3da6d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index d40660bdc72..e419bd8a544 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 6ec39174d2d..0474a43c2f1 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 937c64be1c7..1354f3b8653 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index bf1a2279d8b..8f2643ee3b4 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 33704a42321..c206f942289 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 55180c56871..67be2e17243 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py index 535c4e21d87..0da94e1e36f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 8f869340bd8..f4191edc678 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 9c0a698ee52..f7792850b42 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 8b68612d1d8..f10a82c0aed 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 0cb21ab37ac..bd4f350033e 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index e459f95847d..e3a6968bcd2 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -863,6 +863,25 @@ def run_relatedness(self, data=None, **options): return self._post(category='analysis', resource='run', subcategory='variant/relatedness', data=data, **options) + def run_roh(self, data=None, **options): + """ + Analysis to calculate and visualise regions of homozygosity (ROHs) for + a given sample. + PATH: /{apiVersion}/analysis/variant/roh/run + + :param dict data: ROH parameters. (REQUIRED) + :param str study: Study [[organization@]project:]study where study and + project can be either the ID or UUID. + :param str job_id: Job ID. It must be a unique string within the + study. An ID will be autogenerated automatically if not provided. + :param str job_description: Job description. + :param str job_depends_on: Comma separated list of existing job IDs + the job will depend on. + :param str job_tags: Job tags. + """ + + return self._post(category='analysis', resource='run', subcategory='variant/roh', data=data, **options) + def run_rvtests(self, data=None, **options): """ Rvtests is a flexible software package for genetic association diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 33301600c61..cb9694bcda3 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-03-12 + Autogenerated on: 2024-03-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java index ffcbb073b44..8d48fc14e61 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java @@ -526,7 +526,7 @@ public class FieldConstants { + " Default: 1000"; public static final String ROH_HOMOZYG_SNP_DESCRIPTION = "Plink's parameter to set the minimum number of snps in a ROH. Default: 100"; public static final String ROH_HOMOZYG_HET_DESCRIPTION = "Plink's parameter to set the maximum number of heterozygous calls in a ROH." - + " Default: unlimited."; + + " Default: -1 that means 'unlimited'."; public static final String ROH_HOMOZYG_DENSITY_DESCRIPTION = "Plink's parameter to set the maximum inverse ROH density (kb/SNP)." + " Minimum ROH density: 1 SNP per X kb. Default: 50"; public static final String ROH_HOMOZYG_GAP_DESCRIPTION = "Plink's parameter to set the maximum gap length in kb between two" diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/RohWrapperParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/RohWrapperParams.java index 0bd973d5e76..329f2f2c4e6 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/RohWrapperParams.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/RohWrapperParams.java @@ -36,7 +36,7 @@ public class RohWrapperParams extends ToolParams { private Integer homozygWindowMissing; @DataField(id = "homozygWindowThreshold", description = FieldConstants.ROH_HOMOZYG_WINDOW_THRESHOLD_DESCRIPTION, defaultValue = "0.05") - private Float homozygWindowThreshold; + private Double homozygWindowThreshold; @DataField(id = "homozygKb", description = FieldConstants.ROH_HOMOZYG_KB_DESCRIPTION, defaultValue = "1000") private Integer homozygKb; @@ -44,7 +44,7 @@ public class RohWrapperParams extends ToolParams { @DataField(id = "homozygSnp", description = FieldConstants.ROH_HOMOZYG_SNP_DESCRIPTION, defaultValue = "100") private Integer homozygSnp; - @DataField(id = "homozygHet", description = FieldConstants.ROH_HOMOZYG_HET_DESCRIPTION, defaultValue = "unlimited") + @DataField(id = "homozygHet", description = FieldConstants.ROH_HOMOZYG_HET_DESCRIPTION, defaultValue = "-1") private Integer homozygHet; @DataField(id = "homozygDensity", description = FieldConstants.ROH_HOMOZYG_DENSITY_DESCRIPTION, defaultValue = "50") @@ -60,7 +60,7 @@ public RohWrapperParams() { } public RohWrapperParams(String sampleId, String chromosome, String filter, Integer genotypeQuality, Boolean skipGenotypeQuality, - Integer homozygWindowSnp, Integer homozygWindowHet, Integer homozygWindowMissing, Float homozygWindowThreshold, + Integer homozygWindowSnp, Integer homozygWindowHet, Integer homozygWindowMissing, Double homozygWindowThreshold, Integer homozygKb, Integer homozygSnp, Integer homozygHet, String homozygDensity, String homozygGap, String outdir) { this.sampleId = sampleId; @@ -174,11 +174,11 @@ public RohWrapperParams setHomozygWindowMissing(Integer homozygWindowMissing) { return this; } - public Float getHomozygWindowThreshold() { + public Double getHomozygWindowThreshold() { return homozygWindowThreshold; } - public RohWrapperParams setHomozygWindowThreshold(Float homozygWindowThreshold) { + public RohWrapperParams setHomozygWindowThreshold(Double homozygWindowThreshold) { this.homozygWindowThreshold = homozygWindowThreshold; return this; }