client: generate client, #TASK-5795, #TASK-5343

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;
     }

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<Candidate> 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<Candidate> 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());

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);

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<Job> runRelatedness() throws Exception {
         return openCGAClient.getVariantClient().runRelatedness(relatednessAnalysisParams, queryParams);
     }
 
+    private RestResponse<Job> 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<Job> 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<Job> runRvtests() throws Exception {
         logger.debug("Executing runRvtests in Analysis - Variant command line");
 

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 {
 

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.

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.