From cd4c96caf1cb7afcdec5f54a7de72bde4f63820e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Wed, 9 Nov 2022 13:52:55 +0100 Subject: [PATCH] analysis: remove HS metrics from alignment QC analysis, and generate CLI, #TASK-2303, #TASK-2304 --- .../alignment/qc/AlignmentQcAnalysis.java | 61 +------------------ .../executors/AlignmentCommandExecutor.java | 2 - .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../AnalysisAlignmentCommandExecutor.java | 2 - .../AnalysisAlignmentCommandOptions.java | 16 ++--- .../AnalysisClinicalCommandOptions.java | 4 +- .../AnalysisVariantCommandOptions.java | 10 +-- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 6 +- opencga-client/src/main/R/R/AllGenerics.R | 22 +++---- .../src/main/R/R/Clinical-methods.R | 8 +-- 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 +- opencga-client/src/main/R/R/Panel-methods.R | 4 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- 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 | 12 ++-- .../client/rest/clients/AdminClient.java | 4 +- .../client/rest/clients/AlignmentClient.java | 12 ++-- .../rest/clients/ClinicalAnalysisClient.java | 8 +-- .../client/rest/clients/CohortClient.java | 4 +- .../rest/clients/DiseasePanelClient.java | 4 +- .../client/rest/clients/FamilyClient.java | 4 +- .../client/rest/clients/FileClient.java | 4 +- .../client/rest/clients/GA4GHClient.java | 4 +- .../client/rest/clients/IndividualClient.java | 4 +- .../client/rest/clients/JobClient.java | 4 +- .../client/rest/clients/MetaClient.java | 4 +- .../client/rest/clients/ProjectClient.java | 4 +- .../client/rest/clients/SampleClient.java | 4 +- .../client/rest/clients/StudyClient.java | 4 +- .../client/rest/clients/UserClient.java | 4 +- .../client/rest/clients/VariantClient.java | 14 ++--- .../rest/clients/VariantOperationClient.java | 4 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 9 ++- .../src/main/javascript/ClinicalAnalysis.js | 8 ++- 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 +- 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 | 4 +- .../rest_clients/alignment_client.py | 17 +++--- .../rest_clients/clinical_analysis_client.py | 11 ++-- .../pyopencga/rest_clients/cohort_client.py | 4 +- .../rest_clients/disease_panel_client.py | 4 +- .../pyopencga/rest_clients/family_client.py | 4 +- .../pyopencga/rest_clients/file_client.py | 4 +- .../pyopencga/rest_clients/ga4gh_client.py | 4 +- .../rest_clients/individual_client.py | 4 +- .../pyopencga/rest_clients/job_client.py | 4 +- .../pyopencga/rest_clients/meta_client.py | 4 +- .../pyopencga/rest_clients/project_client.py | 4 +- .../pyopencga/rest_clients/sample_client.py | 4 +- .../pyopencga/rest_clients/study_client.py | 4 +- .../pyopencga/rest_clients/user_client.py | 4 +- .../pyopencga/rest_clients/variant_client.py | 23 ++++--- .../rest_clients/variant_operation_client.py | 4 +- .../opencga/core/api/FieldConstants.java | 11 +++- .../opencga/core/api/ParamConstants.java | 4 +- .../models/alignment/AlignmentQcParams.java | 49 +++++---------- 80 files changed, 223 insertions(+), 295 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java index 43af49f934c..d4d08bba37f 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java @@ -61,7 +61,6 @@ public class AlignmentQcAnalysis extends OpenCgaToolScopeStudy { private boolean runStats = true; private boolean runFlagStats = true; private boolean runFastqc = true; - private boolean runHsmetrics = true; @Override protected void check() throws Exception { @@ -99,33 +98,10 @@ protected void check() throws Exception { (!analysisParams.isOverwrite() && alignmentQc != null && alignmentQc.getFastQcMetrics() != null)) { runFastqc = false; } - if (skipValues.contains(AlignmentQcParams.HS_METRICS_SKIP_VALUE) - || - (!analysisParams.isOverwrite() && alignmentQc != null && alignmentQc.getHsMetrics() != null) - || - StringUtils.isEmpty(analysisParams.getBedFile()) - || - StringUtils.isEmpty(analysisParams.getDictFile())) { - runHsmetrics = false; - } } } catch (CatalogException e) { throw new ToolException("Error accessing to the BAM file '" + analysisParams.getBamFile() + "'", e); } - - if (runHsmetrics) { - try { - AnalysisUtils.getCatalogFile(analysisParams.getBedFile(), study, catalogManager.getFileManager(), token); - } catch (CatalogException e) { - throw new ToolException("Error accessing to the BED file '" + analysisParams.getBedFile() + "'", e); - } - - try { - AnalysisUtils.getCatalogFile(analysisParams.getDictFile(), study, catalogManager.getFileManager(), token); - } catch (CatalogException e) { - throw new ToolException("Error accessing to the dictionary file '" + analysisParams.getDictFile() + "'", e); - } - } } @Override @@ -136,7 +112,6 @@ protected void run() throws ToolException { String statsJobId = null; String flagStatsJobId = null; String fastQcMetricsJobId = null; - String hsMetricsJobId = null; try { if (runFlagStats) { @@ -189,29 +164,10 @@ protected void run() throws ToolException { addWarning("Error launching job for Alignment FastQC Metrics Analysis: " + e.getMessage()); } - try { - if (runHsmetrics) { - // HS metrics - params = new AlignmentHsMetricsParams(analysisParams.getBamFile(), analysisParams.getBedFile(), - analysisParams.getDictFile(), null).toParams(new ObjectMap(ParamConstants.STUDY_PARAM, study)); - - OpenCGAResult hsMetricsJobResult = catalogManager.getJobManager() - .submit(study, AlignmentHsMetricsAnalysis.ID, Enums.Priority.MEDIUM, params, null, - "Job generated by " + getId() + " - " + getJobId(), Collections.emptyList(), Collections.emptyList(), - token); - hsMetricsJobId = hsMetricsJobResult.first().getId(); - addEvent(Event.Type.INFO, "Submit job " + hsMetricsJobId + " to compute HS metrics (" + AlignmentHsMetricsAnalysis.ID - + ")"); - } - } catch (CatalogException e) { - addWarning("Error launching job for Alignment HS Metrics Analysis: " + e.getMessage()); - } - // Wait for those jobs before saving QC SamtoolsFlagstats samtoolsFlagstats = null; SamtoolsStats samtoolsStats = null; FastQcMetrics fastQcMetrics = null; - HsMetrics hsMetrics = null; if (flagStatsJobId != null) { try { @@ -249,17 +205,6 @@ protected void run() throws ToolException { addWarning("Error waiting for job '" + fastQcMetricsJobId + "' (Alignment FastQC Metrics Analysis): " + e.getMessage()); } } - if (hsMetricsJobId != null) { - try { - if (waitFor(hsMetricsJobId)) { - Job job = getJob(hsMetricsJobId); - logger.info("Alignment HS Metrics Analysis, job.outDir = " + job.getOutDir()); - hsMetrics = AlignmentHsMetricsAnalysis.parseResults(Paths.get(job.getOutDir().getUri().getPath())); - } - } catch (Exception e) { - addWarning("Error waiting for job '" + hsMetricsJobId + "' (Alignment FastQC Metrics Analysis): " + e.getMessage()); - } - } // Update quality control for the catalog file catalogBamFile = AnalysisUtils.getCatalogFile(analysisParams.getBamFile(), study, catalogManager.getFileManager(), token); @@ -284,10 +229,6 @@ protected void run() throws ToolException { qc.getAlignment().setFastQcMetrics(fastQcMetrics); saveQc = true; } - if (hsMetrics != null) { - qc.getAlignment().setHsMetrics(hsMetrics); - saveQc = true; - } if (saveQc) { catalogManager.getFileManager().update(getStudy(), catalogBamFile.getId(), new FileUpdateParams().setQualityControl(qc), @@ -324,7 +265,7 @@ private boolean waitFor(String jobId) throws ToolException { return status.equals(Enums.ExecutionStatus.DONE) ? true : false; } - private Job getJob(String jobId) throws ToolException { + private Job getJob(String jobId) { Job job = null; try { Query query = new Query("id", jobId); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java index 1ed8c9fa275..3553384e71a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java @@ -156,8 +156,6 @@ private void qcRun() throws ToolException { ObjectMap params = new AlignmentQcParams( cliOptions.bamFile, - cliOptions.bedFile, - cliOptions.dictFile, cliOptions.skip, cliOptions.overwrite, cliOptions.outdir 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 1fb4ba6dbfc..30fbe687500 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 2015-2022-09-29 OpenCB +* Copyright 2015-2022-11-09 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. 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 3b7b84a973e..4768c317a04 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 2015-2022-09-29 OpenCB +* Copyright 2015-2022-11-09 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 773f03e4e09..01ad95bf28a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -481,8 +481,6 @@ private RestResponse runQc() throws Exception { } else { ObjectMap beanParams = new ObjectMap(); putNestedIfNotEmpty(beanParams, "bamFile",commandOptions.bamFile, true); - putNestedIfNotEmpty(beanParams, "bedFile",commandOptions.bedFile, true); - putNestedIfNotEmpty(beanParams, "dictFile",commandOptions.dictFile, true); putNestedIfNotEmpty(beanParams, "skip",commandOptions.skip, true); putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true); putNestedIfNotEmpty(beanParams, "outdir",commandOptions.outdir, true); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java index 3d39615f845..96d5394fef8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java @@ -421,7 +421,7 @@ public class RunPicardCommandOptions { } - @Parameters(commandNames = {"qc-run"}, commandDescription ="Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS metrics)") + @Parameters(commandNames = {"qc-run"}, commandDescription ="Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics.") public class RunQcCommandOptions { @ParametersDelegate @@ -448,22 +448,16 @@ public class RunQcCommandOptions { @Parameter(names = {"--job-tags"}, description = "Job tags", required = false, arity = 1) public String jobTags; - @Parameter(names = {"--bam-file"}, description = "The body web service bamFile parameter", required = false, arity = 1) + @Parameter(names = {"--bam-file"}, description = "ID for the BAM file to process.", required = false, arity = 1) public String bamFile; - @Parameter(names = {"--bed-file"}, description = "The body web service bedFile parameter", required = false, arity = 1) - public String bedFile; - - @Parameter(names = {"--dict-file"}, description = "The body web service dictFile parameter", required = false, arity = 1) - public String dictFile; - - @Parameter(names = {"--skip"}, description = "The body web service skip parameter", required = false, arity = 1) + @Parameter(names = {"--skip"}, description = "To skip any alignment QC metrics use the following keywords (separated by commas): stats, flagstats, fastqc", required = false, arity = 1) public String skip; - @Parameter(names = {"--overwrite"}, description = "The body web service overwrite parameter", required = false, help = true, arity = 0) + @Parameter(names = {"--overwrite"}, description = "To overwrite the QC metrics already computed.", required = false, help = true, arity = 0) public boolean overwrite = false; - @Parameter(names = {"--outdir"}, description = "The body web service outdir parameter", required = false, arity = 1) + @Parameter(names = {"--outdir"}, description = "Output dir for the job.", required = false, arity = 1) public String outdir; } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java index da223815b12..609d17c23d2 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java @@ -1613,7 +1613,7 @@ public class QueryVariantCommandOptions { @Parameter(names = {"--file-data"}, description = "Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from 'file' filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP", required = false, arity = 1) public String fileData; - @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) + @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) public String sample; @Parameter(names = {"--sample-data"}, description = "Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10", required = false, arity = 1) @@ -1655,7 +1655,7 @@ public class QueryVariantCommandOptions { @Parameter(names = {"--family-disorder"}, description = "Specify the disorder to use for the family segregation", required = false, arity = 1) public String familyDisorder; - @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]", required = false, arity = 1) + @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]", required = false, arity = 1) public String familySegregation; @Parameter(names = {"--family-members"}, description = "Sub set of the members of a given family", required = false, arity = 1) 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 f39995b6ddc..fd3404d008b 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 @@ -1296,7 +1296,7 @@ public class MetadataCommandOptions { @Parameter(names = {"--file"}, description = "Filter variants from the files specified. This will set includeFile parameter when not provided", required = false, arity = 1) public String file; - @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) + @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) public String sample; @Parameter(names = {"--include-study"}, description = "List of studies to include in the result. Accepts 'all' and 'none'.", required = false, arity = 1) @@ -1577,7 +1577,7 @@ public class QueryCommandOptions { @Parameter(names = {"--file-data"}, description = "Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from 'file' filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP", required = false, arity = 1) public String fileData; - @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) + @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) public String sample; @Parameter(names = {"--genotype"}, description = "Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set 'includeSample' parameter when not provided", required = false, arity = 1) @@ -1634,7 +1634,7 @@ public class QueryCommandOptions { @Parameter(names = {"--family-disorder"}, description = "Specify the disorder to use for the family segregation", required = false, arity = 1) public String familyDisorder; - @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]", required = false, arity = 1) + @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]", required = false, arity = 1) public String familySegregation; @Parameter(names = {"--family-members"}, description = "Sub set of the members of a given family", required = false, arity = 1) @@ -1853,7 +1853,7 @@ public class AggregationStatsSampleCommandOptions { @Parameter(names = {"--filter"}, description = "Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: PASS,LowGQX", required = false, arity = 1) public String filter; - @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) + @Parameter(names = {"--sample"}, description = "Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. ", required = false, arity = 1) public String sample; @Parameter(names = {"--genotype"}, description = "Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set 'includeSample' parameter when not provided", required = false, arity = 1) @@ -1868,7 +1868,7 @@ public class AggregationStatsSampleCommandOptions { @Parameter(names = {"--family-disorder"}, description = "Specify the disorder to use for the family segregation", required = false, arity = 1) public String familyDisorder; - @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]", required = false, arity = 1) + @Parameter(names = {"--family-segregation"}, description = "Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]", required = false, arity = 1) public String familySegregation; @Parameter(names = {"--family-members"}, description = "Sub set of the members of a given family", required = false, arity = 1) diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 8101fc8058a..0dec819f31f 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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 42fd548fc6e..7a24169eea1 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -165,13 +165,13 @@ setMethod("alignmentClient", "OpencgaR", function(OpencgaR, endpointName, params subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), #' @section Endpoint /{apiVersion}/analysis/alignment/qc/run: - #' Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS metrics). + #' Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics. #' @param study study. #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. #' @param jobDependsOn Comma separated list of existing job IDs the job will depend on. #' @param jobDescription Job description. #' @param jobTags Job tags. - #' @param data Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and hybrid-selection metrics. The BAM file is mandatory ever but the BED fileand the dictionary files are only mandatory for computing hybrid-selection (HS) metrics. In order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc and hsmetrics. + #' @param data Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics. The BAM file ID is mandatory and in order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc. runQc=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="alignment/qc", subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 034a4e0a0a6..21e928c6dc8 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,42 +10,42 @@ setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, variableSet, study, studies, templateId, group, members, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, group, templateId, study, members, studies, variableSet, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, members, file, files, folder, annotationSet, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, files, file, annotationSet, folder, members, 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")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, samples, sample, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, annotationSet, individuals, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, family, families, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, cohorts, cohort, annotationSet, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, cohort, cohorts, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## ## PanelClient -setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...) +setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...) standardGeneric("panelClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretations, clinicalAnalyses, clinicalAnalysis, members, interpretation, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, interpretation, interpretations, members, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, file, study, 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 f7fd055e4e2..3ad6e792be6 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, clinicalAnalyses, clinicalAnalysis, members, interpretation, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, interpretation, interpretations, members, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: @@ -531,7 +531,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, clin #' @param filter Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: PASS,LowGQX. #' @param qual Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. e.g.: >123.4. #' @param fileData Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from "file" filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . #' @param sampleData Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. #' @param sampleAnnotation Selects some samples using metadata information from Catalog. e.g. age>20;phenotype=hpo:123,hpo:456;name=smith. #' @param cohort Select variants with calculated stats for the selected cohorts. @@ -545,7 +545,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, clin #' @param score Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. #' @param family Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). #' @param familyDisorder Specify the disorder to use for the family segregation. - #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. #' @param familyMembers Sub set of the members of a given family. #' @param familyProband Specify the proband child to use for the family segregation. #' @param gene List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter. diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 8b95192c983..8adee1daa29 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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("cohortClient", "OpencgaR", function(OpencgaR, members, cohorts, cohort, annotationSet, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, cohorts, annotationSet, 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 fefa330f95f..e7f24fb5470 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, family, families, annotationSet, 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 7bca6768e88..0a3ce48b480 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, members, file, files, folder, annotationSet, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, annotationSet, folder, members, 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 743db285d25..84160d942e3 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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, study, file, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, 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 6b5b6bf7264..7fb2fb05fdd 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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("individualClient", "OpencgaR", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, individuals, 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 79c3b9bf69f..2293bc1ae31 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -40,7 +40,7 @@ #' [*]: 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 af033f70c37..1c79388995e 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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 02048f11773..3b1f3082a63 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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 9340c2e989f..8547c2eec23 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -36,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) { +setMethod("panelClient", "OpencgaR", function(OpencgaR, panels, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/panels/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 8a4eec89ae0..d7c605c4264 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index edc5ff18bed..d2b1a66a63f 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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("sampleClient", "OpencgaR", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, sample, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 7fe35cd1af3..ff57bf11bb7 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, variableSet, study, studies, templateId, group, members, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, group, templateId, study, members, studies, 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 93d858a5438..fbb09adc533 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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, user, users, filterId, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/create: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 4c7ef1d9b95..ac82f504173 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: 2022-09-29 11:52:54 +# Autogenerated on: 2022-11-09 12:56:56 # # 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. @@ -345,7 +345,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N #' @param project Project [user@]project where project can be either the ID or the alias. #' @param study Filter variants from the given studies, these can be either the numeric ID or the alias with the format user@project:study. #' @param file Filter variants from the files specified. This will set includeFile parameter when not provided. - #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . #' @param includeStudy List of studies to include in the result. Accepts 'all' and 'none'. #' @param includeFile List of files to be returned. Accepts 'all' and 'none'. If undefined, automatically includes files used for filtering. If none, no file is included. #' @param includeSample List of samples to be included in the result. Accepts 'all' and 'none'. If undefined, automatically includes samples used for filtering. If none, no sample is included. @@ -432,7 +432,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N #' @param filter Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: PASS,LowGQX. #' @param qual Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. e.g.: >123.4. #' @param fileData Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from "file" filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . #' @param genotype Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set 'includeSample' parameter when not provided. #' @param sampleData Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. #' @param sampleAnnotation Selects some samples using metadata information from Catalog. e.g. age>20;phenotype=hpo:123,hpo:456;name=smith. @@ -451,7 +451,7 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N #' @param score Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. #' @param family Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). #' @param familyDisorder Specify the disorder to use for the family segregation. - #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. #' @param familyMembers Sub set of the members of a given family. #' @param familyProband Specify the proband child to use for the family segregation. #' @param includeStudy List of studies to include in the result. Accepts 'all' and 'none'. @@ -523,12 +523,12 @@ setMethod("variantClient", "OpencgaR", function(OpencgaR, endpointName, params=N #' @param study Filter variants from the given studies, these can be either the numeric ID or the alias with the format user@project:study. #' @param file Filter variants from the files specified. This will set includeFile parameter when not provided. #' @param filter Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: PASS,LowGQX. - #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + #' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . #' @param genotype Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT. This will automatically set 'includeSample' parameter when not provided. #' @param sampleAnnotation Selects some samples using metadata information from Catalog. e.g. age>20;phenotype=hpo:123,hpo:456;name=smith. #' @param family Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). #' @param familyDisorder Specify the disorder to use for the family segregation. - #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + #' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. #' @param familyMembers Sub set of the members of a given family. #' @param familyProband Specify the proband child to use for the family segregation. #' @param ct List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'. 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 5eb47c7bf72..c4138aff873 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 @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -44,7 +44,7 @@ /** * This class contains methods for the Admin webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: admin */ public class AdminClient extends AbstractParentClient { 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 9081ac81fbe..12c8185b358 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: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -49,7 +49,7 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { @@ -251,11 +251,9 @@ public RestResponse runPicard(PicardWrapperParams data, ObjectMap params) t } /** - * Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS - * metrics). - * @param data Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and hybrid-selection metrics. The BAM - * file is mandatory ever but the BED fileand the dictionary files are only mandatory for computing hybrid-selection (HS) metrics. - * In order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc and hsmetrics. + * Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics. + * @param data Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics. The BAM file ID is + * mandatory and in order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc. * @param params Map containing any of the following optional parameters. * study: study. * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. 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 98a11c05bd1..38433c91abb 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 @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -60,7 +60,7 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { @@ -682,7 +682,7 @@ public RestResponse search(ObjectMap params) throws ClientExce * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . * sampleData: Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will * use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be @@ -701,7 +701,7 @@ public RestResponse search(ObjectMap params) throws ClientExce * family: Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). * familyDisorder: Specify the disorder to use for the family segregation. * familySegregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, - * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. * familyMembers: Sub set of the members of a given family. * familyProband: Specify the proband child to use for the family segregation. * gene: List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter. 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 7af0d626cd8..19b4b99db4e 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 @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -46,7 +46,7 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: cohorts */ public class CohortClient extends AbstractParentClient { 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 43fe0b0ed3a..e45b1524790 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: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -44,7 +44,7 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { 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 a07aa7d8b67..2e2eb9642f5 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 @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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 @@ /** * This class contains methods for the Family webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: families */ public class FamilyClient extends AbstractParentClient { 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 de5b13619a5..fc4d7ccf23d 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 @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -52,7 +52,7 @@ /** * This class contains methods for the File webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: files */ public class FileClient extends AbstractParentClient { 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 f7dd9e9b8b0..a4ed8d2a220 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: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -36,7 +36,7 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { 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 e1bc6ee6312..159d3a01d20 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 @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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 @@ /** * This class contains methods for the Individual webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: individuals */ public class IndividualClient extends AbstractParentClient { 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 fb3b7341441..f2e620b83c5 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 @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -46,7 +46,7 @@ /** * This class contains methods for the Job webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: jobs */ public class JobClient extends AbstractParentClient { 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 17236975b97..0b6a1f52a72 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: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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 @@ /** * This class contains methods for the Meta webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: meta */ public class MetaClient extends AbstractParentClient { 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 c0f56fb193f..2f225d35d93 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 @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -41,7 +41,7 @@ /** * This class contains methods for the Project webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: projects */ public class ProjectClient extends AbstractParentClient { 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 45c6d9826dd..ca8c5e80f25 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 @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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 @@ /** * This class contains methods for the Sample webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: samples */ public class SampleClient extends AbstractParentClient { 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 29540ccaf73..5ffd4a16e07 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 @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -54,7 +54,7 @@ /** * This class contains methods for the Study webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: studies */ public class StudyClient extends AbstractParentClient { 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 7e58fa94079..9dd689fff7f 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 @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -46,7 +46,7 @@ /** * This class contains methods for the User webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: users */ public class UserClient extends AbstractParentClient { 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 8f65b6359c9..e77dba24252 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 @@ -61,7 +61,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -70,7 +70,7 @@ /** * This class contains methods for the Variant webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { @@ -513,7 +513,7 @@ public RestResponse runMendelianError(MendelianErrorAnalysisParams data, Ob * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . * includeStudy: List of studies to include in the result. Accepts 'all' and 'none'. * includeFile: List of files to be returned. Accepts 'all' and 'none'. If undefined, automatically includes files used for @@ -665,7 +665,7 @@ public RestResponse runPlink(PlinkWrapperParams data, ObjectMap params) thr * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . * genotype: Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. * HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), @@ -695,7 +695,7 @@ public RestResponse runPlink(PlinkWrapperParams data, ObjectMap params) thr * family: Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). * familyDisorder: Specify the disorder to use for the family segregation. * familySegregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, - * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. * familyMembers: Sub set of the members of a given family. * familyProband: Specify the proband child to use for the family segregation. * includeStudy: List of studies to include in the result. Accepts 'all' and 'none'. @@ -810,7 +810,7 @@ public RestResponse runRvtests(RvtestsWrapperParams data, ObjectMap params) * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . * genotype: Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. * HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), @@ -823,7 +823,7 @@ public RestResponse runRvtests(RvtestsWrapperParams data, ObjectMap params) * family: Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). * familyDisorder: Specify the disorder to use for the family segregation. * familySegregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, - * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. * familyMembers: Sub set of the members of a given family. * familyProband: Specify the proband child to use for the family segregation. * ct: List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' 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 fa1260d30c4..6b14a1781e1 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: 2022-09-29 11:52:54 +* Autogenerated on: 2022-11-09 12:56:55 * * 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. @@ -59,7 +59,7 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + * Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index c8c295eeea1..b3c469ab705 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 9d4c4a96180..a07e02aff42 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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. @@ -188,10 +188,9 @@ export default class Alignment extends OpenCGAParentClass { return this._post("analysis", null, "alignment/picard", null, "run", data, params); } - /** Compute quality control (QC) metrics for a given alignment file (including samtools stats, samtools flag stats, FastQC and HS metrics) - * @param {Object} data - Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and hybrid-selection metrics. - * The BAM file is mandatory ever but the BED fileand the dictionary files are only mandatory for computing hybrid-selection (HS) - * metrics. In order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc and hsmetrics. + /** Compute quality control (QC) metrics for a given alignment file: samtools stats, samtools flag stats and FastQC metrics. + * @param {Object} data - Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics. The BAM file ID + * is mandatory and in order to skip some metrics, use the following keywords (separated by commas): stats, flagstats, fastqc. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - study. * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 57e5cc099d4..b56f6d79795 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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. @@ -581,7 +581,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + * deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined + * and indexed. . * @param {String} [params.sampleData] - Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is * specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can * be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. @@ -600,7 +601,8 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * HOM_ALT). * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, + * compoundHeterozygous ]. * @param {String} [params.familyMembers] - Sub set of the members of a given family. * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. * @param {String} [params.gene] - List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index a918097f9cd..4bcb7ec1180 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 15a08374be5..0978954487f 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 d207e2c30e7..57d0b99535d 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 7d5daf8787f..79c3297810c 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 4b1659a4cfd..72375ae7c7a 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 5a7c31a2fc5..51dbe67b0be 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 5b8ebb096cb..6b9b9bea91b 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 0deeb79b65d..a97cf461da1 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 bcc2e4eb428..191a5385cc9 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 ffc54c300c1..a5b02fe4035 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 ccc4565647e..9788ba04044 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 9ab54db591a..827020aa412 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:55 * * 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 657f77929a7..e216387b8a2 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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. @@ -405,7 +405,8 @@ export default class Variant extends OpenCGAParentClass { * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + * deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined + * and indexed. . * @param {String} [params.includeStudy] - List of studies to include in the result. Accepts 'all' and 'none'. * @param {String} [params.includeFile] - List of files to be returned. Accepts 'all' and 'none'. If undefined, automatically includes * files used for filtering. If none, no file is included. @@ -551,7 +552,8 @@ export default class Variant extends OpenCGAParentClass { * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + * deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined + * and indexed. . * @param {String} [params.genotype] - Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. * HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice * versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with @@ -580,7 +582,8 @@ export default class Variant extends OpenCGAParentClass { * HOM_ALT). * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, + * compoundHeterozygous ]. * @param {String} [params.familyMembers] - Sub set of the members of a given family. * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. * @param {String} [params.includeStudy] - List of studies to include in the result. Accepts 'all' and 'none'. @@ -693,7 +696,8 @@ export default class Variant extends OpenCGAParentClass { * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + * deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined + * and indexed. . * @param {String} [params.genotype] - Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. * HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice * versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with @@ -705,7 +709,8 @@ export default class Variant extends OpenCGAParentClass { * HOM_ALT). * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. + * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, + * compoundHeterozygous ]. * @param {String} [params.familyMembers] - Sub set of the members of a given family. * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. * @param {String} [params.ct] - List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index c5c5c74b912..38def2b2652 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: 2022-09-29 11:52:54 + * Autogenerated on: 2022-11-09 12:56:56 * * 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 8c2b0573b8b..9c20a9a4836 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/admin """ 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 34714d062f8..42923a06d63 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/analysis/alignment """ @@ -227,17 +227,14 @@ def run_picard(self, data=None, **options): def run_qc(self, data=None, **options): """ - Compute quality control (QC) metrics for a given alignment file - (including samtools stats, samtools flag stats, FastQC and HS - metrics). + Compute quality control (QC) metrics for a given alignment file: + samtools stats, samtools flag stats and FastQC metrics. PATH: /{apiVersion}/analysis/alignment/qc/run :param dict data: Alignment quality control (QC) parameters. It - computes: stats, flag stats, fastqc and hybrid-selection metrics. - The BAM file is mandatory ever but the BED fileand the dictionary - files are only mandatory for computing hybrid-selection (HS) - metrics. In order to skip some metrics, use the following keywords - (separated by commas): stats, flagstats, fastqc and hsmetrics. + computes: stats, flag stats and fastqc metrics. The BAM file ID is + mandatory and in order to skip some metrics, use the following + keywords (separated by commas): stats, flagstats, fastqc. (REQUIRED) :param str study: study. :param str job_id: Job ID. It must be a unique string within the 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 da69bba9cd2..b31daa393b8 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/analysis/clinical """ @@ -703,8 +703,9 @@ def query_variant(self, **options): mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case + insensitive. e.g. HG0097:DeNovo Sample must have parents defined + and indexed. . :param str sample_data: Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or @@ -738,7 +739,7 @@ def query_variant(self, **options): :param str family_segregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. + deNovoStrict, mendelianError, compoundHeterozygous ]. :param str family_members: Sub set of the members of a given family. :param str family_proband: Specify the proband child to use for the family segregation. 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 02d9a530bd4..a4b8698b7b7 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/cohorts """ 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 b5264aac46a..8842d0e75f5 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/panels """ 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 4131e31dd03..652927d490c 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/families """ 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 aac1fc1bf87..553644b1c2d 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/files """ 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 ed86850bb01..28db276f65a 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/ga4gh """ 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 d599a25e7a3..a850d62b418 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/individuals """ 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 062f3b6ebd8..58b1a32026d 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/jobs """ 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 ff5b4ca16e2..5b597d48074 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/meta """ 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 51e8e7916a4..c5c1acf073c 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/projects """ 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 446d4a95cbc..388d804b7d2 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/samples """ 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 4f4d013cb36..4a53cb9e790 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/studies """ 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 90349297341..58692be0f32 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/users """ 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 0fe891499e8..95ed3885f5d 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/analysis/variant """ @@ -509,8 +509,9 @@ def metadata(self, **options): mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case + insensitive. e.g. HG0097:DeNovo Sample must have parents defined + and indexed. . :param str include_study: List of studies to include in the result. Accepts 'all' and 'none'. :param str include_file: List of files to be returned. Accepts 'all' @@ -720,8 +721,9 @@ def query(self, **options): mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case + insensitive. e.g. HG0097:DeNovo Sample must have parents defined + and indexed. . :param str genotype: Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will @@ -774,7 +776,7 @@ def query(self, **options): :param str family_segregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. + deNovoStrict, mendelianError, compoundHeterozygous ]. :param str family_members: Sub set of the members of a given family. :param str family_proband: Specify the proband child to use for the family segregation. @@ -935,8 +937,9 @@ def aggregation_stats_sample(self, **options): mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . + deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case + insensitive. e.g. HG0097:DeNovo Sample must have parents defined + and indexed. . :param str genotype: Samples with a specific genotype: {samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)* e.g. HG0097:0/0;HG0098:0/1,1/1. Unphased genotypes (e.g. 0/1, 1/1) will @@ -957,7 +960,7 @@ def aggregation_stats_sample(self, **options): :param str family_segregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. + deNovoStrict, mendelianError, compoundHeterozygous ]. :param str family_members: Sub set of the members of a given family. :param str family_proband: Specify the proband child to use for the family segregation. 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 4416d65cead..58f8e4b5ab2 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: 2022-09-29 11:52:54 + Autogenerated on: 2022-11-09 12:56:55 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. @@ -14,7 +14,7 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 2.4.6-SNAPSHOT [9398b71434a77b1fefbbef5ccac42d25eb6f2070] + Client version: 2.4.11-SNAPSHOT [ad9f2b832fe47e07ac566edd97a65c174b208b2d] PATH: /{apiVersion}/operation """ 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 0962295831d..e25e2751065 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 @@ -2,6 +2,7 @@ import com.beust.jcommander.DynamicParameter; import com.beust.jcommander.Parameter; +import org.opencb.opencga.core.models.alignment.AlignmentQcParams; import java.util.HashMap; import java.util.Map; @@ -430,8 +431,16 @@ public class FieldConstants { public static final String GENOME_PLOT_DESCRIPTION_DESCRIPTION = "Genome plot description."; public static final String GENOME_PLOT_CONFIGURATION_FILE_DESCRIPTION = "Genome plot configuration file."; - // Varaint stats (sample-qc-run) + // Variant stats (sample-qc-run) public static final String VARIANT_STATS_ID_DESCRIPTION = "Variant stats ID."; public static final String VARIANT_STATS_DESCRIPTION_DESCRIPTION = "Variant stats description."; public static final String VARIANT_STATS_QUERY_DESCRIPTION = "Variant stats query in JSON format."; + + // Alignment QC analysis (asample-qc-run) + public static final String ALIGNMENT_QC_BAM_FILE_DESCRIPTION = "ID for the BAM file to process."; + public static final String ALIGNMENT_QC_SKIP_DESCRIPTION = "To skip any alignment QC metrics use the following keywords (separated by" + + " commas): " + AlignmentQcParams.STATS_SKIP_VALUE + ", " + AlignmentQcParams.FLAGSTATS_SKIP_VALUE + ", " + + AlignmentQcParams.FASTQC_METRICS_SKIP_VALUE; + public static final String ALIGNMENT_QC_OVERWRITE_DESCRIPTION = "To overwrite the QC metrics already computed."; + } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index 8004d2a504e..d0f061cbd99 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -579,8 +579,8 @@ public class ParamConstants { public static final String ALIGNMENT_COVERAGE_RATIO_DESCRIPTION = "Compute coverage ratio from file #1 vs file #2, (e.g. somatic vs " + "germline)"; // --------------------------------------------- - public static final String ALIGNMENT_QC_DESCRIPTION = "Compute quality control (QC) metrics for a given alignment file (including " + - "samtools stats, samtools flag stats, FastQC and HS metrics)"; + public static final String ALIGNMENT_QC_DESCRIPTION = "Compute quality control (QC) metrics for a given alignment file:" + + " samtools stats, samtools flag stats and FastQC metrics."; public static final String ALIGNMENT_STATS_DESCRIPTION = "Compute stats (based on samtools/stats command) for a given alignment file"; public static final String ALIGNMENT_FLAG_STATS_DESCRIPTION = "Compute flag stats (based on samtools/flagstat command) for a given " + "alignment file"; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentQcParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentQcParams.java index b4becf1deb0..16507adb547 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentQcParams.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentQcParams.java @@ -1,32 +1,35 @@ package org.opencb.opencga.core.models.alignment; +import org.opencb.commons.annotations.DataField; +import org.opencb.opencga.core.api.FieldConstants; import org.opencb.opencga.core.tools.ToolParams; public class AlignmentQcParams extends ToolParams { - public static String STATS_SKIP_VALUE = "stats"; - public static String FLAGSTATS_SKIP_VALUE = "flagstats"; - public static String FASTQC_METRICS_SKIP_VALUE = "fastqc"; - public static String HS_METRICS_SKIP_VALUE = "hsmetrics"; + public static final String STATS_SKIP_VALUE = "stats"; + public static final String FLAGSTATS_SKIP_VALUE = "flagstats"; + public static final String FASTQC_METRICS_SKIP_VALUE = "fastqc"; - public static final String DESCRIPTION = "Alignment quality control (QC) parameters. It computes: stats, flag stats, fastqc and" - + " hybrid-selection metrics. The BAM file is mandatory ever but the BED fileand the dictionary files are only mandatory for" - + " computing hybrid-selection (HS) metrics. In order to skip some metrics, use the following keywords (separated by commas): " - + "stats, flagstats, fastqc and hsmetrics"; + public static final String DESCRIPTION = "Alignment quality control (QC) parameters. It computes: stats, flag stats and fastqc metrics." + + " The BAM file ID is mandatory and in order to skip some metrics, use the following keywords (separated by commas): " + + STATS_SKIP_VALUE + ", " + FLAGSTATS_SKIP_VALUE + ", " + FASTQC_METRICS_SKIP_VALUE; + @DataField(id = "bamFile", description = FieldConstants.ALIGNMENT_QC_BAM_FILE_DESCRIPTION) private String bamFile; - private String bedFile; - private String dictFile; + + @DataField(id = "skip", description = FieldConstants.ALIGNMENT_QC_SKIP_DESCRIPTION) private String skip; + + @DataField(id = "overwrite", description = FieldConstants.ALIGNMENT_QC_OVERWRITE_DESCRIPTION) private boolean overwrite; + + @DataField(id = "outdir", description = FieldConstants.JOB_OUT_DIR_DESCRIPTION) private String outdir; public AlignmentQcParams() { } - public AlignmentQcParams(String bamFile, String bedFile, String dictFile, String skip, boolean overwrite, String outdir) { + public AlignmentQcParams(String bamFile, String skip, boolean overwrite, String outdir) { this.bamFile = bamFile; - this.bedFile = bedFile; - this.dictFile = dictFile; this.skip = skip; this.overwrite = overwrite; this.outdir = outdir; @@ -36,8 +39,6 @@ public AlignmentQcParams(String bamFile, String bedFile, String dictFile, String public String toString() { final StringBuilder sb = new StringBuilder("AlignmentQcParams{"); sb.append("bamFile='").append(bamFile).append('\''); - sb.append(", bedFile='").append(bedFile).append('\''); - sb.append(", dictFile='").append(dictFile).append('\''); sb.append(", skip='").append(skip).append('\''); sb.append(", overwrite=").append(overwrite); sb.append(", outdir='").append(outdir).append('\''); @@ -54,24 +55,6 @@ public AlignmentQcParams setBamFile(String bamFile) { return this; } - public String getBedFile() { - return bedFile; - } - - public AlignmentQcParams setBedFile(String bedFile) { - this.bedFile = bedFile; - return this; - } - - public String getDictFile() { - return dictFile; - } - - public AlignmentQcParams setDictFile(String dictFile) { - this.dictFile = dictFile; - return this; - } - public String getSkip() { return skip; }