Merge branch 'release-2.4.x' into TASK-2420

opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

@@ -119,7 +119,7 @@ public class VariantAnalysisTest {
     public static Object[][] parameters() {
         return new Object[][]{
                 {MongoDBVariantStorageEngine.STORAGE_ENGINE_ID},
-                {HadoopVariantStorageEngine.STORAGE_ENGINE_ID}
+//                {HadoopVariantStorageEngine.STORAGE_ENGINE_ID}
         };
     }
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2022-09-29 OpenCB
+* Copyright 2015-2022-10-28 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2022-09-29 OpenCB
+* Copyright 2015-2022-10-28 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java

@@ -513,8 +513,8 @@ private RestResponse<Job> runExport() throws Exception {
              putNestedIfNotEmpty(beanParams, "includeSample",commandOptions.includeSample, true);
              putNestedIfNotEmpty(beanParams, "includeFile",commandOptions.includeFile, true);
              putNestedIfNotEmpty(beanParams, "includeSampleData",commandOptions.includeSampleData, true);
-             putNestedIfNotEmpty(beanParams, "includeSampleId",commandOptions.includeSampleId, true);
-             putNestedIfNotEmpty(beanParams, "includeGenotype",commandOptions.includeGenotype, true);
+             putNestedIfNotNull(beanParams, "includeSampleId",commandOptions.includeSampleId, true);
+             putNestedIfNotNull(beanParams, "includeGenotype",commandOptions.includeGenotype, true);
              putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true);
              putNestedIfNotEmpty(beanParams, "qual",commandOptions.qual, true);
              putNestedIfNotEmpty(beanParams, "filter",commandOptions.filter, true);

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)