From a222469d37c8d34a8a85fad4c4eeb5dd2e050e97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Thu, 13 Jun 2024 16:40:55 +0200 Subject: [PATCH] analysis: remove unused parameter 'relatedness method', #TASK-5282, #TASK-5282 On branch TASK-5278 Changes to be committed: modified: opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java modified: opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java modified: opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java modified: opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java modified: opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java --- .../family/qc/FamilyQcLocalAnalysisExecutor.java | 6 +++--- .../opencga/analysis/family/qc/IBDComputation.java | 4 +++- .../cli/internal/options/VariantCommandOptions.java | 3 --- .../org/opencb/opencga/core/api/ParamConstants.java | 1 - .../core/tools/variant/FamilyQcAnalysisExecutor.java | 10 ---------- 5 files changed, 6 insertions(+), 18 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java index 1494dab5e2f..e19608bb184 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java @@ -66,10 +66,10 @@ private void runRelatedness() throws ToolException { if (CollectionUtils.isNotEmpty(qualityControl.getRelatedness())) { for (RelatednessReport relatedness : qualityControl.getRelatedness()) { - if (relatednessMethod.equals(relatedness.getMethod()) && relatednessMaf.equals(relatedness.getMaf())) { + if (IBDComputation.PLINK_IBD_METHOD.equals(relatedness.getMethod()) && relatednessMaf.equals(relatedness.getMaf())) { // Nothing to update - addWarning("Skipping relatedness analysis: it was already computed for method '" + relatednessMethod + "' and MAF '" - + relatednessMaf + "'"); + addWarning("Skipping relatedness analysis: it was already computed for method '" + IBDComputation.PLINK_IBD_METHOD + + "' and MAF '" + relatednessMaf + "'"); qualityControl = null; return; } diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java index 18e4b925e03..2d677a0812b 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/IBDComputation.java @@ -57,6 +57,8 @@ public class IBDComputation { private static final String FREQ_FILENAME = BASENAME + ".frq"; private static final String PRUNE_IN_FILENAME = BASENAME + ".prune.in"; + public static final String PLINK_IBD_METHOD = "PLINK/IBD"; + public static RelatednessReport compute(String study, Family family, List samples, String maf, String haploidCallMode, Map> thresholds, Path resourcesPath, Path outDir, VariantStorageManager storageManager, String token) throws ToolException { @@ -142,7 +144,7 @@ public static RelatednessReport compute(String study, Family family, List0.05") public String relatednessMaf = "cohort:ALL>0.05"; 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 6bf964e760f..3cfa253afa0 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 @@ -1197,7 +1197,6 @@ public class ParamConstants { public static final String ANALYSIS_VARIANT_RELATEDNESS_RUN_METHOD = "The body web service method parameter"; public static final String ANALYSIS_VARIANT_RELATEDNESS_RUN_OUTDIR = "The body web service outdir parameter"; public static final String ANALYSIS_VARIANT_FAMILY_QC_RUN_FAMILY = "The body web service family parameter"; - public static final String ANALYSIS_VARIANT_FAMILY_QC_RUN_RELATEDNESSMETHOD = "The body web service relatednessMethod parameter"; public static final String ANALYSIS_VARIANT_FAMILY_QC_RUN_RELATEDNESSMAF = "The body web service relatednessMaf parameter"; public static final String ANALYSIS_VARIANT_FAMILY_QC_RUN_OUTDIR = "The body web service outdir parameter"; public static final String ANALYSIS_VARIANT_INDIVIDUAL_QC_RUN_INDIVIDUAL = "The body web service individual parameter"; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java index 0383de0156c..dad8f5bfecc 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java @@ -31,7 +31,6 @@ public enum QcType { protected String studyId; protected Family family; - protected String relatednessMethod; protected String relatednessMaf; protected String haploidCallMode; protected Map> relatednessThresholds; @@ -62,15 +61,6 @@ public FamilyQcAnalysisExecutor setFamily(Family family) { return this; } - public String getRelatednessMethod() { - return relatednessMethod; - } - - public FamilyQcAnalysisExecutor setRelatednessMethod(String relatednessMethod) { - this.relatednessMethod = relatednessMethod; - return this; - } - public String getRelatednessMaf() { return relatednessMaf; }