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
opencb · Jun 13, 2024 · a222469 · a222469
1 parent 8da3dea
commit a222469
Show file tree

Hide file tree

Showing 5 changed files with 6 additions and 18 deletions.
diff --git a/...is/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java b/...is/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
@@ -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<String> samples, String maf, String haploidCallMode,
                                             Map<String, Map<String, Float>> thresholds, Path resourcesPath, Path outDir,
                                             VariantStorageManager storageManager, String token) throws ToolException {
@@ -142,7 +144,7 @@ public static RelatednessReport compute(String study, Family family, List<String
         }
 
         RelatednessReport relatedness = new RelatednessReport()
-                .setMethod("PLINK/IBD")
+                .setMethod(PLINK_IBD_METHOD)
                 .setMaf(maf)
                 .setHaploidCallMode(haploidCallMode)
                 .setScores(parseRelatednessScores(outFile, family, thresholds));

diff --git a/...-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java b/...-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
@@ -1587,9 +1587,6 @@ public class FamilyQcCommandOptions {
         @Parameter(names = {"--family"}, description = "Family ID.", required = true)
         public String family;
 
-        @Parameter(names = {"--relatedness-method"}, description = "Method to compute relatedness.")
-        public String relatednessMethod = "PLINK/IBD";
-
         @Parameter(names = {"--relatedness-maf"}, description = "Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35,"
                 + " cohort:ALL>0.05")
         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
@@ -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/...ga-core/src/main/java/org/opencb/opencga/core/tools/variant/FamilyQcAnalysisExecutor.java b/...ga-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<String, Map<String, Float>> 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;
     }