TASK-5278 - Add haploid calls treatment parameter to family-qc and relatedness

biodata-models/src/main/java/org/opencb/biodata/models/clinical/qc/RelatednessReport.java

@@ -27,6 +27,11 @@
 
 public class RelatednessReport {
 
+    public static final String HAPLOID_CALL_MODE_HAPLOID_VALUE = "haploid";
+    public static final String HAPLOID_CALL_MODE_MISSING_VALUE = "missing";
+    public static final String HAPLOID_CALL_MODE_REF_VALUE = "reference";
+    public static final String HAPLOID_CALL_MODE_DEFAUT_VALUE = HAPLOID_CALL_MODE_HAPLOID_VALUE;
+
     // Method., e.g.: Plink/IBD
     @DataField(id = "method",
             description = FieldConstants.RELATEDNESS_REPORT_METHOD_DESCRIPTION)
@@ -37,6 +42,11 @@ public class RelatednessReport {
             description = FieldConstants.RELATEDNESS_REPORT_MAF_DESCRIPTION)
     private String maf;
 
+    // Haploid call mode, i.e., the PLINK/IBD parameter: vcf-half-call
+    @DataField(id = "haploidCallMode",
+            description = FieldConstants.RELATEDNESS_REPORT_HAPLOID_CALL_MODE_DESCRIPTION)
+    private String haploidCallMode;
+
     // Relatedness scores for pair of samples
     @DataField(id = "scores", uncommentedClasses = {"RelatednessScore"},
             description = FieldConstants.RELATEDNESS_REPORT_SCORES_DESCRIPTION)
@@ -47,12 +57,13 @@ public class RelatednessReport {
     private List<String> files;
 
     public RelatednessReport() {
-        this("PLINK/IBD", "cohort:ALL>0.05", new ArrayList<>(), new ArrayList<>());
+        this("PLINK/IBD", "cohort:ALL>0.05", HAPLOID_CALL_MODE_DEFAUT_VALUE, new ArrayList<>(), new ArrayList<>());
     }
 
-    public RelatednessReport(String method, String maf, List<RelatednessScore> scores, List<String> files) {
+    public RelatednessReport(String method, String maf, String haploidCallMode, List<RelatednessScore> scores, List<String> files) {
         this.method = method;
         this.maf = maf;
+        this.haploidCallMode = haploidCallMode;
         this.scores = scores;
         this.files = files;
     }
@@ -62,6 +73,7 @@ public String toString() {
         final StringBuilder sb = new StringBuilder("RelatednessReport{");
         sb.append("method='").append(method).append('\'');
         sb.append(", maf='").append(maf).append('\'');
+        sb.append(", haploidCallMode='").append(haploidCallMode).append('\'');
         sb.append(", scores=").append(scores);
         sb.append(", files=").append(files);
         sb.append('}');
@@ -86,6 +98,15 @@ public RelatednessReport setMaf(String maf) {
         return this;
     }
 
+    public String getHaploidCallMode() {
+        return haploidCallMode;
+    }
+
+    public RelatednessReport setHaploidCallMode(String haploidCallMode) {
+        this.haploidCallMode = haploidCallMode;
+        return this;
+    }
+
     public List<RelatednessScore> getScores() {
         return scores;
     }

biodata-models/src/main/java/org/opencb/biodata/models/constants/FieldConstants.java

@@ -1,5 +1,7 @@
 package org.opencb.biodata.models.constants;
 
+import org.opencb.biodata.models.clinical.qc.RelatednessReport;
+
 public class FieldConstants {
     public static final String PHENOTYPE_AGE_OF_ON_SET = "Indicates the age of on set of the phenotype";
     public static final String PHENOTYPE_STATUS = "Status of phenotype OBSERVED, NOT_OBSERVED, UNKNOWN";
@@ -55,7 +57,11 @@ public class FieldConstants {
     public static final String CLINICAL_CONFIDENCE_DATE_DESCRIPTION = "Date of the clinical confidence";
     public static final String CLINICAL_CONFIDENCE_VALUE_DESCRIPTION = "Date of the clinical confidence";
 
-    public static final String RELATEDNESS_REPORT_MAF_DESCRIPTION = "Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35, cohort:ALL>0.05";
+    public static final String RELATEDNESS_REPORT_MAF_DESCRIPTION = "Minor allele frequency to filter variants, e.g.: 1kg_phase3:CEU>0.35,"
+            + " cohort:ALL>0.05";
+    public static final String RELATEDNESS_REPORT_HAPLOID_CALL_MODE_DESCRIPTION = "Haploid call mode, equivalent to the PLINK/IBD parameter"
+            + " vcf-half-call, accepts the following values: " + RelatednessReport.HAPLOID_CALL_MODE_DEFAUT_VALUE + ", "
+            + RelatednessReport.HAPLOID_CALL_MODE_MISSING_VALUE + " and " + RelatednessReport.HAPLOID_CALL_MODE_REF_VALUE;
     public static final String RELATEDNESS_REPORT_SCORES_DESCRIPTION = "Relatedness scores for pair of samples";
     public static final String RELATEDNESS_REPORT_FILES_DESCRIPTION = "List of files of Relatedness Report";
 
@@ -67,7 +73,8 @@ public class FieldConstants {
     public static final String AUDIT_MESSAGE_DESCRIPTION = "Audit message";
     public static final String AUDIT_ACTION_DESCRIPTION = "Enum action that can have the values "
             + " CREATE_CLINICAL_ANALYSIS, CREATE_INTERPRETATION, UPDATE_CLINICAL_ANALYSIS, DELETE_CLINICAL_ANALYSIS,"
-            + " UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and DELETE_INTERPRETATION";
+            + " UPDATE_INTERPRETATION, REVERT_INTERPRETATION, CLEAR_INTERPRETATION, MERGE_INTERPRETATION, SWAP_INTERPRETATION and"
+            + " DELETE_INTERPRETATION";
     public static final String AUDIT_DATE_DESCRIPTION = "Date of the audit";
 
     public static final String SOFTWARE_NAME = "Software name";
@@ -76,5 +83,5 @@ public class FieldConstants {
     public static final String SOFTWARE_COMMIT = "Software commit";
     public static final String SOFTWARE_WEBSITE = "Software website";
     public static final String SOFTWARE_PARAMS = "Software params";
-    
+
 }