Add logging for specific use case

hms-dbmi · Mar 23, 2024 · 0ac2ce0 · 0ac2ce0
1 parent 1f16776
commit 0ac2ce0
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java b/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java
@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.Serializable;
 import java.math.BigInteger;
@@ -11,6 +13,9 @@
 import java.util.stream.Collectors;
 
 public class VariableVariantMasks implements Serializable {
+
+	private static Logger log = LoggerFactory.getLogger(VariableVariantMasks.class);
+
 	private static final long serialVersionUID = 6225420483804601477L;
 	private static final String oneone = "11";
 	private static final char one = '1';

diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMaskBitmaskImpl.java
@@ -81,4 +81,11 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(bitmask);
     }
+
+    @Override
+    public String toString() {
+        return "VariantMaskBitmaskImpl{" +
+                "bitmask=" + bitmask.toString() +
+                '}';
+    }
 }
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
@@ -246,6 +246,20 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
                 }
 
                 VariableVariantMasks mergeResult = VariableVariantMasks.append(entry.getValue(), variantStore1PatientCount, variantMasks2, variantStore2PatientCount);
+                if (entry.getKey().equals("chr3,11805,T,A,LINC01986,splice_donor_region_variant")) {
+                    log.info("Mask 1: " + Optional.ofNullable(entry.getValue().heterozygousMask).map(VariantMask::toString).orElse("empty"));
+                    log.info("Mask 2: " + Optional.ofNullable(variantMasks2.heterozygousMask).map(VariantMask::toString).orElse("empty"));
+                    log.info("Merged mask: " + Optional.ofNullable(mergeResult.heterozygousMask).map(VariantMask::toString).orElse("empty"));
+
+                    Set<Integer> patientIds1 = VariableVariantMasks.patientMaskToPatientIdSet(Optional.ofNullable(entry.getValue().heterozygousMask).orElse(VariantMask.emptyInstance()), Arrays.asList(variantStore1.getPatientIds()));
+                    log.info("Patients 1: " + Joiner.on(",").join(patientIds1));
+
+                    Set<Integer> patientIds2 = VariableVariantMasks.patientMaskToPatientIdSet(Optional.ofNullable(variantMasks2.heterozygousMask).orElse(VariantMask.emptyInstance()), Arrays.asList(variantStore2.getPatientIds()));
+                    log.info("Patients 2: " + Joiner.on(",").join(patientIds2));
+
+                    Set<Integer> mergedPatientIds = VariableVariantMasks.patientMaskToPatientIdSet(Optional.ofNullable(mergeResult.heterozygousMask).orElse(VariantMask.emptyInstance()), Arrays.asList(mergedVariantStore.getPatientIds()));
+                    log.info("Merged patient ids: " + Joiner.on(",").join(mergedPatientIds));
+                }
                 mergedMasks.put(entry.getKey(), mergeResult);
             }
             // Any entry in the second set that is not in the merged set can be merged with an empty variant mask,
@@ -285,8 +299,8 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
             ConcurrentHashMap<String, VariableVariantMasks> maskMap = merged.get(key);
             maskMap.keySet().stream().sorted().limit(5).forEach(variantSpec -> {
                 VariableVariantMasks variableVariantMasks = maskMap.get(variantSpec);
-                VariantMask union = Optional.ofNullable(variableVariantMasks.heterozygousMask).orElse(VariantMask.emptyInstance()).union(Optional.ofNullable(variableVariantMasks.homozygousMask).orElse(VariantMask.emptyInstance()));
-                Set<Integer> patientsWithVariant = VariableVariantMasks.patientMaskToPatientIdSet(union, Arrays.asList(mergedVariantStore.getPatientIds()));
+                VariantMask heteroMask = Optional.ofNullable(variableVariantMasks.heterozygousMask).orElse(VariantMask.emptyInstance());
+                Set<Integer> patientsWithVariant = VariableVariantMasks.patientMaskToPatientIdSet(heteroMask, Arrays.asList(mergedVariantStore.getPatientIds()));
                 log.info("Patients with variant [" + variantSpec + "]: " + Joiner.on(",").join(patientsWithVariant));
             });