Merge master, fix unrelated VDS-making breakage [VS-1777]

.dockstore.yml

@@ -343,7 +343,7 @@ workflows:
          branches:
              - master
              - ah_var_store
-             - vs_1739_cmrg_learnings
+             - vs_1777_build_failure
          tags:
              - /.*/
    - name: GvsIngestTieout

build.gradle

@@ -74,7 +74,7 @@ final guavaVersion = System.getProperty('guava.version', '32.1.3-jre')
 final log4j2Version = System.getProperty('log4j2Version', '2.24.1')
 final testNGVersion = System.getProperty('testNGVersion', '7.7.0')
 final googleCloudNioVersion = System.getProperty('googleCloudNioVersion','0.127.8')
-final gklVersion = System.getProperty('gklVersion', '0.9.0')
+final gklVersion = System.getProperty('gklVersion', '0.9.1')
 
 final baseJarName = 'gatk'
 final secondaryBaseJarName = 'hellbender'

build_docker_remote.sh

@@ -131,16 +131,6 @@ fi
 echo "- name: 'gcr.io/cloud-builders/docker'" >> cloudbuild.yaml
 echo "  args: [ 'push', '${DOCKER_IMAGE_TAG}' ]" >> cloudbuild.yaml
 
-echo "steps:" >> cloudbuild.yaml
-echo "- name: 'gcr.io/cloud-builders/docker'" >> cloudbuild.yaml
-if [ -n "$RELEASE" ]; then
-  echo "  args: [ 'build', '-t', '${DOCKER_IMAGE_TAG}', '--build-arg', 'RELEASE=true', '.' ]" >> cloudbuild.yaml
-else
-  echo "  args: [ 'build', '-t', '${DOCKER_IMAGE_TAG}', '.' ]" >> cloudbuild.yaml
-fi
-echo "- name: 'gcr.io/cloud-builders/docker'" >> cloudbuild.yaml
-echo "  args: [ 'push', '${DOCKER_IMAGE_TAG}' ]" >> cloudbuild.yaml
-
 echo "Building image with the tag ${DOCKER_IMAGE_TAG}..."
 
 SUBMIT_COMMAND="gcloud builds submit --config cloudbuild.yaml --timeout=24h --machine-type n1_highcpu_32"

scripts/variantstore/wdl/GvsCreateVDS.wdl

@@ -175,6 +175,7 @@ task CreateVds {
 
         account_name=$(gcloud config list account --format "value(core.account)")
 
+        apt-get update
         apt install --assume-yes python3.11-venv
         python3 -m venv ./localvenv
         . ./localvenv/bin/activate

scripts/variantstore/wdl/GvsUtils.wdl

@@ -131,9 +131,9 @@ task GetToolVersions {
     # GVS generally uses the smallest `alpine` version of the Google Cloud SDK as it suffices for most tasks, but
     # there are a handful of tasks that require the larger GNU libc-based `slim`.
     String cloud_sdk_slim_docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:524.0.0-slim"
-    String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2025-10-28-alpine-4a74414607d9"
+    String variants_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/variants:2025-12-05-alpine-11ede1e609a0"
     String variants_nirvana_docker = "us.gcr.io/broad-dsde-methods/variantstore:nirvana_2022_10_19"
-    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2025-10-17-gatkbase-0a4709121758"
+    String gatk_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/gatk:2025-12-05-gatkbase-36ee09833e27"
     String real_time_genomics_docker = "docker.io/realtimegenomics/rtg-tools:latest"
     String gotc_imputation_docker = "us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.5-1.10.2-0.1.16-1649948623"
     String plink_docker = "us-central1-docker.pkg.dev/broad-dsde-methods/gvs/plink2:2024-04-23-slim-a0a65f52cc0e"

src/main/java/org/broadinstitute/hellbender/tools/funcotator/TranscriptSelectionMode.java

@@ -84,8 +84,8 @@ public enum TranscriptSelectionMode {
      *      no appris tag present
      */
     BEST_EFFECT {
-        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts) {
-            return new BestEffectGencodeFuncotationComparator(userRequestedTranscripts);
+        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts) {
+            return new BestEffectGencodeFuncotationComparator(userRequestedTranscripts, preferMANETranscripts);
         }
     },
 
@@ -160,21 +160,21 @@ public Comparator<GencodeFuncotation> getComparator(final Set<String> userReques
      *      no appris tag present
      */
     CANONICAL {
-        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts) {
-            return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts);
+        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts) {
+            return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts, preferMANETranscripts);
         }
     },
 
     /**
      * Same as CANONICAL, but indicates that no transcripts should be dropped.  Render all overlapping transcripts.
      */
     ALL {
-        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts) {
-            return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts);
+        public Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts) {
+            return new CanonicalGencodeFuncotationComparator(userRequestedTranscripts, preferMANETranscripts);
         }
     };
 
-    public abstract Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts);
+    public abstract Comparator<GencodeFuncotation> getComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts);
 
     private static class ComparatorByUserTranscript implements Comparator<GencodeFuncotation> {
 
@@ -199,6 +199,24 @@ else if ( (!FuncotatorUtils.isFuncotationInTranscriptList(a, userRequestedTransc
         }
     }
 
+    private static class ComparatorByManeStatus implements Comparator<GencodeFuncotation> {
+
+        public ComparatorByManeStatus() {}
+
+        @Override
+        public int compare(final GencodeFuncotation a, final GencodeFuncotation b) {
+            if((a.isManeTranscript()) && (!b.isManeTranscript())) {
+                return -1;
+            }
+            else if((!a.isManeTranscript()) && (b.isManeTranscript())) {
+                return 1;
+            }
+            else {
+                return 0;
+            }
+        }
+    }
+
     private static class ComparatorByIgrStatus implements Comparator<GencodeFuncotation> {
 
         public ComparatorByIgrStatus(){}
@@ -360,6 +378,7 @@ else if ( (a.getAnnotationTranscript() == null ) && (b.getAnnotationTranscript()
     static class BestEffectGencodeFuncotationComparator implements Comparator<GencodeFuncotation> {
 
         private final Comparator<GencodeFuncotation> byUserTranscript;
+        private final Comparator<GencodeFuncotation> byManeStatus;
         private final Comparator<GencodeFuncotation> byIgrStatus;
         private final Comparator<GencodeFuncotation> byVariantClassification;
         private final Comparator<GencodeFuncotation> byProteinCodingStatus;
@@ -368,10 +387,11 @@ static class BestEffectGencodeFuncotationComparator implements Comparator<Gencod
         private final Comparator<GencodeFuncotation> byTranscriptLength;
         private final Comparator<GencodeFuncotation> byTranscriptName;
 
-        private final Comparator<GencodeFuncotation> chainedComparator;
+        private Comparator<GencodeFuncotation> chainedComparator;
 
-        public BestEffectGencodeFuncotationComparator( final Set<String> userRequestedTranscripts ) {
+        public BestEffectGencodeFuncotationComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts) {
             byUserTranscript = new ComparatorByUserTranscript(userRequestedTranscripts);
+            byManeStatus = new ComparatorByManeStatus();
             byIgrStatus = new ComparatorByIgrStatus();
             byVariantClassification = new ComparatorByVariantClassification();
             byProteinCodingStatus = new ComparatorByProteinCodingStatus();
@@ -380,8 +400,16 @@ public BestEffectGencodeFuncotationComparator( final Set<String> userRequestedTr
             byTranscriptLength = new ComparatorByTranscriptSequenceLength();
             byTranscriptName = new ComparatorByTranscriptName();
 
-            chainedComparator = byUserTranscript
-                    .thenComparing(byIgrStatus)
+            // Always start with the user transcript comparator
+            chainedComparator = byUserTranscript;
+
+            // Next highest level of priority is MANE transcripts if the user has specified this preference
+            if(preferMANETranscripts) {
+                chainedComparator = chainedComparator.thenComparing(byManeStatus);
+            }
+
+            // Add the rest of the BEST_EFFECT comparators
+            chainedComparator = chainedComparator.thenComparing(byIgrStatus)
                     .thenComparing(byVariantClassification)
                     .thenComparing(byProteinCodingStatus)
                     .thenComparing(byLocusLevel)
@@ -411,6 +439,7 @@ public int compare( final GencodeFuncotation a, final GencodeFuncotation b ) {
     static class CanonicalGencodeFuncotationComparator implements Comparator<GencodeFuncotation> {
 
         private final Comparator<GencodeFuncotation> byUserTranscript;
+        private final Comparator<GencodeFuncotation> byManeStatus;
         private final Comparator<GencodeFuncotation> byIgrStatus;
         private final Comparator<GencodeFuncotation> byVariantClassification;
         private final Comparator<GencodeFuncotation> byProteinCodingStatus;
@@ -419,10 +448,11 @@ static class CanonicalGencodeFuncotationComparator implements Comparator<Gencode
         private final Comparator<GencodeFuncotation> byTranscriptLength;
         private final Comparator<GencodeFuncotation> byTranscriptName;
 
-        private final Comparator<GencodeFuncotation> chainedComparator;
+        private Comparator<GencodeFuncotation> chainedComparator;
 
-        public CanonicalGencodeFuncotationComparator(final Set<String> userRequestedTranscripts ) {
+        public CanonicalGencodeFuncotationComparator(final Set<String> userRequestedTranscripts, final boolean preferMANETranscripts) {
             byUserTranscript = new ComparatorByUserTranscript(userRequestedTranscripts);
+            byManeStatus = new ComparatorByManeStatus();
             byIgrStatus = new ComparatorByIgrStatus();
             byVariantClassification = new ComparatorByVariantClassification();
             byProteinCodingStatus = new ComparatorByProteinCodingStatus();
@@ -431,8 +461,16 @@ public CanonicalGencodeFuncotationComparator(final Set<String> userRequestedTran
             byTranscriptLength = new ComparatorByTranscriptSequenceLength();
             byTranscriptName = new ComparatorByTranscriptName();
 
-            chainedComparator = byUserTranscript
-                    .thenComparing(byProteinCodingStatus)
+            // Always start with the user transcript comparator
+            chainedComparator = byUserTranscript;
+
+            // Next highest level of priority is MANE transcripts if the user has specified this preference
+            if(preferMANETranscripts) {
+                chainedComparator = chainedComparator.thenComparing(byManeStatus);
+            }
+
+            // Add the rest of the CANONICAL comparators
+            chainedComparator = chainedComparator.thenComparing(byProteinCodingStatus)
                     .thenComparing(byLocusLevel)
                     .thenComparing(byApprisRank)
                     .thenComparing(byIgrStatus)

src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotation.java

@@ -79,6 +79,7 @@ public class GencodeFuncotation implements Funcotation {
     private Integer                              transcriptLength;
     private String                               version;
     private String                               geneTranscriptType;
+    private Boolean                              isManeTranscript;
 
     //------------------------------------------------------------
     // Fields for overriding serialized values:
@@ -150,6 +151,7 @@ public class GencodeFuncotation implements Funcotation {
         this.transcriptLength = that.transcriptLength;
         this.version = that.version;
         this.geneTranscriptType = that.geneTranscriptType;
+        this.isManeTranscript = that.isManeTranscript;
         this.hugoSymbolSerializedOverride = that.hugoSymbolSerializedOverride;
         this.ncbiBuildSerializedOverride = that.ncbiBuildSerializedOverride;
         this.chromosomeSerializedOverride = that.chromosomeSerializedOverride;
@@ -703,6 +705,10 @@ public void setGeneTranscriptType(final String geneTranscriptType) {
         this.geneTranscriptType = geneTranscriptType;
     }
 
+    public Boolean isManeTranscript() { return isManeTranscript; }
+
+    public void setManeTranscript(final Boolean isManeTranscript) { this.isManeTranscript = isManeTranscript; }
+
     public void setDataSourceName(final String dataSourceName) {
         this.dataSourceName = dataSourceName;
     }

src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationBuilder.java

@@ -320,6 +320,11 @@ public GencodeFuncotationBuilder setGeneTranscriptType(final String geneTranscri
         return this;
     }
 
+    public GencodeFuncotationBuilder setManeTranscript(final Boolean isManeTranscript) {
+        gencodeFuncotation.setManeTranscript(isManeTranscript);
+        return this;
+    }
+
     /**
      * Set the Data Source Name {@link String} in the {@link GencodeFuncotation}.
      * @param name The {@link String} containing the Data Source Name for the {@link GencodeFuncotation}.