Merge pull request #653 from TheJacksonLaboratory/release-v2.0.1

Release v2.0.1
TheJacksonLaboratory · Apr 16, 2024 · d95d3fb · d95d3fb
2 parents 012e3aa + 616f894
commit d95d3fb
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,18 @@
 Changelog
 =========
 
+-------------------
+latest
+-------------------
+
+-------------------
+v2.0.1 (2024-04-16)
+-------------------
+
+- Bug fix - When running with a VCF file, the TSV report will only include the diseases with a mutation
+  in the associated gene, *unless* the ``--sdwndv`` is provided via CLI. Previously, the TSV reports included
+  the diseases with no mutation regardless of the ``--sdwndv`` option.
+
 -------------------
 v2.0.0 (2023-12-29)
 -------------------

diff --git a/docs/conf.py b/docs/conf.py
@@ -56,7 +56,7 @@
 # The short X.Y version.
 version = u'2.0'
 # The full version, including alpha/beta/rc tags.
-release = u'2.0.0'
+release = u'2.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/running.rst b/docs/running.rst
@@ -76,7 +76,8 @@ The configuration options tweak the analysis.
 * ``--sdwndv``: show diseases even if no deleterious variants are found in the gene associated with the disease.
   The option is a flag (takes no value) and its presence will lead to showing *all* diseases,
   even those with no deleterious variants.
-  Only applicable to the HTML report when running with a VCF file (genotype-aware mode).
+  Only applicable to the HTML and TSV reports when running with a VCF file (genotype-aware mode).
+  The JSON report will include *all* diseases all the time.
 * ``--transcript-db``: transcript database (default: ``RefSeq``), see :ref:`rsttx-dbs` for more info.
 * ``--use-orphanet``: use `Orphanet <https://www.orpha.net/consor/cgi-bin/index.php>`_ annotations (default: ``false``).
 * ``--strict``: use strict penalties if the genotype does not match the disease model

diff --git a/lirical-background/pom.xml b/lirical-background/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/lirical-cli/pom.xml b/lirical-cli/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java
@@ -16,7 +16,7 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer> {
 
-    public static final String VERSION = "lirical v2.0.0";
+    public static final String VERSION = "lirical v2.0.1";
     public static final int WIDTH = 120;
     public static final String FOOTER = "\nSee the full documentation at https://thejacksonlaboratory.github.io/LIRICAL/stable";
 

diff --git a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/OutputCommand.java b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/OutputCommand.java
@@ -72,6 +72,7 @@ protected OutputOptions createOutputOptions(String prefix) {
         LrThreshold lrThreshold = output.lrThreshold == null ? LrThreshold.notInitialized() : LrThreshold.setToUserDefinedThreshold(output.lrThreshold);
         MinDiagnosisCount minDiagnosisCount = output.minDifferentialsToShow == null ? MinDiagnosisCount.notInitialized() : MinDiagnosisCount.setToUserDefinedMinCount(output.minDifferentialsToShow);
         return new OutputOptions(lrThreshold, minDiagnosisCount, runConfiguration.pathogenicityThreshold,
-                output.displayAllVariants, output.outdir, prefix);
+                output.displayAllVariants, runConfiguration.showDiseasesWithNoDeleteriousVariants,
+                output.outdir, prefix);
     }
 }
diff --git a/lirical-configuration/pom.xml b/lirical-configuration/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -34,10 +34,6 @@
             <groupId>org.monarchinitiative.phenol</groupId>
             <artifactId>phenol-annotations</artifactId>
         </dependency>
-        <dependency>
-            <groupId>ch.qos.logback</groupId>
-            <artifactId>logback-classic</artifactId>
-        </dependency>
     </dependencies>
 
     <build>

diff --git a/lirical-core/pom.xml b/lirical-core/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/...src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java b/...src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java
@@ -78,5 +78,22 @@ public enum GenotypeLrMatchType {
      */
     @Deprecated(forRemoval = true)
     // REMOVE(v3.0.0)
-    UNKNOWN
+            UNKNOWN;
+
+    /**
+     * Returns {@code true} if the genotype LR match indicates that the enclosing {@link GenotypeLrWithExplanation}
+     * was created for a gene that contains deleterious variants. This includes the genotype LRs generated
+     * for ClinVar variants, using the LIRICAL genotype model, etc...
+     * <p>
+     * Returns {@code false} if the genotype LR represents state with no deleterious variants in a gene.
+     */
+    public boolean hasDeleteriousVariants() {
+        return switch (this) {
+            case NO_VARIANTS_DETECTED_AD, NO_VARIANTS_DETECTED_AR, UNKNOWN -> false;
+            case ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD, LIRICAL_GT_MODEL,
+                    ONE_DELETERIOUS_CLINVAR_VARIANT_IN_AD, TWO_DELETERIOUS_CLINVAR_VARIANTS_IN_AR,
+                    TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR, ONE_DELETERIOUS_VARIANT_IN_AR,
+                    HIGH_NUMBER_OF_OBSERVED_PREDICTED_PATHOGENIC_VARIANTS -> true;
+        };
+    }
 }
diff --git a/lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/OutputOptions.java b/lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/OutputOptions.java
@@ -7,20 +7,26 @@ public final class OutputOptions {
     private final LrThreshold lrThreshold;
     private final MinDiagnosisCount minDiagnosisCount;
     private final float pathogenicityThreshold;
+    // If set to true, all variants, pathogenic, VUSs, and benign will be shown in the report.
     private final boolean displayAllVariants;
+    // If set to true, all differential diagnoses, even those with no deleterious variants in the associated gene
+    // will be shown in the report.
+    private final boolean showDiseasesWithNoDeleteriousVariants;
     private final Path outputDirectory;
     private final String prefix;
 
     public OutputOptions(LrThreshold lrThreshold,
                          MinDiagnosisCount minDiagnosisCount,
                          float pathogenicityThreshold,
                          boolean displayAllVariants,
+                         boolean showDiseasesWithNoDeleteriousVariants,
                          Path outputDirectory,
                          String prefix) {
         this.lrThreshold = lrThreshold;
         this.minDiagnosisCount = minDiagnosisCount;
         this.pathogenicityThreshold = pathogenicityThreshold;
         this.displayAllVariants = displayAllVariants;
+        this.showDiseasesWithNoDeleteriousVariants = showDiseasesWithNoDeleteriousVariants;
         this.outputDirectory = outputDirectory;
         this.prefix = prefix;
     }
@@ -41,6 +47,10 @@ public boolean displayAllVariants() {
         return displayAllVariants;
     }
 
+    public boolean showDiseasesWithNoDeleteriousVariants() {
+        return showDiseasesWithNoDeleteriousVariants;
+    }
+
     public Path outputDirectory() {
         return outputDirectory;
     }
@@ -58,13 +68,14 @@ public boolean equals(Object obj) {
                 Objects.equals(this.minDiagnosisCount, that.minDiagnosisCount) &&
                 Float.floatToIntBits(this.pathogenicityThreshold) == Float.floatToIntBits(that.pathogenicityThreshold) &&
                 this.displayAllVariants == that.displayAllVariants &&
+                this.showDiseasesWithNoDeleteriousVariants == that.showDiseasesWithNoDeleteriousVariants &&
                 Objects.equals(this.outputDirectory, that.outputDirectory) &&
                 Objects.equals(this.prefix, that.prefix);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(lrThreshold, minDiagnosisCount, pathogenicityThreshold, displayAllVariants, outputDirectory, prefix);
+        return Objects.hash(lrThreshold, minDiagnosisCount, pathogenicityThreshold, displayAllVariants, showDiseasesWithNoDeleteriousVariants, outputDirectory, prefix);
     }
 
     @Override
@@ -74,6 +85,7 @@ public String toString() {
                 "minDiagnosisCount=" + minDiagnosisCount + ", " +
                 "pathogenicityThreshold=" + pathogenicityThreshold + ", " +
                 "displayAllVariants=" + displayAllVariants + ", " +
+                "showDiseasesWithNoDeleteriousVariants=" + showDiseasesWithNoDeleteriousVariants + ", " +
                 "outputDirectory=" + outputDirectory + ", " +
                 "prefix=" + prefix + ']';
     }

diff --git a/...test/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchTypeTest.java b/...test/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchTypeTest.java
@@ -0,0 +1,33 @@
+package org.monarchinitiative.lirical.core.likelihoodratio;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.CsvSource;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+
+public class GenotypeLrMatchTypeTest {
+
+    @ParameterizedTest
+    @CsvSource(
+            {
+                    "NO_VARIANTS_DETECTED_AD,                                  false",
+                    "NO_VARIANTS_DETECTED_AR,                                  false",
+                    "UNKNOWN,                                                  false",
+                    "ONE_P_OR_LP_CLINVAR_ALLELE_IN_AD,                         true",
+                    "LIRICAL_GT_MODEL,                                         true",
+                    "ONE_DELETERIOUS_CLINVAR_VARIANT_IN_AD,                    true",
+                    "TWO_DELETERIOUS_CLINVAR_VARIANTS_IN_AR,                   true",
+                    "TWO_P_OR_LP_CLINVAR_ALLELES_IN_AR,                        true",
+                    "ONE_DELETERIOUS_VARIANT_IN_AR,                            true",
+                    "HIGH_NUMBER_OF_OBSERVED_PREDICTED_PATHOGENIC_VARIANTS,    true",
+            }
+    )
+    public void hasDeleteriousVariants(String value, boolean expected) {
+        // We depend on correctness of `hasDeleteriousVariants` in HTML and TSV report generators,
+        // where we may choose to only show the diff dgs with a deleterious variant.
+        GenotypeLrMatchType glmt = GenotypeLrMatchType.valueOf(value);
+
+        assertThat(glmt.hasDeleteriousVariants(), equalTo(expected));
+    }
+}
diff --git a/lirical-exomiser-db-adapter/pom.xml b/lirical-exomiser-db-adapter/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/lirical-io/pom.xml b/lirical-io/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>LIRICAL</artifactId>
         <groupId>org.monarchinitiative.lirical</groupId>
-        <version>2.0.0</version>
+        <version>2.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/HtmlTemplate.java b/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/HtmlTemplate.java
@@ -6,7 +6,10 @@
 import org.monarchinitiative.lirical.core.analysis.AnalysisResults;
 import org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation;
 import org.monarchinitiative.lirical.core.model.Gene2Genotype;
-import org.monarchinitiative.lirical.core.output.*;
+import org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata;
+import org.monarchinitiative.lirical.core.output.LrThreshold;
+import org.monarchinitiative.lirical.core.output.MinDiagnosisCount;
+import org.monarchinitiative.lirical.core.output.OutputOptions;
 import org.monarchinitiative.lirical.io.output.svg.Lr2Svg;
 import org.monarchinitiative.phenol.annotations.formats.GeneIdentifier;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoDisease;
@@ -70,7 +73,8 @@ public class HtmlTemplate extends LiricalTemplate {
         cfg.setClassForTemplateLoading(HtmlTemplate.class, "");
         templateData.put("postprobthreshold", String.format("%.1f%%", 100 * this.lrThreshold.getThreshold()));
         int N = totalDetailedDiagnosesToShow(analysisResults);
-        List<SparklinePacket> sparklinePackets = SparklinePacket.sparklineFactory(analysisResults, diseases, hpo, N);
+        List<SparklinePacket> sparklinePackets = SparklinePacket.sparklineFactory(analysisResults, diseases, hpo,
+                outputOptions.showDiseasesWithNoDeleteriousVariants(), N);
         this.templateData.put("sparkline", sparklinePackets);
         if (symbolsWithoutGeneIds != null && !symbolsWithoutGeneIds.isEmpty()) {
             this.templateData.put("geneSymbolsWithoutIds", symbolsWithoutGeneIds);
@@ -81,6 +85,7 @@ public class HtmlTemplate extends LiricalTemplate {
         List<ImprobableDifferential> improbableDifferentials = new ArrayList<>();
         AtomicInteger rank = new AtomicInteger();
         analysisResults.resultsWithDescendingPostTestProbability().sequential()
+                .filter(handleCasesWithNoDeleteriousVariants(outputOptions.showDiseasesWithNoDeleteriousVariants()))
                 .forEachOrdered(result -> {
                     int current = rank.incrementAndGet();
 

diff --git a/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/LiricalTemplate.java b/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/LiricalTemplate.java
@@ -3,6 +3,7 @@
 import freemarker.template.Configuration;
 import freemarker.template.Version;
 import org.monarchinitiative.lirical.core.analysis.AnalysisData;
+import org.monarchinitiative.lirical.core.analysis.TestResult;
 import org.monarchinitiative.lirical.core.exception.LiricalRuntimeException;
 import org.monarchinitiative.lirical.core.model.Gene2Genotype;
 import org.monarchinitiative.lirical.core.model.LiricalVariant;
@@ -17,6 +18,7 @@
 import java.nio.file.Path;
 import java.util.*;
 import java.util.function.Function;
+import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
 /**
@@ -126,4 +128,21 @@ private boolean isPassingPathogenicThreshold(LiricalVariant lv) {
         return lv.pathogenicityScore().orElse(0f) >= pathogenicityThreshold;
     }
 
+    /**
+     * Include the result from the differential diagnoses
+     * IF we are interested the diseases with no deleterious variants
+     * OR if the genotype LR represents a situation where some pathogenic variants were found in the associated gene
+     * OR if genotype LR is missing (phenotype only mode).
+     *
+     * @param showDiseasesWithNoDeleteriousVariants set to {@code true} if you wish to see the differential diagnoses
+     *                                              with no deleterious variants regardless of anything.
+     */
+    static Predicate<TestResult> handleCasesWithNoDeleteriousVariants(boolean showDiseasesWithNoDeleteriousVariants) {
+        return r ->
+                showDiseasesWithNoDeleteriousVariants
+                        || r.genotypeLr()
+                        .map(g -> g.matchType().hasDeleteriousVariants())
+                        .orElse(true);
+    }
+
 }
diff --git a/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/SparklinePacket.java b/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/SparklinePacket.java
@@ -41,6 +41,7 @@ public class SparklinePacket {
     public static List<SparklinePacket> sparklineFactory(AnalysisResults results,
                                                          HpoDiseases diseases,
                                                          MinimalOntology ontology,
+                                                         boolean showDiseasesWithNoDeleteriousVariants,
                                                          int N) {
         if (results.isEmpty())
             return List.of();
@@ -53,6 +54,7 @@ public static List<SparklinePacket> sparklineFactory(AnalysisResults results,
         Map<TermId, HpoDisease> diseaseById = diseases.diseaseById();
         Sparkline2Svg sparkline2Svg = new Sparkline2Svg(topResult, true, ontology);
         results.resultsWithDescendingPostTestProbability()
+                .filter(LiricalTemplate.handleCasesWithNoDeleteriousVariants(showDiseasesWithNoDeleteriousVariants))
                 .limit(N)
                 .forEachOrdered(result -> {
                     double posttestProb = result.posttestProbability();

diff --git a/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/TsvTemplate.java b/lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/TsvTemplate.java
@@ -43,6 +43,7 @@ public class TsvTemplate extends LiricalTemplate {
         Map<TermId, HpoDisease> diseaseById = diseases.diseaseById();
         List<TsvDifferential> diff = new ArrayList<>();
         analysisResults.resultsWithDescendingPostTestProbability().sequential()
+                .filter(handleCasesWithNoDeleteriousVariants(outputOptions.showDiseasesWithNoDeleteriousVariants()))
                 .forEachOrdered(result -> {
                     int current = rank.incrementAndGet();
                     List<VisualizableVariant> variants = result.genotypeLr()

diff --git a/...o/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java b/...o/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java
@@ -63,7 +63,7 @@ public void writeExampleAnalysisOutput() throws Exception {
         AnalysisResults results = createTestAnalysisResults();
         AnalysisResultsMetadata metadata = createTestMetadata();
         Path current = Path.of(".");
-        OutputOptions oo = new OutputOptions(LrThreshold.notInitialized(), MinDiagnosisCount.setToUserDefinedMinCount(2), 1.f, true, current, "test");
+        OutputOptions oo = new OutputOptions(LrThreshold.notInitialized(), MinDiagnosisCount.setToUserDefinedMinCount(2), 1.f, true, false, current, "test");
         writer.process(analysisData, results, metadata, oo);
 
         String output = readFileIntoString(TEST_OUTPUT);

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
     <groupId>org.monarchinitiative.lirical</groupId>
     <artifactId>LIRICAL</artifactId>
     <packaging>pom</packaging>
-    <version>2.0.0</version>
+    <version>2.0.1</version>
     <modules>
         <module>lirical-core</module>
         <module>lirical-io</module>