From 49f85e6a37759a54b60109c2791bd77ea2859f07 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 29 Dec 2023 10:52:48 -0500 Subject: [PATCH 1/6] Next development iteration `v2.0.1-SNAPSHOT`. --- CHANGELOG.rst | 5 +++++ docs/conf.py | 2 +- lirical-background/pom.xml | 2 +- lirical-cli/pom.xml | 2 +- .../main/java/org/monarchinitiative/lirical/cli/Main.java | 4 ++-- lirical-configuration/pom.xml | 2 +- lirical-core/pom.xml | 2 +- lirical-exomiser-db-adapter/pom.xml | 2 +- lirical-io/pom.xml | 2 +- pom.xml | 2 +- 10 files changed, 15 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 717bf6194..c4ccfd45d 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,11 @@ Changelog ========= +------------------- +latest +------------------- + + ------------------- v2.0.0 (2023-12-29) ------------------- diff --git a/docs/conf.py b/docs/conf.py index 1040ed3b6..8a33908f7 100644 --- 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-SNAPSHOT' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/lirical-background/pom.xml b/lirical-background/pom.xml index 93eea09cb..bf7c0821f 100644 --- a/lirical-background/pom.xml +++ b/lirical-background/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 diff --git a/lirical-cli/pom.xml b/lirical-cli/pom.xml index 5eaf9d43a..3d7ecd79f 100644 --- a/lirical-cli/pom.xml +++ b/lirical-cli/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 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 index 2d2263999..b73d7e605 100644 --- a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java +++ b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java @@ -16,9 +16,9 @@ footer = Main.FOOTER) public class Main implements Callable { - public static final String VERSION = "lirical v2.0.0"; + public static final String VERSION = "lirical v2.0.1-SNAPSHOT"; public static final int WIDTH = 120; - public static final String FOOTER = "\nSee the full documentation at https://thejacksonlaboratory.github.io/LIRICAL/stable"; + public static final String FOOTER = "\nSee the full documentation at https://thejacksonlaboratory.github.io/LIRICAL/latest"; private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder() .commands(bold, fg_blue, underline) diff --git a/lirical-configuration/pom.xml b/lirical-configuration/pom.xml index d7d879bab..f5469f948 100644 --- a/lirical-configuration/pom.xml +++ b/lirical-configuration/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 diff --git a/lirical-core/pom.xml b/lirical-core/pom.xml index c68f5623f..89b0e790a 100644 --- a/lirical-core/pom.xml +++ b/lirical-core/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 diff --git a/lirical-exomiser-db-adapter/pom.xml b/lirical-exomiser-db-adapter/pom.xml index 349d7f8b1..e9e4f1f11 100644 --- a/lirical-exomiser-db-adapter/pom.xml +++ b/lirical-exomiser-db-adapter/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 diff --git a/lirical-io/pom.xml b/lirical-io/pom.xml index 8f00a38ed..1c59fec76 100644 --- a/lirical-io/pom.xml +++ b/lirical-io/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.0 + 2.0.1-SNAPSHOT 4.0.0 diff --git a/pom.xml b/pom.xml index 87f24f63e..48eeb6eda 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.monarchinitiative.lirical LIRICAL pom - 2.0.0 + 2.0.1-SNAPSHOT lirical-core lirical-io From b15fadc93e0ed77a21612c920f9a2f5bc5dd2b4b Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Thu, 11 Jan 2024 22:00:38 -0500 Subject: [PATCH 2/6] Remove misplaced dependency from `lirical-configuration` POM. --- lirical-configuration/pom.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/lirical-configuration/pom.xml b/lirical-configuration/pom.xml index f5469f948..7b2af034c 100644 --- a/lirical-configuration/pom.xml +++ b/lirical-configuration/pom.xml @@ -34,10 +34,6 @@ org.monarchinitiative.phenol phenol-annotations - - ch.qos.logback - logback-classic - From a888b3ef2372ccc01dec713c712138072b299b65 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 1 Mar 2024 15:15:05 -0500 Subject: [PATCH 3/6] In genotype-aware mode, do not include the differential diagnoses in HTML and TSV reports, unless there is a predicted deleterious variant in the associated gene. --- docs/running.rst | 3 +- .../lirical/cli/cmd/OutputCommand.java | 3 +- .../likelihoodratio/GenotypeLrMatchType.java | 19 ++++++++++- .../lirical/core/output/OutputOptions.java | 14 +++++++- .../GenotypeLrMatchTypeTest.java | 33 +++++++++++++++++++ .../lirical/io/output/HtmlTemplate.java | 9 +++-- .../lirical/io/output/LiricalTemplate.java | 19 +++++++++++ .../lirical/io/output/SparklinePacket.java | 2 ++ .../lirical/io/output/TsvTemplate.java | 1 + 9 files changed, 97 insertions(+), 6 deletions(-) create mode 100644 lirical-core/src/test/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchTypeTest.java diff --git a/docs/running.rst b/docs/running.rst index 3345cbd18..7ce2fe5ab 100644 --- 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 `_ annotations (default: ``false``). * ``--strict``: use strict penalties if the genotype does not match the disease model 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 index 3e3801310..e78906ff4 100644 --- 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-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java b/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java index 2cb60c4b7..da7b4fb73 100644 --- a/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java +++ b/lirical-core/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 with some deleterious variants in the gene were observed or if the LR was produced using + * the LIRICAL genotype model, etc... + *

+ * 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 index cccf2465f..38b6765e3 100644 --- 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 @@ -7,7 +7,11 @@ 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; @@ -15,12 +19,14 @@ 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/lirical-core/src/test/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchTypeTest.java b/lirical-core/src/test/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchTypeTest.java new file mode 100644 index 000000000..4528894b5 --- /dev/null +++ b/lirical-core/src/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)); + } +} \ No newline at end of file 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 index faaf94390..fdfd5a554 100644 --- 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 sparklinePackets = SparklinePacket.sparklineFactory(analysisResults, diseases, hpo, N); + List 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 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 index 094364ec8..d096ff950 100644 --- 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 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 index 92b549edd..a8b464c19 100644 --- 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 sparklineFactory(AnalysisResults results, HpoDiseases diseases, MinimalOntology ontology, + boolean showDiseasesWithNoDeleteriousVariants, int N) { if (results.isEmpty()) return List.of(); @@ -53,6 +54,7 @@ public static List sparklineFactory(AnalysisResults results, Map 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 index bd18cef51..fb0d084fd 100644 --- 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 diseaseById = diseases.diseaseById(); List diff = new ArrayList<>(); analysisResults.resultsWithDescendingPostTestProbability().sequential() + .filter(handleCasesWithNoDeleteriousVariants(outputOptions.showDiseasesWithNoDeleteriousVariants())) .forEachOrdered(result -> { int current = rank.incrementAndGet(); List variants = result.genotypeLr() From 47a192a714f2e3be05427f76af275309a7b0809a Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 1 Mar 2024 15:22:48 -0500 Subject: [PATCH 4/6] Update Javadoc. --- .../lirical/core/likelihoodratio/GenotypeLrMatchType.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java b/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java index da7b4fb73..e79547adb 100644 --- a/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java +++ b/lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrMatchType.java @@ -82,8 +82,8 @@ public enum GenotypeLrMatchType { /** * Returns {@code true} if the genotype LR match indicates that the enclosing {@link GenotypeLrWithExplanation} - * was created for a gene with some deleterious variants in the gene were observed or if the LR was produced using - * the LIRICAL genotype model, etc... + * was created for a gene that contains deleterious variants. This includes the genotype LRs generated + * for ClinVar variants, using the LIRICAL genotype model, etc... *

* Returns {@code false} if the genotype LR represents state with no deleterious variants in a gene. */ From 03b0bee4b1db81f7b283469a65f3f0560c7b4028 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Fri, 1 Mar 2024 15:26:32 -0500 Subject: [PATCH 5/6] Fix the test. --- .../lirical/io/output/JsonAnalysisResultWriterTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java b/lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java index 1db72d236..da336e35b 100644 --- a/lirical-io/src/test/java/org/monarchinitiative/lirical/io/output/JsonAnalysisResultWriterTest.java +++ b/lirical-io/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); From 616f8941f76c7c313efe267ec13d2ec289ae2209 Mon Sep 17 00:00:00 2001 From: Daniel Danis Date: Tue, 16 Apr 2024 10:20:42 -0400 Subject: [PATCH 6/6] Bump release to `v2.0.1`. --- CHANGELOG.rst | 7 +++++++ docs/conf.py | 2 +- lirical-background/pom.xml | 2 +- lirical-cli/pom.xml | 2 +- .../main/java/org/monarchinitiative/lirical/cli/Main.java | 4 ++-- lirical-configuration/pom.xml | 2 +- lirical-core/pom.xml | 2 +- lirical-exomiser-db-adapter/pom.xml | 2 +- lirical-io/pom.xml | 2 +- pom.xml | 2 +- 10 files changed, 17 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c4ccfd45d..f0bb456ff 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,13 @@ 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 index 8a33908f7..128f6cc2c 100644 --- 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'2.0.1-SNAPSHOT' +release = u'2.0.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/lirical-background/pom.xml b/lirical-background/pom.xml index bf7c0821f..ff7cb8592 100644 --- a/lirical-background/pom.xml +++ b/lirical-background/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 diff --git a/lirical-cli/pom.xml b/lirical-cli/pom.xml index 3d7ecd79f..8eb14dbc6 100644 --- a/lirical-cli/pom.xml +++ b/lirical-cli/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 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 index b73d7e605..6ce4835e0 100644 --- a/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java +++ b/lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/Main.java @@ -16,9 +16,9 @@ footer = Main.FOOTER) public class Main implements Callable { - public static final String VERSION = "lirical v2.0.1-SNAPSHOT"; + 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/latest"; + public static final String FOOTER = "\nSee the full documentation at https://thejacksonlaboratory.github.io/LIRICAL/stable"; private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder() .commands(bold, fg_blue, underline) diff --git a/lirical-configuration/pom.xml b/lirical-configuration/pom.xml index 7b2af034c..7a5e5c79b 100644 --- a/lirical-configuration/pom.xml +++ b/lirical-configuration/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 diff --git a/lirical-core/pom.xml b/lirical-core/pom.xml index 89b0e790a..859f88a03 100644 --- a/lirical-core/pom.xml +++ b/lirical-core/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 diff --git a/lirical-exomiser-db-adapter/pom.xml b/lirical-exomiser-db-adapter/pom.xml index e9e4f1f11..fdb3da230 100644 --- a/lirical-exomiser-db-adapter/pom.xml +++ b/lirical-exomiser-db-adapter/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 diff --git a/lirical-io/pom.xml b/lirical-io/pom.xml index 1c59fec76..029496981 100644 --- a/lirical-io/pom.xml +++ b/lirical-io/pom.xml @@ -5,7 +5,7 @@ LIRICAL org.monarchinitiative.lirical - 2.0.1-SNAPSHOT + 2.0.1 4.0.0 diff --git a/pom.xml b/pom.xml index 48eeb6eda..2b3242fa5 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.monarchinitiative.lirical LIRICAL pom - 2.0.1-SNAPSHOT + 2.0.1 lirical-core lirical-io