Update pom.xml svart-2.0.0-RC6 -> RC7

Author: julesjacobsen

exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/commands/AnnotateCommandRunner.java

@@ -25,7 +25,7 @@
 import org.monarchinitiative.svart.GenomicRegion;
 import org.monarchinitiative.svart.GenomicVariant;
 import org.monarchinitiative.svart.assembly.GenomicAssembly;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Component;

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverter.java

@@ -25,8 +25,8 @@
 import org.monarchinitiative.exomiser.core.model.SvMetaType;
 import org.monarchinitiative.svart.*;
 import org.monarchinitiative.svart.assembly.GenomicAssembly;
-import org.monarchinitiative.svart.util.VariantTrimmer;
-import org.monarchinitiative.svart.util.VcfConverter;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
+import org.monarchinitiative.svart.vcf.VcfConverter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryImpl.java

@@ -33,7 +33,7 @@
 import org.monarchinitiative.exomiser.core.model.VariantAnnotation;
 import org.monarchinitiative.exomiser.core.model.VariantEvaluation;
 import org.monarchinitiative.svart.GenomicVariant;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/JannovarAnnotationServiceTest.java

@@ -25,7 +25,7 @@
 import htsjdk.variant.variantcontext.VariantContext;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.svart.GenomicVariant;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 
 import static org.hamcrest.CoreMatchers.*;
 import static org.hamcrest.MatcherAssert.assertThat;

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/JannovarStructuralVariantAnnotatorTest.java

@@ -29,7 +29,7 @@
 import org.monarchinitiative.exomiser.core.model.ChromosomalRegionIndex;
 import org.monarchinitiative.exomiser.core.model.VariantAnnotation;
 import org.monarchinitiative.svart.*;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 
 import java.nio.file.Path;
 import java.util.List;

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/JannovarVariantAnnotatorTest.java

@@ -29,7 +29,7 @@
 import org.monarchinitiative.exomiser.core.model.*;
 import org.monarchinitiative.svart.GenomicVariant;
 import org.monarchinitiative.svart.*;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 
 import java.util.List;
 import java.util.Map;
@@ -60,7 +60,7 @@ private GenomicVariant variant(String contig, int start, String ref, String alt)
 
     @Test
     void testGetAnnotationsForUnknownContigVariant() {
-        assertThrows(CoordinatesOutOfBoundsException.class, () -> annotate(instance, "UNKNOWN", 1, "A", "T"));
+        assertThrows(CoordinatesOutOfBoundsException.class, () -> annotate(instance, "UNKNOWN", 2, "A", "T"));
     }
 
     @Test

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantContextConverterTest.java

@@ -25,7 +25,7 @@
 import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.svart.*;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 
 import static org.hamcrest.CoreMatchers.*;
 import static org.hamcrest.MatcherAssert.assertThat;

exomiser-data-genome/src/main/java/org/monarchinitiative/exomiser/data/genome/model/parsers/AlfaAlleleParser.java

@@ -11,7 +11,7 @@
 import org.monarchinitiative.exomiser.core.proto.AlleleProto.FrequencySource;
 import org.monarchinitiative.exomiser.data.genome.model.Allele;
 import org.monarchinitiative.svart.Strand;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

exomiser-data-genome/src/main/java/org/monarchinitiative/exomiser/data/genome/model/parsers/VcfAlleleParser.java

@@ -23,7 +23,7 @@
 import org.monarchinitiative.exomiser.core.genome.Contigs;
 import org.monarchinitiative.exomiser.data.genome.model.Allele;
 import org.monarchinitiative.svart.Strand;
-import org.monarchinitiative.svart.util.VariantTrimmer;
+import org.monarchinitiative.svart.sequence.VariantTrimmer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

pom.xml

@@ -94,7 +94,7 @@
         <sonar.organization>exomiser</sonar.organization>
         <sonar.language>java</sonar.language>
         <jannovar.version>0.41</jannovar.version>
-        <svart.version>2.0.0-RC6</svart.version>
+        <svart.version>2.0.0-RC7</svart.version>
         <htsjdk.version>3.0.5</htsjdk.version>
         <guava.version>31.1-jre</guava.version>
         <protobuf.version>3.21.12</protobuf.version>