Fixing SVTYPE=CNV for DRAGEN CNV (#74)

Closes: #74
Related-Issue: #74
Projected-Results-Impact: none

README.md

@@ -1,5 +1,6 @@
 [![Continuous Integration](https://github.com/bihealth/varfish-annotator/actions/workflows/ci.yml/badge.svg)](https://github.com/bihealth/varfish-annotator/actions?query=workflow%3Acontinuous-integration)
 [![Coverage Status](https://coveralls.io/repos/github/bihealth/varfish-annotator/badge.svg?branch=main)](https://coveralls.io/github/bihealth/varfish-annotator?branch=main)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/varfish-annotator-cli/README.html)
 
 # VarFish Annotator
 
@@ -174,3 +175,15 @@ The folder `/tests` contains some data sets that are appropriate for system (aka
 You can build the data sets with the `build.sh` script that is available in each folder.
 This script also serves for documenting the test data's provenance.
 The Jannovar software must be available as `jannovar` (e.g., through bioconda) on your `PATH` and you will need `samtools`.
+
+## Using JDK >=18
+
+The **tests** use [junit5-system-exit](https://github.com/tginsberg/junit5-system-exit) for detecting `System.exit()` calls.
+In JDK 18 you have to use the `-Djava.security.manager=allow` flag.
+Issue [tginsberg/junit5-system-exit#10](https://github.com/tginsberg/junit5-system-exit/issues/10) tracks this issue.
+
+## Developing on Windows
+
+There is an issue with removing temporary directories on Windows.
+Apparently, HTSJDK does not properly close files.
+Set `-Djunit.jupiter.tempdir.cleanup.mode.default=NEVER` to work around this issue.

pom.xml

@@ -14,9 +14,8 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
 		<hamcrest.version>1.3</hamcrest.version>
-		<junit.jupiter.version>5.7.2</junit.jupiter.version>
-		<junit.platform.version>1.7.2</junit.platform.version>
-		<guava.version>30.0-jre</guava.version>
+		<junit.jupiter.version>5.9.0</junit.jupiter.version>
+		<guava.version>31.1-jre</guava.version>
 		<fmt-maven-plugin.version>2.5.1</fmt-maven-plugin.version>
 		<checkstyle.version>7</checkstyle.version>
 		<slf4j.version>1.7.24</slf4j.version>

tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected

@@ -1,2 +1,2 @@
 release	chromosome	chromosome_no	bin	chromosome2	chromosome_no2	bin2	pe_orientation	start	end	start_ci_left	start_ci_right	end_ci_left	end_ci_right	case_id	set_id	sv_uuid	caller	sv_type	sv_sub_type	info	num_hom_alt	num_hom_ref	num_het	num_hemi_alt	num_hemi_ref	genotype
-GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""backgroundCarriers""":0,"""affectedCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ft""":{"""LowQual"""},"""gq""":14,"""pec""":0,"""pev""":0,"""src""":34,"""srv""":4,"""cn""":2},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":35,"""pec""":0,"""pev""":0,"""src""":29,"""srv""":2,"""cn""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""gq""":67,"""pec""":0,"""pev""":0,"""src""":32,"""srv""":1,"""cn""":2}}
+GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":{"""LowQual"""},"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}

varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java

@@ -247,7 +247,11 @@ private void annotateSvVcf(
 
     // Write out header.
     try {
-      gtWriter.append(Joiner.on("\t").join(gtRecordBuilder.getHeaders()) + "\n");
+      gtWriter.append(
+          GenotypeRecord.tsvHeader(
+                  !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS),
+                  !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS))
+              + "\n");
       // Write feature-effects header.
       featureEffectsWriter.append(Joiner.on("\t").join(HEADERS_FEATURE_EFFECTS) + "\n");
     } catch (IOException e) {
@@ -481,10 +485,14 @@ private void annotateVariantContext(
       }
 
       // Write out record with the genotype.
-      final List<Object> gtOutRec =
+      final GenotypeRecord gtOutRec =
           gtRecordBuilder.buildRecord(variantId, svGenomeVar, ctx, genomeVersion, i);
       try {
-        gtWriter.append(Joiner.on("\t").useForNull(".").join(gtOutRec) + "\n");
+        gtWriter.append(
+            gtOutRec.toTsv(
+                    !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_CHROM2_COLUMNS),
+                    !args.getOptOutFeatures().contains(GtRecordBuilder.FEATURE_DBCOUNTS_COLUMNS))
+                + "\n");
       } catch (IOException e) {
         throw new VarfishAnnotatorException("Problem writing to genotypes call file.", e);
       }

varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf37Chr1Test.java

@@ -103,8 +103,11 @@ void runTest(
       }
     } else {
       Assertions.assertEquals(
-          expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8"));
-      Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8"));
+          expectedDbInfos,
+          FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n"));
+      Assertions.assertEquals(
+          expectedGts,
+          FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"));
     }
   }
 

varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/AnnotateGatkHcVcf38Chr1Test.java

@@ -96,8 +96,11 @@ void runTest(
       }
     } else {
       Assertions.assertEquals(
-          expectedDbInfos, FileUtils.readFileToString(outputDbInfoPath, "utf-8"));
-      Assertions.assertEquals(expectedGts, FileUtils.readFileToString(outputGtsPath, "utf-8"));
+          expectedDbInfos,
+          FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n"));
+      Assertions.assertEquals(
+          expectedGts,
+          FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"));
     }
   }
 

varfish-annotator-cli/src/test/java/com/github/bihealth/varfish_annotator/annotate/RunWithRealWorldData37Test.java

@@ -103,11 +103,11 @@ void runTest(
       }
     } else {
       Assertions.assertEquals(
-          FileUtils.readFileToString(expectedDbInfosPath, "utf-8"),
-          FileUtils.readFileToString(outputDbInfoPath, "utf-8"));
+          FileUtils.readFileToString(expectedDbInfosPath, "utf-8").replaceAll("\\r\\n?", "\n"),
+          FileUtils.readFileToString(outputDbInfoPath, "utf-8").replaceAll("\\r\\n?", "\n"));
       Assertions.assertEquals(
-          FileUtils.readFileToString(expectedGtsPath, "utf-8"),
-          FileUtils.readFileToString(outputGtsPath, "utf-8"));
+          FileUtils.readFileToString(expectedGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"),
+          FileUtils.readFileToString(outputGtsPath, "utf-8").replaceAll("\\r\\n?", "\n"));
     }
   }