Adding explicit support for SV/CNV calling tools (#68)

Closes: #68
Related-Issue: #68
Projected-Results-Impact: none

varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/CallerSupportDragenCnv.java

@@ -0,0 +1,33 @@
+package com.github.bihealth.varfish_annotator.annotate_svs;
+
+import htsjdk.variant.vcf.VCFFilterHeaderLine;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+
+/** Import SV caller support for Dragen CNV. */
+public class CallerSupportDragenCnv extends CallerSupportBase {
+
+  public SvCaller getSvCaller() {
+    return SvCaller.DRAGEN_CNV;
+  }
+
+  public boolean isCompatible(VCFHeader vcfHeader) {
+    boolean seenDragenVersionHeaderLine = false;
+    boolean seenDragenCommandLineHeaderLine = false;
+    for (VCFHeaderLine headerLine : vcfHeader.getOtherHeaderLines()) {
+      if (headerLine.getKey().equals("DRAGENVersion")) {
+        seenDragenVersionHeaderLine = true;
+      } else if (headerLine.getKey().equals("DRAGENCommandLine")) {
+        seenDragenCommandLineHeaderLine = true;
+      }
+    }
+
+    final VCFFilterHeaderLine cnvBinSupportRatio =
+        vcfHeader.getFilterHeaderLine("cnvBinSupportRatio");
+    boolean seenCnvBinSupportRatioFilter = (cnvBinSupportRatio != null);
+
+    return seenDragenVersionHeaderLine
+        && seenDragenCommandLineHeaderLine
+        && seenCnvBinSupportRatioFilter;
+  }
+}

varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/CallerSupportDragenSv.java

@@ -0,0 +1,32 @@
+package com.github.bihealth.varfish_annotator.annotate_svs;
+
+import com.github.bihealth.varfish_annotator.utils.HtsjdkUtils;
+import htsjdk.variant.vcf.VCFFilterHeaderLine;
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+import htsjdk.variant.vcf.VCFInfoHeaderLine;
+
+/** Import SV caller support for Dragen SV. */
+public class CallerSupportDragenSv extends CallerSupportBase {
+
+  public SvCaller getSvCaller() {
+    return SvCaller.DRAGEN_SV;
+  }
+
+  public boolean isCompatible(VCFHeader vcfHeader) {
+    boolean seenSourceDragen = false;
+    for (VCFHeaderLine headerLine : HtsjdkUtils.getSourceHeaderLines(vcfHeader)) {
+      final String value = headerLine.getValue();
+      if (value.startsWith("DRAGEN")) {
+        seenSourceDragen = true;
+      }
+    }
+
+    final VCFFilterHeaderLine minQualFilter = vcfHeader.getFilterHeaderLine("MinQUAL");
+    boolean seenMinQualFilter = (minQualFilter != null);
+    final VCFInfoHeaderLine mateIdInfo = vcfHeader.getInfoHeaderLine("MATEID");
+    boolean seenMateIdInfo = (mateIdInfo != null);
+
+    return seenSourceDragen && seenMinQualFilter && seenMateIdInfo;
+  }
+}

varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/utils/HtsjdkUtils.java

@@ -0,0 +1,18 @@
+package com.github.bihealth.varfish_annotator.utils;
+
+import htsjdk.variant.vcf.VCFHeader;
+import htsjdk.variant.vcf.VCFHeaderLine;
+import java.util.ArrayList;
+import java.util.List;
+
+public class HtsjdkUtils {
+  public static List<VCFHeaderLine> getSourceHeaderLines(VCFHeader vcfHeader) {
+    final ArrayList<VCFHeaderLine> result = new ArrayList<>();
+    for (VCFHeaderLine headerLine : vcfHeader.getOtherHeaderLines()) {
+      if (headerLine.getKey().equals("source")) {
+        result.add(headerLine);
+      }
+    }
+    return result;
+  }
+}

varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/CallerSupportDragenCnvTest.java

@@ -0,0 +1,48 @@
+package com.github.bihealth.varfish_annotator.annotate_svs;
+
+import com.github.bihealth.varfish_annotator.ResourceUtils;
+import htsjdk.variant.vcf.VCFFileReader;
+import htsjdk.variant.vcf.VCFHeader;
+import java.io.File;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+public class CallerSupportDragenCnvTest {
+
+  @TempDir public File tmpFolder;
+  File vcfFile;
+  File otherVcfFile;
+  CallerSupportDragenCnv callerSupport;
+
+  @BeforeEach
+  void initEach() {
+    vcfFile = new File(tmpFolder + "/vcf-header.vcf");
+    ResourceUtils.copyResourceToFile("/callers-sv/dragen-cnv-head.vcf", vcfFile);
+    otherVcfFile = new File(tmpFolder + "/incompatible.vcf");
+    ResourceUtils.copyResourceToFile("/callers-sv/delly2-head.vcf", otherVcfFile);
+    callerSupport = new CallerSupportDragenCnv();
+  }
+
+  @Test
+  void testGetSvCaller() {
+    Assertions.assertEquals(SvCaller.DRAGEN_CNV, callerSupport.getSvCaller());
+  }
+
+  @Test
+  void testIsCompatiblePositive() {
+    final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
+    final VCFHeader vcfHeader = vcfReader.getHeader();
+
+    Assertions.assertTrue(callerSupport.isCompatible(vcfHeader));
+  }
+
+  @Test
+  void testIsCompatibleNegative() {
+    final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
+    final VCFHeader vcfHeader = vcfReader.getHeader();
+
+    Assertions.assertTrue(callerSupport.isCompatible(vcfHeader));
+  }
+}

varfish-annotator-core/src/test/java/com/github/bihealth/varfish_annotator/annotate_svs/CallerSupportDragenSvTest.java

@@ -0,0 +1,48 @@
+package com.github.bihealth.varfish_annotator.annotate_svs;
+
+import com.github.bihealth.varfish_annotator.ResourceUtils;
+import htsjdk.variant.vcf.VCFFileReader;
+import htsjdk.variant.vcf.VCFHeader;
+import java.io.File;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+public class CallerSupportDragenSvTest {
+
+  @TempDir public File tmpFolder;
+  File vcfFile;
+  File otherVcfFile;
+  CallerSupportDragenSv callerSupport;
+
+  @BeforeEach
+  void initEach() {
+    vcfFile = new File(tmpFolder + "/vcf-header.vcf");
+    ResourceUtils.copyResourceToFile("/callers-sv/dragen-sv-head.vcf", vcfFile);
+    otherVcfFile = new File(tmpFolder + "/incompatible.vcf");
+    ResourceUtils.copyResourceToFile("/callers-sv/delly2-head.vcf", otherVcfFile);
+    callerSupport = new CallerSupportDragenSv();
+  }
+
+  @Test
+  void testGetSvCaller() {
+    Assertions.assertEquals(SvCaller.DRAGEN_SV, callerSupport.getSvCaller());
+  }
+
+  @Test
+  void testIsCompatiblePositive() {
+    final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
+    final VCFHeader vcfHeader = vcfReader.getHeader();
+
+    Assertions.assertTrue(callerSupport.isCompatible(vcfHeader));
+  }
+
+  @Test
+  void testIsCompatibleNegative() {
+    final VCFFileReader vcfReader = new VCFFileReader(vcfFile, false);
+    final VCFHeader vcfHeader = vcfReader.getHeader();
+
+    Assertions.assertTrue(callerSupport.isCompatible(vcfHeader));
+  }
+}