Merge branch 'release-2.2.x'

Author: imedina

biodata-external/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>biodata</artifactId>
         <groupId>org.opencb.biodata</groupId>
-        <version>2.2.0</version>
+        <version>2.2.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-formats/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.2.0</version>
+        <version>2.2.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-formats/src/main/java/org/opencb/biodata/formats/variant/vcf4/FullVcfCodec.java

@@ -203,4 +203,8 @@ public LazyGenotypesContext.LazyData createGenotypeMap(final String str,
         return new LazyGenotypesContext.LazyData(genotypes, header.getSampleNamesInOrder(), header.getSampleNameToOffset());
     }
 
+    public void setLineNumber(int lineNumber) {
+        lineNo = lineNumber;
+    }
+
 }

biodata-models/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.2.0</version>
+        <version>2.2.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-tools/pom.xml

@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.biodata</groupId>
         <artifactId>biodata</artifactId>
-        <version>2.2.0</version>
+        <version>2.2.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

biodata-tools/src/main/java/org/opencb/biodata/tools/variant/normalizer/extensions/SvVariantNormalizerExtension.java

@@ -71,61 +71,70 @@ public void init() {
 
     @Override
     protected boolean canUseExtension(VariantFileMetadata fileMetadata) {
-        // canCalculateVaf is calculated in the init() method after checking the VCF header fields
-        return SUPPORTED_SVTYPE_CALLERS.containsKey(caller) || SUPPORTED_SVLEN_CALLERS.containsKey(caller);
+        // First, check if the caller is registered because it does not use standard names
+        if (SUPPORTED_SVTYPE_CALLERS.containsKey(caller) || SUPPORTED_SVLEN_CALLERS.containsKey(caller)) {
+            return true;
+        }
+
+        // Second, if the VCF header contains standard SV info fields, in this case we always add EXT fields
+        for (VariantFileHeaderComplexLine complexLine : fileMetadata.getHeader().getComplexLines()) {
+            if (complexLine.getKey().equals("INFO")) {
+                if (complexLine.getId().equals("SVTYPE") || complexLine.getId().equals("SVLEN")) {
+                    return true;
+                }
+            }
+        }
+
+        return false;
     }
 
     @Override
     protected void normalizeHeader(VariantFileMetadata fileMetadata) {
-        if (SUPPORTED_SVTYPE_CALLERS.containsKey(caller)) {
-            // Add EXT_SVTYPE
-            VariantFileHeaderComplexLine newSampleMetadataLine = new VariantFileHeaderComplexLine( "INFO",
-                    EXT_SVTYPE,
-                    "Variant SVTYPE obtained from " + SUPPORTED_SVTYPE_CALLERS.get(caller)
-                            + ", several variant callers supported. NOTE: this is a OpenCB extension field.",
-                    "1",
-                    "String",
-                    Collections.emptyMap());
-            fileMetadata.getHeader().getComplexLines().add(newSampleMetadataLine);
-        }
-
-        if (SUPPORTED_SVLEN_CALLERS.containsKey(caller)) {
-            // Add EXT_SVLEN
-            VariantFileHeaderComplexLine newSampleMetadataLine = new VariantFileHeaderComplexLine( "INFO",
-                    EXT_SVLEN,
-                    "Variant SVLEN obtained from " + SUPPORTED_SVLEN_CALLERS.get(caller)
-                            + ", several variant callers supported. NOTE: this is a OpenCB extension field.",
-                    "1",
-                    "Integer",
-                    Collections.emptyMap());
-            fileMetadata.getHeader().getComplexLines().add(newSampleMetadataLine);
-        }
+        // Add EXT_SVTYPE
+        VariantFileHeaderComplexLine extSvtypeFileMetadataLine = new VariantFileHeaderComplexLine( "INFO",
+                EXT_SVTYPE,
+                "Variant SVTYPE obtained from " + SUPPORTED_SVTYPE_CALLERS.getOrDefault(caller, "SVTYPE")
+                        + ", several variant callers supported. NOTE: this is a OpenCB extension field.",
+                "1",
+                "String",
+                Collections.emptyMap());
+        fileMetadata.getHeader().getComplexLines().add(extSvtypeFileMetadataLine);
+
+        // Add EXT_SVLEN
+        VariantFileHeaderComplexLine extSvlenFileMetadataLine = new VariantFileHeaderComplexLine( "INFO",
+                EXT_SVLEN,
+                "Variant SVLEN obtained from " + SUPPORTED_SVLEN_CALLERS.getOrDefault(caller, "SVLEN")
+                        + ", several variant callers supported. NOTE: this is a OpenCB extension field.",
+                "1",
+                "Integer",
+                Collections.emptyMap());
+        fileMetadata.getHeader().getComplexLines().add(extSvlenFileMetadataLine);
     }
 
     @Override
     protected void normalizeFile(Variant variant, StudyEntry study, FileEntry file) {
-        // Check if we can get SVTYPE from this caller
-        if (SUPPORTED_SVTYPE_CALLERS.containsKey(caller)) {
-            VariantType svtype = parseSvtype(file);
-            // Check returned svtype, some variants could miss the svtype
-            if (svtype != null) {
-                study.addFileData(file.getFileId(), EXT_SVTYPE, svtype.name());
-            }
+        // GET SVTYPE and check value, some variants could miss the SVTYPE
+        VariantType svtype = parseSvtype(file);
+        if (svtype != null) {
+            study.addFileData(file.getFileId(), EXT_SVTYPE, svtype.name());
         }
 
-        // Check if we can get SVLEN from this caller
-        if (SUPPORTED_SVLEN_CALLERS.containsKey(caller)) {
-            String svlen = file.getData().get(SUPPORTED_SVLEN_CALLERS.get(caller));
-            // Check returned svlen, some variants could miss the svlen
-            if (StringUtils.isNotEmpty(svlen)) {
+        // Get SVLEN and check value, some variants could miss the SVLEN
+        String svlen = file.getData().get(SUPPORTED_SVLEN_CALLERS.getOrDefault(caller, "SVLEN"));
+        if (StringUtils.isNotEmpty(svlen)) {
+            try {
+                // Make sure SVLEN is a positive number
+                int i = Math.abs(Integer.parseInt(svlen));
+                study.addFileData(file.getFileId(), EXT_SVLEN, String.valueOf(i));
+            } catch (NumberFormatException e) {
                 study.addFileData(file.getFileId(), EXT_SVLEN, svlen);
             }
         }
     }
 
     private VariantType parseSvtype(FileEntry file) {
         VariantType SVTYPE = null;
-        String fileSvType = file.getData().get(SUPPORTED_SVTYPE_CALLERS.get(caller));
+        String fileSvType = file.getData().get(SUPPORTED_SVTYPE_CALLERS.getOrDefault(caller, "SVTYPE"));
 
         if (StringUtils.isNotEmpty(fileSvType)) {
             switch (fileSvType.toUpperCase()) {

pom.xml

@@ -20,7 +20,7 @@
 
     <groupId>org.opencb.biodata</groupId>
     <artifactId>biodata</artifactId>
-    <version>2.2.0</version>
+    <version>2.2.1</version>
     <packaging>pom</packaging>
 
     <name>Biodata</name>
@@ -35,7 +35,7 @@
     </modules>
 
     <properties>
-        <biodata.version>2.2.0</biodata.version>
+        <biodata.version>2.2.1</biodata.version>
         <commons.version>4.2.0</commons.version>
         <collections.version>4.4</collections.version>
         <avro.version>1.7.7</avro.version>