models: Replace FileEntry.call with dedicated model #179

biodata-models/src/main/avro/variant.avdl

@@ -147,6 +147,18 @@ protocol Variants {
         union { null, float } pValue = null;
     }
 
+    record OriginalCall {
+        /**
+         * Original variant ID before normalization including all secondary alternates.
+         */
+        string variantId;
+
+        /**
+         * Alternate allele index of the original multi-allellic variant call in which was decomposed.
+         */
+        union {null, int} alleleIndex;
+    }
+
     record FileEntry {
         /**
          * Unique identifier of the source file.
@@ -158,7 +170,7 @@ protocol Variants {
          *
          * {position}:{reference}:{alternate}(,{other_alternate})*:{allele_index}
          */
-        union { null, string } call;
+        union { null, OriginalCall } call;
 
         /**
          * Optional data that probably depend on the format of the file the

biodata-models/src/main/java/org/opencb/biodata/models/variant/StudyEntry.java

@@ -146,16 +146,6 @@ public String getSampleDataKeysAsString() {
         return impl.getSampleDataKeys() == null ? null : String.join(":", impl.getSampleDataKeys());
     }
 
-    @Deprecated
-    public List<String> getFormat() {
-        return getSampleDataKeys();
-    }
-
-    @Deprecated
-    public StudyEntry setFormat(List<String> value) {
-        return setSampleDataKeys(value);
-    }
-
     /**
      * Do not modify this list
      * @return
@@ -266,53 +256,6 @@ public List<String> getSampleData(int samplePosition) {
         }
     }
 
-    @Deprecated
-    public List<List<String>> getSamplesData() {
-        List<SampleEntry> samples = impl.getSamples();
-        if (samples == null) {
-            return null;
-        } else {
-            return samples.stream().map(SampleEntry::getData).collect(Collectors.toList());
-        }
-    }
-
-    @Deprecated
-    public void setSamplesData(List<List<String>> value) {
-        if (value == null) {
-            impl.setSamples(null);
-        } else {
-            impl.setSamples(value.stream().map(s -> new SampleEntry(null, null, s)).collect(Collectors.toList()));
-        }
-    }
-
-    @Deprecated
-    public Map<String, Map<String, String>> getSamplesDataAsMap() {
-        requireSamplesPosition();
-
-        Map<String, Map<String, String>> samplesDataMap = new HashMap<>();
-        for (Map.Entry<String, Integer> entry : samplesPosition.entrySet()) {
-            samplesDataMap.put(entry.getKey(), getSampleDataAsMap(entry.getKey()));
-        }
-
-        return Collections.unmodifiableMap(samplesDataMap);
-    }
-
-    @Deprecated
-    public Map<String, String> getSampleDataAsMap(String sampleName) {
-        requireSamplesPosition();
-        if (samplesPosition.containsKey(sampleName)) {
-            HashMap<String, String> sampleDataMap = new HashMap<>();
-            Iterator<String> iterator = getSampleDataKeys().iterator();
-            List<String> sampleDataList = getSampleData(sampleName);
-            for (String data : sampleDataList) {
-                sampleDataMap.put(iterator.next(), data);
-            }
-
-            return Collections.unmodifiableMap(sampleDataMap);
-        }
-        return null;
-    }
-
     public StudyEntry addSampleData(String sampleName, Map<String, String> sampleData) {
         if (getSampleDataKeys() == null) {
             setSampleDataKeys(new ArrayList<>(sampleData.keySet()));
@@ -524,7 +467,7 @@ public String getFileId() {
 
     public void setFileId(String fileId) {
         if (impl.getFiles().isEmpty()) {
-            impl.getFiles().add(new FileEntry(fileId, "", new HashMap<>()));
+            impl.getFiles().add(new FileEntry(fileId, null, new HashMap<>()));
         } else {
             impl.getFiles().get(0).setFileId(fileId);
         }

biodata-models/src/main/java/org/opencb/biodata/models/variant/VariantBuilder.java

@@ -91,7 +91,7 @@ public class VariantBuilder {
     private List<String> sampleDataKeys;
     private List<SampleEntry> samples;
     private Map<String, String> fileData;
-    private String call;
+    private OriginalCall call;
 
     private String variantString;
 
@@ -414,7 +414,7 @@ public VariantBuilder addFileData(String key, String value) {
         return this;
     }
 
-    public VariantBuilder setCall(String call) {
+    public VariantBuilder setCall(OriginalCall call) {
         checkFile("set call");
         this.call = call;
         return this;
@@ -612,9 +612,16 @@ public VariantProto.Variant buildProtoVariant(VariantProto.VariantOrBuilder reus
                     .setStudyId(studyId);
 
             if (fileId != null) {
-                studyBuilder.addFiles(VariantProto.FileEntry.newBuilder()
+                VariantProto.FileEntry.Builder fileBuilder = VariantProto.FileEntry.newBuilder()
                         .setFileId(fileId)
-                        .putAllData(fileData));
+                        .putAllData(fileData);
+                if (call != null) {
+                    fileBuilder.setCall(VariantProto.OriginalCall
+                            .newBuilder()
+                            .setVariantId(call.getVariantId())
+                            .setAlleleIndex(call.getAlleleIndex()));
+                }
+                studyBuilder.addFiles(fileBuilder);
             }
 
             for (int i = 1; i < alternates.size(); i++) {
@@ -1153,7 +1160,7 @@ private void parseStructuralVariationFileData(String key, String value) {
                     if (alternates.size() > 1) {
                         throw new IllegalArgumentException("Found SVINSSEQ in a multi allelic variant!");
                     } else {
-                        setCall(start + ":" + reference + ":" + alternates.get(0) + ":" + 0);
+                        setCall(new OriginalCall(toString(), 0));
                         setAlternate(reference + value);
                     }
                 }
@@ -1344,7 +1351,7 @@ public String toString() {
                     + start + "-"
                     + end + ":"
                     + reference + ":"
-                    + (alternates == null ? "null" : String.join(",", alternates));
+                    + (alternates == null ? "-" : String.join(",", alternates));
     }
 
     private static <T> void ifNotNull(T value, Consumer<T> setter) {

biodata-models/src/main/proto/protobuf/opencb/variant.proto

@@ -127,9 +127,22 @@ message VariantStats {
     string mgfGenotype = 13;
 }
 
+message OriginalCall {
+    /**
+     * Original variant ID before normalization including all secondary alternates.
+     */
+    string variantId = 1;
+
+    /**
+     * Alternate allele index of the original multi-allellic variant call in which was decomposed.
+     */
+    int32 alleleIndex = 2;
+}
+
+
 message FileEntry {
     string fileId = 1;
-    string call = 2;
+    OriginalCall call = 2;
     map<string, string> data = 3;
 }
 

biodata-models/src/test/java/org/opencb/biodata/models/variant/VariantBuilderTest.java

@@ -99,7 +99,7 @@ public void buildSVInsertion() {
         assertEquals(length, v.getLength().intValue());
         assertEquals(length, v.getLengthAlternate().intValue());
         assertEquals(1, v.getLengthReference().intValue());
-        assertEquals("1000:A:<INS>:0", v.getStudies().get(0).getFiles().get(0).getCall());
+        assertEquals(new OriginalCall("1:1000:A:<INS>", 0), v.getStudies().get(0).getFiles().get(0).getCall());
 
     }
 

biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java

@@ -313,7 +313,7 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                 }
                 // Iterate keyFields sorting by position, so the generated variants are ordered. Do not modify original order!
                 for (VariantKeyFields keyFields : sortByPosition(keyFieldsList)) {
-                    String call = start + ":" + reference + ":" + alternate + ":" + keyFields.getNumAllele();
+                    OriginalCall call = new OriginalCall(variant.toString(), keyFields.getNumAllele());
                     Variant normalizedVariant = newVariant(variant, keyFields, sv);
                     if (keyFields.getPhaseSet() != null) {
                         StudyEntry studyEntry = new StudyEntry();
@@ -361,15 +361,18 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                             && keyFieldsList.get(0).getReference().equals(reference)
                             && keyFieldsList.get(0).getAlternate().equals(alternate);
 
-                    String callPrefix;
+                    String originalCall;
                     if (entry.getFiles() != null
                             && !entry.getFiles().isEmpty()
-                            && StringUtils.isNotEmpty(entry.getFiles().get(0).getCall())) {
-                        String call = entry.getFiles().get(0).getCall();
-                        // Remove allele index
-                        callPrefix = call.substring(0, call.lastIndexOf(':') + 1);
+                            && entry.getFiles().get(0).getCall() != null
+                            && StringUtils.isNotEmpty(entry.getFiles().get(0).getCall().getVariantId())) {
+                        originalCall = entry.getFiles().get(0).getCall().getVariantId();
                     } else {
-                        callPrefix = start + ":" + reference + ":" + String.join(",", originalAlternates) + ":";
+                        StringBuilder sb = new StringBuilder(variant.toString());
+                        for (int i = 1; i < originalAlternates.size(); i++) {
+                            sb.append(",").append(originalAlternates.get(i));
+                        }
+                        originalCall = sb.toString();
                     }
 
                     // Iterate keyFields sorting by position, so the generated variants are ordered. Do not modify original order!
@@ -378,13 +381,12 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                         if (keyFields.alternate.equals(VariantBuilder.REF_ONLY_ALT)) {
                             continue;
                         }
-                        String call = callPrefix + keyFields.getNumAllele();
 
                         final Variant normalizedVariant;
                         final StudyEntry normalizedEntry;
                         final List<SampleEntry> samples;
                         if (reuse && keyFieldsList.size() == 1) {   //Only reuse for non multiallelic variants
-                            //Reuse variant. Set new fields.
+                            //callReuse variant. Set new fields.
                             normalizedVariant = variant;
                             variant.setStart(keyFields.getStart());
                             variant.setEnd(keyFields.getEnd());
@@ -397,7 +399,12 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
 //                                variant.setSv(sv);
 //                            }
                             normalizedEntry = entry;
-                            entry.getFiles().forEach(fileEntry -> fileEntry.setCall(sameVariant ? null : call));
+                            if (!sameVariant) {
+                                OriginalCall call = new OriginalCall(originalCall.toString(), keyFields.numAllele);
+                                entry.getFiles().forEach(fileEntry -> {
+                                    fileEntry.setCall(call);
+                                });
+                            }
                             samples = entry.getSamples();
                         } else {
                             normalizedVariant = newVariant(variant, keyFields, sv);
@@ -408,9 +415,15 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                             normalizedEntry.setSampleDataKeys(entry.getSampleDataKeys());
 
                             List<FileEntry> files = new ArrayList<>(entry.getFiles().size());
+                            OriginalCall call;
+                            if (sameVariant) {
+                                call = null;
+                            } else {
+                                call = new OriginalCall(originalCall, keyFields.numAllele);
+                            }
                             for (FileEntry file : entry.getFiles()) {
                                 HashMap<String, String> fileData = new HashMap<>(file.getData());
-                                files.add(new FileEntry(file.getFileId(), sameVariant ? null : call, fileData));
+                                files.add(new FileEntry(file.getFileId(), call, fileData));
                             }
                             normalizedEntry.setFiles(files);
                             normalizedVariant.addStudyEntry(normalizedEntry);
@@ -461,6 +474,7 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                                 // for all mnv-phased variants
                                 if (normalizedEntry.getFiles().size() == 0) {
                                     // Use mnv string as file Id so that it can be later identified.
+                                    OriginalCall call = new OriginalCall(originalCall, keyFields.numAllele);
                                     normalizedEntry.setFiles(Collections.singletonList(new FileEntry(keyFields.getPhaseSet(), call, null)));
                                 }
                             }
@@ -470,7 +484,7 @@ public List<Variant> normalize(List<Variant> batch, boolean reuse) throws NonSta
                             normalizedVariants.add(normalizedVariant);
 
                         } catch (Exception e) {
-                            logger.warn("Error parsing variant " + call + ", numAllele " + keyFields.getNumAllele(), e);
+                            logger.warn("Error parsing variant " + originalCall + ", numAllele " + keyFields.getNumAllele(), e);
                             throw e;
                         }
                     }

biodata-tools/src/main/java/org/opencb/biodata/tools/variant/converters/VariantContextConverter.java

@@ -25,6 +25,7 @@
 import org.apache.commons.lang3.tuple.MutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.opencb.biodata.models.variant.StudyEntry;
+import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.protobuf.VariantProto;
 import org.opencb.biodata.tools.Converter;
 import org.opencb.commons.datastore.core.ObjectMap;
@@ -202,10 +203,10 @@ protected Set<Integer> getNoCallAlleleIdx(List<String> alleleList) {
     protected static Map<Integer, Character> buildReferenceAllelesMap(Iterator<String> callsIterator) {
         Map<Integer, Character> referenceAlleles = new HashMap<>();
         callsIterator.forEachRemaining(call -> {
-            String[] split = splitCall(call);
-            if (split != null) {
-                String originalReference = VariantContextConverter.getOriginalReference(split);
-                Integer originalPosition = VariantContextConverter.getOriginalPosition(split);
+            if (call != null) {
+                Variant originalVariant = new Variant(call.split(",")[0]);
+                String originalReference = originalVariant.getReference();
+                Integer originalPosition = originalVariant.getStart();
                 for (int i = 0; i < originalReference.length(); i++) {
                     referenceAlleles.put(originalPosition + i, originalReference.charAt(i));
                 }
@@ -375,74 +376,6 @@ protected VariantContext makeVariantContext(String chromosome, int start, int en
         return variantContextBuilder.make();
     }
 
-    protected static String[] splitCall(String call) {
-        if (StringUtils.isNotEmpty(call)) {
-            int idx1 = call.indexOf(':');
-            int idx2 = call.indexOf(':', idx1 + 1);
-            int idx3 = call.lastIndexOf(':'); // Get lastIndexOf, as it may be other intermediate ':' from symbolic or breakend alleles
-            return new String[]{
-                    call.substring(0, idx1),
-                    call.substring(idx1 + 1, idx2),
-                    call.substring(idx2 + 1, idx3),
-                    call.substring(idx3 + 1)
-            };
-        } else {
-            return null;
-        }
-    }
-
-    /**
-     * Assumes that ori is in the form "POS:REF:ALT_0(,ALT_N)*:ALT_IDX".
-     * ALT_N is the n-th allele if this is the n-th variant resultant of a multiallelic vcf row
-     *
-     * @param ori
-     * @return
-     */
-    protected static List<String> getOriginalAlleles(String[] ori) {
-        if (ori != null && ori.length == 4) {
-            String[] multiAllele = ori[2].split(",");
-            if (multiAllele.length != 1) {
-                ArrayList<String> alleles = new ArrayList<>(multiAllele.length + 1);
-                alleles.add(ori[1]);
-                alleles.addAll(Arrays.asList(multiAllele));
-                return alleles;
-            } else {
-                return Arrays.asList(ori[1], ori[2]);
-            }
-        }
-
-        return null;
-    }
-
-    protected static String getOriginalReference(String[] ori) {
-        if (ori != null && ori.length == 4) {
-            return ori[1];
-        }
-        return null;
-    }
-
-    protected static String getOriginalAlleleIndex(String[] ori) {
-        if (ori != null && ori.length == 4) {
-            return ori[3];
-        }
-        return null;
-    }
-
-    /**
-     * Assumes that ori is in the form "POS:REF:ALT_0(,ALT_N)*:ALT_IDX".
-     *
-     * @param ori
-     * @return
-     */
-    protected static Integer getOriginalPosition(String[] ori) {
-
-        if (ori != null && ori.length == 4) {
-            return Integer.parseInt(ori[0]);
-        }
-
-        return null;
-    }
-
     protected abstract Object getStudy(T variant);
 
     protected abstract Iterator<String> getStudiesId(T variant);