public static void main(String[] args) {
    LinkedHashMap<Integer, String> hashmap = new LinkedHashMap<Integer, String>();

    hashmap.put(1, "apple");
    hashmap.put(2, "lemon");
    hashmap.put(3, "orange");
    hashmap.put(4, "banana");
    hashmap.put(5, "litchi");
    hashmap.put(6, "mango");
    hashmap.put(7, "papaya");

    System.out.println(hashmap);

    System.out.println(valuesBetween(2, 5, hashmap));

    //        // note insertion order lost
    //        Map map1 = new HashMap<>();
    //        //for (int i = 1; i < 15; i++) {
    //        for (int i = 14; i > 0; i--) {
    //            map1.put(String.format("%04d", i), "");
    //            System.out.println(String.format("%04d:", i) + map1);
    //        }
    //
    //        map1 = new LinkedHashMap<>();
    //        //for (int i = 1; i < 15; i++) {
    //        for (int i = 14; i > 0; i--) {
    //            map1.put(String.format("%04d", i), "");
    //            System.out.println(String.format("%04d:", i) + map1);
    //        }

    Map<String, String> myMap = new HashMap<>();
    myMap.put("A", "1");
    myMap.put("B", "1");
    myMap.put("C", "1");
    System.out.println(myMap);

    myMap = new LinkedHashMap<>();
    myMap.put("A", "1");
    myMap.put("C", "1");
    myMap.put("B", "1");

    NavigableMap<Integer, String> map = new TreeMap<Integer, String>();

    map.put(0, "Kid");
    map.put(11, "Teens");
    map.put(20, "Twenties");
    map.put(30, "Thirties");
    map.put(40, "Forties");
    map.put(50, "Senior");
    map.put(100, "OMG OMG OMG!");

    System.out.println(map.get(map.floorKey(13)));
    System.out.println(map.get(map.higherKey(20)));
  }
  public void remove(OIdentifiable identifiable) {
    if (removeFromNewEntries(identifiable)) {
      if (size >= 0) size--;
    } else {
      final Change counter = changes.get(identifiable);
      if (counter == null) {
        // Not persistent keys can only be in changes or newEntries
        if (identifiable.getIdentity().isPersistent()) {
          changes.put(identifiable, new DiffChange(-1));
          size = -1;
        } else
          // Return immediately to prevent firing of event
          return;
      } else {
        counter.decrement();

        if (size >= 0)
          if (counter.isUndefined()) size = -1;
          else size--;
      }
    }

    if (this.owner != null) ORecordInternal.unTrack(this.owner, identifiable);

    if (updateOwner)
      fireCollectionChangedEvent(
          new OMultiValueChangeEvent<OIdentifiable, OIdentifiable>(
              OMultiValueChangeEvent.OChangeType.REMOVE, identifiable, null, identifiable, false));
  }
  public void add(final OIdentifiable identifiable) {
    if (identifiable == null)
      throw new NullPointerException("Impossible to add a null identifiable in a ridbag");
    if (identifiable.getIdentity().isValid()) {
      Change counter = changes.get(identifiable);
      if (counter == null) changes.put(identifiable, new DiffChange(1));
      else {
        if (counter.isUndefined()) {
          counter = getAbsoluteValue(identifiable);
          changes.put(identifiable, counter);
        }
        counter.increment();
      }
    } else {
      final OModifiableInteger counter = newEntries.get(identifiable);
      if (counter == null) newEntries.put(identifiable, new OModifiableInteger(1));
      else counter.increment();
    }

    if (size >= 0) size++;

    if (this.owner != null) ORecordInternal.track(this.owner, identifiable);

    if (updateOwner)
      fireCollectionChangedEvent(
          new OMultiValueChangeEvent<OIdentifiable, OIdentifiable>(
              OMultiValueChangeEvent.OChangeType.ADD, identifiable, identifiable, null, false));
  }
  private Map.Entry<OIdentifiable, Integer> nextChangedNotRemovedSBTreeEntry(
      Iterator<Map.Entry<OIdentifiable, Integer>> iterator) {
    while (iterator.hasNext()) {
      final Map.Entry<OIdentifiable, Integer> entry = iterator.next();
      final Change change = changes.get(entry.getKey());
      if (change == null) return entry;

      final int newValue = change.applyTo(entry.getValue());

      if (newValue > 0)
        return new Map.Entry<OIdentifiable, Integer>() {
          @Override
          public OIdentifiable getKey() {
            return entry.getKey();
          }

          @Override
          public Integer getValue() {
            return newValue;
          }

          @Override
          public Integer setValue(Integer value) {
            throw new UnsupportedOperationException();
          }
        };
    }

    return null;
  }
  private AbsoluteChange getAbsoluteValue(OIdentifiable identifiable) {
    final OSBTreeBonsai<OIdentifiable, Integer> tree = loadTree();
    try {
      Integer oldValue;

      if (tree == null) oldValue = 0;
      else oldValue = tree.get(identifiable);

      if (oldValue == null) oldValue = 0;

      final Change change = changes.get(identifiable);

      return new AbsoluteChange(change == null ? oldValue : change.applyTo(oldValue));
    } finally {
      releaseTree();
    }
  }
 @Override
 public <T> T getProperty(String key, Class<T> targetType, T defaultValue) {
   Object originalValue = configMap.get(key);
   if (originalValue == null && key.contains(".")) {
     originalValue = configMap.navigate(key.split("\\."));
     if (originalValue != null) {
       try {
         configMap.put(key, originalValue);
       } catch (Exception e) {
         // ignore
       }
     }
   }
   if (originalValue != null) {
     T value = conversionService.convert(originalValue, targetType);
     return DefaultGroovyMethods.asBoolean(value) ? value : defaultValue;
   }
   return defaultValue;
 }
    @Override
    public void remove() {
      if (currentRemoved)
        throw new IllegalStateException("Current element has already been removed");

      if (currentValue == null)
        throw new IllegalStateException("Next method was not called for given iterator");

      if (removeFromNewEntries(currentValue)) {
        if (size >= 0) size--;
      } else {
        Change counter = changedValues.get(currentValue);
        if (counter != null) {
          counter.decrement();
          if (size >= 0)
            if (counter.isUndefined()) size = -1;
            else size--;
        } else {
          if (nextChange != null) {
            changedValues.put(currentValue, new DiffChange(-1));
            changedValuesIterator =
                changedValues.tailMap(nextChange.getKey(), false).entrySet().iterator();
          } else {
            changedValues.put(currentValue, new DiffChange(-1));
          }

          size = -1;
        }
      }

      if (OSBTreeRidBag.this.owner != null)
        ORecordInternal.unTrack(OSBTreeRidBag.this.owner, currentValue);

      if (updateOwner)
        fireCollectionChangedEvent(
            new OMultiValueChangeEvent<OIdentifiable, OIdentifiable>(
                OMultiValueChangeEvent.OChangeType.REMOVE,
                currentValue,
                null,
                currentValue,
                false));
      currentRemoved = true;
    }
  @Override
  public boolean contains(OIdentifiable identifiable) {
    if (newEntries.containsKey(identifiable)) return true;

    Change counter = changes.get(identifiable);

    if (counter != null) {
      AbsoluteChange absoluteValue = getAbsoluteValue(identifiable);

      if (counter.isUndefined()) {
        changes.put(identifiable, absoluteValue);
      }

      counter = absoluteValue;
    } else {
      counter = getAbsoluteValue(identifiable);
    }

    return counter.applyTo(0) > 0;
  }
  @Override
  public int serialize(byte[] stream, int offset, UUID ownerUuid) {
    for (Map.Entry<OIdentifiable, OModifiableInteger> entry : newEntries.entrySet()) {
      OIdentifiable identifiable = entry.getKey();
      assert identifiable instanceof ORecord;
      Change c = changes.get(identifiable);

      final int delta = entry.getValue().intValue();
      if (c == null) changes.put(identifiable, new DiffChange(delta));
      else c.applyDiff(delta);
    }
    newEntries.clear();

    final ORecordSerializationContext context;
    boolean remoteMode =
        ODatabaseRecordThreadLocal.INSTANCE.get().getStorage() instanceof OStorageProxy;
    if (remoteMode) {
      context = null;
    } else context = ORecordSerializationContext.getContext();

    // make sure that we really save underlying record.
    if (collectionPointer == null) {
      if (context != null) {
        final int clusterId = getHighLevelDocClusterId();
        assert clusterId > -1;
        collectionPointer =
            ODatabaseRecordThreadLocal.INSTANCE
                .get()
                .getSbTreeCollectionManager()
                .createSBTree(clusterId, ownerUuid);
      }
    }

    OBonsaiCollectionPointer collectionPointer;
    if (this.collectionPointer != null) collectionPointer = this.collectionPointer;
    else {
      collectionPointer = OBonsaiCollectionPointer.INVALID;
    }

    OLongSerializer.INSTANCE.serializeLiteral(collectionPointer.getFileId(), stream, offset);
    offset += OLongSerializer.LONG_SIZE;

    OBonsaiBucketPointer rootPointer = collectionPointer.getRootPointer();
    OLongSerializer.INSTANCE.serializeLiteral(rootPointer.getPageIndex(), stream, offset);
    offset += OLongSerializer.LONG_SIZE;

    OIntegerSerializer.INSTANCE.serializeLiteral(rootPointer.getPageOffset(), stream, offset);
    offset += OIntegerSerializer.INT_SIZE;

    // Keep this section for binary compatibility with versions older then 1.7.5
    OIntegerSerializer.INSTANCE.serializeLiteral(size, stream, offset);
    offset += OIntegerSerializer.INT_SIZE;

    if (context == null) {
      ChangeSerializationHelper.INSTANCE.serializeChanges(
          changes, OLinkSerializer.INSTANCE, stream, offset);
    } else {
      context.push(new ORidBagUpdateSerializationOperation(changes, collectionPointer));

      // 0-length serialized list of changes
      OIntegerSerializer.INSTANCE.serializeLiteral(0, stream, offset);
      offset += OIntegerSerializer.INT_SIZE;
    }

    return offset;
  }
  @Test
  public void testRandom() throws Exception {
    Directory directory = newDirectory();
    final Random r = random();
    final IndexWriterConfig iwc =
        LuceneTestCase.newIndexWriterConfig(r, new MockAnalyzer(r))
            .setMaxBufferedDocs(IndexWriterConfig.DISABLE_AUTO_FLUSH)
            .setRAMBufferSizeMB(
                scaledRandomIntBetween(16, 64)); // we might index a lot - don't go crazy here
    RandomIndexWriter indexWriter = new RandomIndexWriter(r, directory, iwc);
    int numUniqueChildValues = scaledRandomIntBetween(100, 2000);
    String[] childValues = new String[numUniqueChildValues];
    for (int i = 0; i < numUniqueChildValues; i++) {
      childValues[i] = Integer.toString(i);
    }

    IntOpenHashSet filteredOrDeletedDocs = new IntOpenHashSet();

    int childDocId = 0;
    int numParentDocs = scaledRandomIntBetween(1, numUniqueChildValues);
    ObjectObjectOpenHashMap<String, NavigableMap<String, FloatArrayList>> childValueToParentIds =
        new ObjectObjectOpenHashMap<>();
    for (int parentDocId = 0; parentDocId < numParentDocs; parentDocId++) {
      boolean markParentAsDeleted = rarely();
      boolean filterMe = rarely();
      String parent = Integer.toString(parentDocId);
      Document document = new Document();
      document.add(
          new StringField(UidFieldMapper.NAME, Uid.createUid("parent", parent), Field.Store.YES));
      document.add(new StringField(TypeFieldMapper.NAME, "parent", Field.Store.NO));
      if (markParentAsDeleted) {
        filteredOrDeletedDocs.add(parentDocId);
        document.add(new StringField("delete", "me", Field.Store.NO));
      }
      if (filterMe) {
        filteredOrDeletedDocs.add(parentDocId);
        document.add(new StringField("filter", "me", Field.Store.NO));
      }
      indexWriter.addDocument(document);

      int numChildDocs = scaledRandomIntBetween(0, 100);
      for (int i = 0; i < numChildDocs; i++) {
        boolean markChildAsDeleted = rarely();
        String childValue = childValues[random().nextInt(childValues.length)];

        document = new Document();
        document.add(
            new StringField(
                UidFieldMapper.NAME,
                Uid.createUid("child", Integer.toString(childDocId++)),
                Field.Store.NO));
        document.add(new StringField(TypeFieldMapper.NAME, "child", Field.Store.NO));
        document.add(
            new StringField(
                ParentFieldMapper.NAME, Uid.createUid("parent", parent), Field.Store.NO));
        document.add(new StringField("field1", childValue, Field.Store.NO));
        if (markChildAsDeleted) {
          document.add(new StringField("delete", "me", Field.Store.NO));
        }
        indexWriter.addDocument(document);

        if (!markChildAsDeleted) {
          NavigableMap<String, FloatArrayList> parentIdToChildScores;
          if (childValueToParentIds.containsKey(childValue)) {
            parentIdToChildScores = childValueToParentIds.lget();
          } else {
            childValueToParentIds.put(childValue, parentIdToChildScores = new TreeMap<>());
          }
          if (!markParentAsDeleted && !filterMe) {
            FloatArrayList childScores = parentIdToChildScores.get(parent);
            if (childScores == null) {
              parentIdToChildScores.put(parent, childScores = new FloatArrayList());
            }
            childScores.add(1f);
          }
        }
      }
    }

    // Delete docs that are marked to be deleted.
    indexWriter.deleteDocuments(new Term("delete", "me"));
    indexWriter.commit();

    IndexReader indexReader = DirectoryReader.open(directory);
    IndexSearcher searcher = new IndexSearcher(indexReader);
    Engine.Searcher engineSearcher =
        new Engine.Searcher(ChildrenQueryTests.class.getSimpleName(), searcher);
    ((TestSearchContext) SearchContext.current())
        .setSearcher(new ContextIndexSearcher(SearchContext.current(), engineSearcher));

    int max = numUniqueChildValues / 4;
    for (int i = 0; i < max; i++) {
      // Simulate a parent update
      if (random().nextBoolean()) {
        final int numberOfUpdatableParents = numParentDocs - filteredOrDeletedDocs.size();
        int numberOfUpdates =
            RandomInts.randomIntBetween(
                random(), 0, Math.min(numberOfUpdatableParents, TEST_NIGHTLY ? 25 : 5));
        for (int j = 0; j < numberOfUpdates; j++) {
          int parentId;
          do {
            parentId = random().nextInt(numParentDocs);
          } while (filteredOrDeletedDocs.contains(parentId));

          String parentUid = Uid.createUid("parent", Integer.toString(parentId));
          indexWriter.deleteDocuments(new Term(UidFieldMapper.NAME, parentUid));

          Document document = new Document();
          document.add(new StringField(UidFieldMapper.NAME, parentUid, Field.Store.YES));
          document.add(new StringField(TypeFieldMapper.NAME, "parent", Field.Store.NO));
          indexWriter.addDocument(document);
        }

        indexReader.close();
        indexReader = DirectoryReader.open(indexWriter.w, true);
        searcher = new IndexSearcher(indexReader);
        engineSearcher =
            new Engine.Searcher(ChildrenConstantScoreQueryTests.class.getSimpleName(), searcher);
        ((TestSearchContext) SearchContext.current())
            .setSearcher(new ContextIndexSearcher(SearchContext.current(), engineSearcher));
      }

      String childValue = childValues[random().nextInt(numUniqueChildValues)];
      int shortCircuitParentDocSet = random().nextInt(numParentDocs);
      ScoreType scoreType = ScoreType.values()[random().nextInt(ScoreType.values().length)];
      // leave min/max set to 0 half the time
      int minChildren = random().nextInt(2) * scaledRandomIntBetween(0, 110);
      int maxChildren = random().nextInt(2) * scaledRandomIntBetween(minChildren, 110);

      QueryBuilder queryBuilder =
          hasChildQuery("child", constantScoreQuery(termQuery("field1", childValue)))
              .scoreType(scoreType.name().toLowerCase(Locale.ENGLISH))
              .minChildren(minChildren)
              .maxChildren(maxChildren)
              .setShortCircuitCutoff(shortCircuitParentDocSet);
      // Using a FQ, will invoke / test the Scorer#advance(..) and also let the Weight#scorer not
      // get live docs as acceptedDocs
      queryBuilder = filteredQuery(queryBuilder, notFilter(termFilter("filter", "me")));
      Query query = parseQuery(queryBuilder);
      BitSetCollector collector = new BitSetCollector(indexReader.maxDoc());
      int numHits = 1 + random().nextInt(25);
      TopScoreDocCollector actualTopDocsCollector = TopScoreDocCollector.create(numHits);
      searcher.search(query, MultiCollector.wrap(collector, actualTopDocsCollector));
      FixedBitSet actualResult = collector.getResult();

      FixedBitSet expectedResult = new FixedBitSet(indexReader.maxDoc());
      TopScoreDocCollector expectedTopDocsCollector = TopScoreDocCollector.create(numHits);
      if (childValueToParentIds.containsKey(childValue)) {
        LeafReader slowLeafReader = SlowCompositeReaderWrapper.wrap(indexReader);
        final FloatArrayList[] scores = new FloatArrayList[slowLeafReader.maxDoc()];
        Terms terms = slowLeafReader.terms(UidFieldMapper.NAME);
        if (terms != null) {
          NavigableMap<String, FloatArrayList> parentIdToChildScores = childValueToParentIds.lget();
          TermsEnum termsEnum = terms.iterator(null);
          DocsEnum docsEnum = null;
          for (Map.Entry<String, FloatArrayList> entry : parentIdToChildScores.entrySet()) {
            int count = entry.getValue().elementsCount;
            if (count >= minChildren && (maxChildren == 0 || count <= maxChildren)) {
              TermsEnum.SeekStatus seekStatus =
                  termsEnum.seekCeil(Uid.createUidAsBytes("parent", entry.getKey()));
              if (seekStatus == TermsEnum.SeekStatus.FOUND) {
                docsEnum =
                    termsEnum.docs(slowLeafReader.getLiveDocs(), docsEnum, DocsEnum.FLAG_NONE);
                expectedResult.set(docsEnum.nextDoc());
                scores[docsEnum.docID()] = new FloatArrayList(entry.getValue());
              } else if (seekStatus == TermsEnum.SeekStatus.END) {
                break;
              }
            }
          }
        }
        MockScorer mockScorer = new MockScorer(scoreType);
        final LeafCollector leafCollector =
            expectedTopDocsCollector.getLeafCollector(slowLeafReader.getContext());
        leafCollector.setScorer(mockScorer);
        for (int doc = expectedResult.nextSetBit(0);
            doc < slowLeafReader.maxDoc();
            doc =
                doc + 1 >= expectedResult.length()
                    ? DocIdSetIterator.NO_MORE_DOCS
                    : expectedResult.nextSetBit(doc + 1)) {
          mockScorer.scores = scores[doc];
          leafCollector.collect(doc);
        }
      }

      assertBitSet(actualResult, expectedResult, searcher);
      assertTopDocs(actualTopDocsCollector.topDocs(), expectedTopDocsCollector.topDocs());
    }

    indexWriter.close();
    indexReader.close();
    directory.close();
  }
  @Override
  public QueryResult<Variant> getAllVariantsByRegionAndStudy(
      Region region, String sourceId, QueryOptions options) {
    Long start, end, dbstart, dbend;
    start = System.currentTimeMillis();
    QueryResult<Variant> queryResult =
        new QueryResult<>(
            String.format("%s:%d-%d", region.getChromosome(), region.getStart(), region.getEnd()));
    List<Variant> results = new LinkedList<>();

    boolean includeSamples;
    boolean includeStats;
    boolean includeEffects;
    if (!options.containsKey("samples")
        && !options.containsKey("stats")
        && !options.containsKey("effects")) {
      includeSamples = true;
      includeStats = true;
      includeEffects = true;
    } else {
      includeSamples = options.containsKey("samples") && options.getBoolean("samples");
      includeStats = options.containsKey("stats") && options.getBoolean("stats");
      includeEffects = options.containsKey("effects") && options.getBoolean("effects");
    }

    try {
      String startRow = buildRowkey(region.getChromosome(), Long.toString(region.getStart()));
      String stopRow = buildRowkey(region.getChromosome(), Long.toString(region.getEnd()));
      HTable table = new HTable(admin.getConfiguration(), tableName);
      dbstart = System.currentTimeMillis();
      Scan regionScan = new Scan(startRow.getBytes(), stopRow.getBytes());
      ResultScanner scanres = table.getScanner(regionScan);
      dbend = System.currentTimeMillis();
      queryResult.setDbTime(dbend - dbstart);

      // Iterate over results and, optionally, their samples and statistics
      for (Result result : scanres) {
        String[] rowkeyParts = new String(result.getRow(), CHARSET_UTF_8).split("_");
        String chromosome = rowkeyParts[0].replaceFirst("^0+(?!$)", "");
        int position = Integer.parseInt(rowkeyParts[1]);

        // Get basic result fields from Protocol Buffers message
        NavigableMap<byte[], byte[]> infoMap = result.getFamilyMap("i".getBytes());
        byte[] byteInfo = infoMap.get((sourceId + "_data").getBytes());
        VariantFieldsProtos.VariantInfo protoInfo =
            VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
        String reference = protoInfo.getReference();
        String alternate = StringUtils.join(protoInfo.getAlternateList(), ",");
        String format = StringUtils.join(protoInfo.getFormatList(), ":");
        Variant variant = new Variant(chromosome, position, position, reference, alternate);

        // Set samples if requested
        if (includeSamples) {
          NavigableMap<byte[], byte[]> sampleMap = result.getFamilyMap("d".getBytes());
          Map<String, Map<String, String>> resultSampleMap = new HashMap<>();

          // Set samples
          for (byte[] s : sampleMap.keySet()) {
            String sampleName = (new String(s, CHARSET_UTF_8)).replaceAll(sourceId + "_", "");
            VariantFieldsProtos.VariantSample sample =
                VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
            String sample1 = sample.getSample();
            String[] values = sample1.split(":");
            String[] fields = format.split(":");
            Map<String, String> singleSampleMap = new HashMap<>();
            for (int i = 0; i < fields.length; i++) {
              singleSampleMap.put(fields[i], values[i]);
            }
            // TODO
            //                        variant.addSampleData(sampleName, singleSampleMap);
          }
        }

        // Set stats if requested
        if (includeStats) {
          byte[] byteStats = infoMap.get((sourceId + "_stats").getBytes());
          VariantFieldsProtos.VariantStats protoStats =
              VariantFieldsProtos.VariantStats.parseFrom(byteStats);
          VariantStats variantStats =
              new VariantStats(
                  chromosome,
                  position,
                  reference,
                  alternate,
                  protoStats.getMaf(),
                  protoStats.getMgf(),
                  protoStats.getMafAllele(),
                  protoStats.getMgfGenotype(),
                  protoStats.getMissingAlleles(),
                  protoStats.getMissingGenotypes(),
                  protoStats.getMendelianErrors(),
                  protoStats.getIsIndel(),
                  protoStats.getCasesPercentDominant(),
                  protoStats.getControlsPercentDominant(),
                  protoStats.getCasesPercentRecessive(),
                  protoStats.getControlsPercentRecessive());
          variant.setStats(variantStats);
        }

        if (includeEffects) {
          QueryResult<VariantEffect> queryEffects = getEffectsByVariant(variant, options);
          variant.setEffect(queryEffects.getResult());
        }

        results.add(variant);
      }
    } catch (IOException e) {
      System.err.println(e.getClass().getName() + ": " + e.getMessage());
    }
    queryResult.setResult(results);
    queryResult.setNumResults(results.size());
    end = System.currentTimeMillis();
    queryResult.setTime(end - start);
    return queryResult;
  }
  public List<Variant> getRecordSimpleStats(
      String study, int missing_gt, float maf, String maf_allele) {
    BasicDBObject compare =
        new BasicDBObject("studies.stats.allele_maf", maf_allele)
            .append("studies.stats.MAF", maf)
            .append("studies.stats.missing", missing_gt);
    List<Get> hbaseQuery = new ArrayList<>();
    DBCollection collection = db.getCollection("variants");
    Iterator<DBObject> result = collection.find(compare);
    String chromosome = new String();
    while (result.hasNext()) {
      DBObject variant = result.next();
      String position = variant.get("_id").toString();
      // hbase query construction
      Get get = new Get(position.getBytes());
      hbaseQuery.add(get);
    }
    // Complete results, from HBase

    tableName = study;
    effectTableName = tableName + "effect";
    Map<String, Variant> resultsMap = new HashMap<>();

    try {
      HTable table = new HTable(admin.getConfiguration(), tableName);
      HTable effectTable = new HTable(admin.getConfiguration(), effectTableName);
      Result[] hbaseResultEffect = effectTable.get(hbaseQuery);
      Result[] hbaseResultStats = table.get(hbaseQuery);

      //            List<Variant> results = new LinkedList<>();
      for (Result r : hbaseResultStats) {
        String position = new String(r.getRow(), CHARSET_UTF_8);
        String[] aux = position.split("_");
        String inner_position = aux[1];
        String chr = aux[0];
        // position parsing
        if (chr.startsWith("0")) {
          chr = chr.substring(1);
        }
        while (inner_position.startsWith("0")) {
          inner_position = inner_position.substring(1);
        }
        List<VariantFieldsProtos.VariantSample> samples = new LinkedList<>();
        NavigableMap<byte[], byte[]> infoMap = r.getFamilyMap("i".getBytes());
        byte[] byteStats = infoMap.get((study + "_stats").getBytes());
        VariantFieldsProtos.VariantStats stats =
            VariantFieldsProtos.VariantStats.parseFrom(byteStats);
        byte[] byteInfo = infoMap.get((study + "_data").getBytes());
        VariantFieldsProtos.VariantInfo info = VariantFieldsProtos.VariantInfo.parseFrom(byteInfo);
        String alternate = StringUtils.join(info.getAlternateList(), ", ");
        String reference = info.getReference();
        Variant partialResult =
            new Variant(
                chr,
                Integer.parseInt(inner_position),
                Integer.parseInt(inner_position),
                reference,
                alternate);
        String format = StringUtils.join(info.getFormatList(), ":");
        NavigableMap<byte[], byte[]> sampleMap = r.getFamilyMap("d".getBytes());
        Map<String, Map<String, String>> resultSampleMap = new HashMap<>();
        //                StringBuilder sampleRaw = new StringBuilder();
        for (byte[] s : sampleMap.keySet()) {
          String qual = (new String(s, CHARSET_UTF_8)).replaceAll(study + "_", "");
          VariantFieldsProtos.VariantSample sample =
              VariantFieldsProtos.VariantSample.parseFrom(sampleMap.get(s));
          String sample1 = sample.getSample();
          String[] values = sample1.split(":");
          String[] fields = format.split(":");
          Map<String, String> singleSampleMap = new HashMap<>();
          for (int i = 0; i < fields.length; i++) {
            singleSampleMap.put(fields[i], values[i]);
          }
          resultSampleMap.put(qual, singleSampleMap);
        }
        VariantStats variantStats =
            new VariantStats(
                chromosome,
                Integer.parseInt(inner_position),
                reference,
                alternate,
                stats.getMaf(),
                stats.getMgf(),
                stats.getMafAllele(),
                stats.getMgfGenotype(),
                stats.getMissingAlleles(),
                stats.getMissingGenotypes(),
                stats.getMendelianErrors(),
                stats.getIsIndel(),
                stats.getCasesPercentDominant(),
                stats.getControlsPercentDominant(),
                stats.getCasesPercentRecessive(),
                stats.getControlsPercentRecessive());
        partialResult.setStats(variantStats);
        resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
      }

      for (Result r : hbaseResultEffect) {
        if (!r.isEmpty()) {
          NavigableMap<byte[], byte[]> effectMap = r.getFamilyMap("e".getBytes());
          Variant partialResult = resultsMap.get(new String(r.getRow(), CHARSET_UTF_8));
          System.out.println("Recuperado " + partialResult.toString());
          String s = partialResult.getReference() + "_" + partialResult.getAlternate();
          VariantEffectProtos.EffectInfo effectInfo =
              VariantEffectProtos.EffectInfo.parseFrom(effectMap.get(s.getBytes()));
          VariantEffect variantEffect =
              new VariantEffect(
                  partialResult.getChromosome(),
                  (int) partialResult.getStart(),
                  partialResult.getReference(),
                  partialResult.getAlternate(),
                  effectInfo.getFeatureId(),
                  effectInfo.getFeatureName(),
                  effectInfo.getFeatureType(),
                  effectInfo.getFeatureBiotype(),
                  effectInfo.getFeatureChromosome(),
                  effectInfo.getFeatureStart(),
                  effectInfo.getFeatureEnd(),
                  effectInfo.getFeatureStrand(),
                  effectInfo.getSnpId(),
                  effectInfo.getAncestral(),
                  effectInfo.getAlternative(),
                  effectInfo.getGeneId(),
                  effectInfo.getTranscriptId(),
                  effectInfo.getGeneName(),
                  effectInfo.getConsequenceType(),
                  effectInfo.getConsequenceTypeObo(),
                  effectInfo.getConsequenceTypeDesc(),
                  effectInfo.getConsequenceTypeType(),
                  effectInfo.getAaPosition(),
                  effectInfo.getAminoacidChange(),
                  effectInfo.getCodonChange());
          resultsMap.put(new String(r.getRow(), CHARSET_UTF_8), partialResult);
        }
      }
    } catch (InvalidProtocolBufferException e) {
      System.err.println(e.getClass().getName() + ": " + e.getMessage());
    } catch (IOException e) {
      System.err.println(e.getClass().getName() + ": " + e.getMessage());
    }

    List<Variant> results = new ArrayList<>(resultsMap.values());
    return results;
  }
Beispiel #13
0
 @Override
 public List<ITEM> findEquals(KEY key) {
   key = getKey(key);
   return list(navigableMap.get(key));
 }