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;
}
@Override
public List<ITEM> findEquals(KEY key) {
key = getKey(key);
return list(navigableMap.get(key));
}
