下面列出了org.apache.commons.lang3.tuple.Triple#getLeft ( ) 实例代码，或者点击链接到github查看源代码，也可以在右侧发表评论。
private SqlgVertex internalStreamVertex(Object... keyValues) {
Preconditions.checkState(this.sqlDialect.supportsStreamingBatchMode(), "Streaming batch mode is not supported.");
final String label = ElementHelper.getLabelValue(keyValues).orElse(Vertex.DEFAULT_LABEL);
SchemaTable schemaTablePair = SchemaTable.from(this, label);
SchemaTable streamingBatchModeVertexSchemaTable = this.tx().getBatchManager().getStreamingBatchModeVertexSchemaTable();
if (streamingBatchModeVertexSchemaTable != null && !streamingBatchModeVertexSchemaTable.toString().equals(schemaTablePair.toString())) {
throw new IllegalStateException("Streaming batch mode must occur for one label at a time. Expected \"" + streamingBatchModeVertexSchemaTable + "\" found \"" + label + "\". First commit the transaction or call SqlgGraph.flush() before streaming a different label");
}
List<String> keys = this.tx().getBatchManager().getStreamingBatchModeVertexKeys();
Triple<Map<String, PropertyType>, Map<String, Object>, Map<String, Object>> keyValueMapTriple = SqlgUtil.validateVertexKeysValues(this.sqlDialect, keyValues, keys);
final Pair<Map<String, Object>, Map<String, Object>> keyValueMapPair = Pair.of(keyValueMapTriple.getMiddle(), keyValueMapTriple.getRight());
final Map<String, PropertyType> columns = keyValueMapTriple.getLeft();
this.tx().readWrite();
this.getTopology().ensureVertexLabelExist(schemaTablePair.getSchema(), schemaTablePair.getTable(), columns);
return new SqlgVertex(this, false, true, schemaTablePair.getSchema(), schemaTablePair.getTable(), keyValueMapPair);
}
AesCbcHmacSha2Encryptor(String name, byte[] key, byte[] iv, byte[] authenticationData, Provider provider) throws InvalidKeyException, NoSuchAlgorithmException, NoSuchPaddingException, InvalidAlgorithmParameterException {
// Split the key to get the AES key, the HMAC key and the HMAC
// object
Triple<byte[], byte[], Mac> parameters = GetAlgorithmParameters(name, key);
// Save the MAC provider and key
_hmac = parameters.getRight();
_hmac_key = parameters.getMiddle();
// Create the AES encryptor
_inner = new AesCbc.AesCbcEncryptor(parameters.getLeft(), iv, provider);
_aad_length = toBigEndian(authenticationData.length * 8);
// Prime the hash.
_hmac.update(authenticationData);
_hmac.update(iv);
}
@Override
public void migrateConfig(List<Triple<Character, String, String>> oldConfig){
for(Triple<Character, String, String> entry:oldConfig){
if (entry.getLeft() == 'B'){
BooleanValue value;
switch(entry.getMiddle()){
case "disableMod": value = ClientSettings.disableMod; break;
case "enableDoubleTap": value = ClientSettings.enableDoubleTap; break;
case "enableAllDirs": value = ClientSettings.enableAllDirs; break;
case "flyOnGround": value = ClientSettings.flyOnGround; break;
default: continue;
}
BetterSprintingMod.config.set(value, entry.getRight().equalsIgnoreCase("true"));
}
else if (entry.getLeft() == 'I' && entry.getMiddle().equals("flySpeedBoost")){
BetterSprintingMod.config.set(ClientSettings.flySpeedBoost, Integer.parseInt(entry.getRight()));
}
else if (entry.getLeft() == 'S' && entry.getMiddle().equals("sprintKeyMode") && entry.getRight().equals("HOLD")){
BetterSprintingMod.config.set(ClientSettings.sprintKeyMode, SprintKeyMode.HOLD);
}
}
}
@Override
public void migrateConfig(List<Triple<Character, String, String>> oldConfig){
for(Triple<Character, String, String> entry:oldConfig){
if (entry.getLeft() == 'B'){
BooleanValue value;
switch(entry.getMiddle()){
case "disableClientMod": value = ServerSettings.disableClientMod; break;
case "enableSurvivalFlyBoost": value = ServerSettings.enableSurvivalFlyBoost; break;
case "enableAllDirs": value = ServerSettings.enableAllDirs; break;
default: continue;
}
BetterSprintingMod.config.set(value, entry.getRight().equalsIgnoreCase("true"));
}
}
}
@Override
public void writeToParcel(Parcel dest, int flags) {
dest.writeInt(initPosition);
dest.writeInt(shouldWaitForPageLoaded ? 1 : 0);
dest.writeInt(attachments.size());
for (Triple<AttachmentModel, String, String> tuple : attachments) {
AttachmentModel attachment = tuple.getLeft();
dest.writeInt(attachment.type);
dest.writeInt(attachment.size);
dest.writeString(attachment.thumbnail);
dest.writeString(attachment.path);
dest.writeInt(attachment.width);
dest.writeInt(attachment.height);
dest.writeString(attachment.originalName);
dest.writeInt(attachment.isSpoiler ? 1 : 0);
dest.writeString(tuple.getMiddle());
dest.writeString(tuple.getRight());
}
}
@Override
public Vertex addVertex(Object... keyValues) {
if (this.tx().isInStreamingBatchMode()) {
throw SqlgExceptions.invalidMode(String.format("Transaction is in %s, use streamVertex(Object ... keyValues)", this.tx().getBatchModeType().toString()));
}
if (this.tx().isInStreamingWithLockBatchMode()) {
return internalStreamVertex(keyValues);
} else {
Triple<Map<String, PropertyType>, Map<String, Object>, Map<String, Object>> keyValueMapTriple = SqlgUtil.validateVertexKeysValues(this.sqlDialect, keyValues);
final Pair<Map<String, Object>, Map<String, Object>> keyValueMapPair = Pair.of(keyValueMapTriple.getMiddle(), keyValueMapTriple.getRight());
final Map<String, PropertyType> columns = keyValueMapTriple.getLeft();
final String label = ElementHelper.getLabelValue(keyValues).orElse(Vertex.DEFAULT_LABEL);
SchemaTable schemaTablePair = SchemaTable.from(this, label);
this.tx().readWrite();
this.getTopology().threadWriteLock();
VertexLabel vertexLabel = this.getTopology().ensureVertexLabelExist(schemaTablePair.getSchema(), schemaTablePair.getTable(), columns);
if (!vertexLabel.hasIDPrimaryKey()) {
Preconditions.checkArgument(columns.keySet().containsAll(vertexLabel.getIdentifiers()), "identifiers must be present %s", vertexLabel.getIdentifiers());
}
return new SqlgVertex(this, false, false, schemaTablePair.getSchema(), schemaTablePair.getTable(), keyValueMapPair);
}
}
/**
* Get the detailed pages under this group
*/
public static ArrayList<String> groupToPages(Triple<String, GoogleWebmasterFilter.FilterOperator, UrlTrieNode> group) {
ArrayList<String> ret = new ArrayList<>();
if (group.getMiddle().equals(GoogleWebmasterFilter.FilterOperator.EQUALS)) {
if (group.getRight().isExist()) {
ret.add(group.getLeft());
}
} else if (group.getMiddle().equals(GoogleWebmasterFilter.FilterOperator.CONTAINS)) {
UrlTrie trie = new UrlTrie(group.getLeft(), group.getRight());
Iterator<Pair<String, UrlTrieNode>> iterator = new UrlTriePostOrderIterator(trie, 1);
while (iterator.hasNext()) {
Pair<String, UrlTrieNode> next = iterator.next();
if (next.getRight().isExist()) {
ret.add(next.getLeft());
}
}
}
return ret;
}
private TicketReservationDescriptor toReservationDescriptor(String reservationId, Triple<TicketReservation, List<Ticket>, Event> triple) {
List<SerializablePair<TicketCategory, List<Ticket>>> tickets = triple.getMiddle().stream().collect(Collectors.groupingBy(Ticket::getCategoryId)).entrySet().stream()
.map(entry -> SerializablePair.of(eventManager.getTicketCategoryById(entry.getKey(), triple.getRight().getId()), entry.getValue()))
.collect(Collectors.toList());
TicketReservation reservation = triple.getLeft();
return new TicketReservationDescriptor(reservation,
ticketReservationManager.loadAdditionalInfo(reservationId),
ticketReservationManager.orderSummaryForReservationId(reservationId, triple.getRight()), tickets);
}
private List<GrpcService> buildQueryResponse(Set<String> queryCondition, Boolean accurate) {
List<GrpcService> services = Lists.newArrayList();
Map<String, Pair<Set<GrpcHost>, Set<GrpcHost>>> servicesPassing = registryRepository.getAllPassingService();
for (Iterator<String> it = queryCondition.iterator(); it.hasNext();) {
String serviceKey = it.next();
Triple<String, String, String> appNameServiceVersion = getAppNameServiceVersion(serviceKey);
Pair<Set<GrpcHost>, Set<GrpcHost>> providerConsumer = servicesPassing.get(serviceKey);
GrpcService service = new GrpcService(appNameServiceVersion.getLeft(), appNameServiceVersion.getRight(),
appNameServiceVersion.getMiddle());
service.setProviderHost(providerConsumer.getLeft());
service.setConsumerHost(providerConsumer.getRight());
services.add(service);
}
return services;
}
private List<AltSiteRecord> createDesignMatrixOfSingleContext(final Triple<String, Nucleotide, ReadOrientation> transition,
final int refDepth, final int altDepth,
final int refF1R2, final int altF1R2,
final int numExamples) {
final List<AltSiteRecord> altDesignMatrix = new ArrayList<>(numExamples);
final String refContext = transition.getLeft();
final Nucleotide altAllele = transition.getMiddle();
IntStream.range(0, numExamples).forEach(i ->
altDesignMatrix.add(new AltSiteRecord(refContext, refDepth, altDepth, refF1R2, altF1R2, altAllele)));
return altDesignMatrix;
}
@Override
public Map<String, PrimitiveTypeProvider> convert(Triple<String, String, String> data) {
final HashMap<String, PrimitiveTypeProvider> map = new HashMap<>(2);
String id = "v_" + data.getLeft() + "_" + data.getMiddle();
map.put(SimpleFulltextFeatureDescriptor.FIELDNAMES[0], PrimitiveTypeProvider.fromObject(id));
map.put(SimpleFulltextFeatureDescriptor.FIELDNAMES[1], PrimitiveTypeProvider.fromObject(data.getRight()));
return map;
}
private void onItemBroken(PlayerEntity player, ItemStack stack)
{
int scrappingLevel = EnchantmentHelper.getEnchantmentLevel(SurvivalistMod.SCRAPING.get(), stack);
if (player.getClass().getName().equals("com.rwtema.extrautils2.fakeplayer.XUFakePlayer"))
return;
boolean fortune = rnd.nextDouble() > 0.9 / (1 + scrappingLevel);
ItemStack ret = null;
for (Triple<ItemStack, ItemStack, ItemStack> scraping : scrapingRegistry)
{
ItemStack source = scraping.getLeft();
if (source.getItem() != stack.getItem())
continue;
ItemStack good = scraping.getMiddle();
ItemStack bad = scraping.getRight();
ret = fortune ? good.copy() : bad.copy();
break;
}
if (ret != null)
{
SurvivalistMod.LOGGER.debug("Item broke (" + stack + ") and the player got " + ret + " in return!");
SurvivalistMod.channel.sendTo(new ScrapingMessage(stack, ret), ((ServerPlayerEntity) player).connection.netManager, NetworkDirection.PLAY_TO_CLIENT);
ItemHandlerHelper.giveItemToPlayer(player, ret);
}
}
public int getParcelSize() {
int total = 12;
for (Triple<AttachmentModel, String, String> tuple : attachments) {
total += 40;
AttachmentModel attachment = tuple.getLeft();
String hash = tuple.getMiddle();
String post = tuple.getRight();
if (attachment.thumbnail != null) total += attachment.thumbnail.length()*2;
if (attachment.path != null) total += attachment.path.length()*2;
if (attachment.originalName != null) total += attachment.originalName.length()*2;
if (hash != null) total += hash.length()*2;
if (post != null) total += post.length()*2;
}
return total;
}
private static int findTab(List<Triple<String, String, String>> list, String tabUrl, String tabTitle) {
for (int i=0; i<list.size(); ++i) {
Triple<String, String, String> triple = list.get(i);
if (tabUrl == null) {
if (triple.getLeft() == null && tabTitle.equals(triple.getRight())) {
return i;
}
} else {
if (tabUrl.equals(triple.getLeft())) {
return i;
}
}
}
return -1;
}
private Edge addEdgeInternal(boolean complete, String label, Vertex inVertex, Object... keyValues) {
if (null == inVertex) throw Graph.Exceptions.argumentCanNotBeNull("vertex");
if (this.removed) {
throw new IllegalStateException(String.format("Vertex with id %s was removed.", id().toString()));
}
ElementHelper.validateLabel(label);
Preconditions.checkArgument(!label.contains("."), String.format("Edge label may not contain a '.' , the edge will be stored in the schema of the owning vertex. label = %s", label));
ElementHelper.legalPropertyKeyValueArray(keyValues);
if (ElementHelper.getIdValue(keyValues).isPresent())
throw Edge.Exceptions.userSuppliedIdsNotSupported();
List<String> previousBatchModeKeys;
if (complete) {
previousBatchModeKeys = this.sqlgGraph.tx().getBatchManager().getStreamingBatchModeEdgeKeys();
} else {
previousBatchModeKeys = Collections.emptyList();
}
Triple<Map<String, PropertyType>, Map<String, Object>, Map<String, Object>> keyValueMapTriple = SqlgUtil.validateVertexKeysValues(this.sqlgGraph.getSqlDialect(), keyValues, previousBatchModeKeys);
if (!complete && keyValueMapTriple.getRight().size() != keyValueMapTriple.getMiddle().size()) {
throw Property.Exceptions.propertyValueCanNotBeNull();
}
final Pair<Map<String, Object>, Map<String, Object>> keyValueMapPair = Pair.of(keyValueMapTriple.getMiddle(), keyValueMapTriple.getRight());
final Map<String, PropertyType> columns = keyValueMapTriple.getLeft();
Optional<VertexLabel> outVertexLabelOptional = this.sqlgGraph.getTopology().getVertexLabel(this.schema, this.table);
Optional<VertexLabel> inVertexLabelOptional = this.sqlgGraph.getTopology().getVertexLabel(((SqlgVertex) inVertex).schema, ((SqlgVertex) inVertex).table);
Preconditions.checkState(outVertexLabelOptional.isPresent(), "Out VertexLabel must be present. Not found for %s", this.schema + "." + this.table);
Preconditions.checkState(inVertexLabelOptional.isPresent(), "In VertexLabel must be present. Not found for %s", ((SqlgVertex) inVertex).schema + "." + ((SqlgVertex) inVertex).table);
this.sqlgGraph.getTopology().threadWriteLock();
//noinspection OptionalGetWithoutIsPresent
EdgeLabel edgeLabel = this.sqlgGraph.getTopology().ensureEdgeLabelExist(label, outVertexLabelOptional.get(), inVertexLabelOptional.get(), columns);
if (!edgeLabel.hasIDPrimaryKey()) {
Preconditions.checkArgument(columns.keySet().containsAll(edgeLabel.getIdentifiers()), "identifiers must be present %s", edgeLabel.getIdentifiers());
}
return new SqlgEdge(this.sqlgGraph, complete, this.schema, label, (SqlgVertex) inVertex, this, keyValueMapPair);
}
private Triple<ValidationResult, Event, Ticket> assignTicket(UpdateTicketOwnerForm updateTicketOwner,
Optional<Errors> bindingResult,
Locale fallbackLocale,
Optional<UserDetails> userDetails,
Triple<Event, TicketReservation, Ticket> result,
String formPrefix) {
Ticket t = result.getRight();
final Event event = result.getLeft();
if(t.getLockedAssignment()) {
//in case of locked assignment, fullName and Email will be overwritten
updateTicketOwner.setFirstName(t.getFirstName());
updateTicketOwner.setLastName(t.getLastName());
updateTicketOwner.setFullName(t.getFullName());
updateTicketOwner.setEmail(t.getEmail());
}
final TicketReservation ticketReservation = result.getMiddle();
List<TicketFieldConfiguration> fieldConf = ticketFieldRepository.findAdditionalFieldsForEvent(event.getId());
var sameCountryValidator = new SameCountryValidator(configurationManager, extensionManager, event, ticketReservation.getId(), vatChecker);
AdvancedTicketAssignmentValidator advancedValidator = new AdvancedTicketAssignmentValidator(sameCountryValidator,
new GroupManager.WhitelistValidator(event.getId(), groupManager));
var additionalServiceIds = new HashSet<>(additionalServiceItemRepository.findAdditionalServiceIdsByReservationUuid(t.getTicketsReservationId()));
var ticketFieldFilterer = new Validator.TicketFieldsFilterer(fieldConf, ticketUUID -> t.getCategoryId(), additionalServiceIds, ticketRepository.findFirstTicketInReservation(t.getTicketsReservationId()));
Validator.AdvancedValidationContext context = new Validator.AdvancedValidationContext(updateTicketOwner, fieldConf, t.getCategoryId(), t.getUuid(), formPrefix);
ValidationResult validationResult = Validator.validateTicketAssignment(updateTicketOwner, ticketFieldFilterer.getFieldsForTicket(t.getUuid()), bindingResult, event, formPrefix, sameCountryValidator)
.or(Validator.performAdvancedValidation(advancedValidator, context, bindingResult.orElse(null)))
.ifSuccess(() -> updateTicketOwner(updateTicketOwner, fallbackLocale, t, event, ticketReservation, userDetails));
return Triple.of(validationResult, event, ticketRepository.findByUUID(t.getUuid()));
}
public void setupNotificationChannels() {
if (SDK_INT >= android.os.Build.VERSION_CODES.O) {
// Each triple contains the channel ID, name, and importance level
List<Triple<String, String, Integer>> notificationTripleList =
new ArrayList<Triple<String, String, Integer>>() {{
add(Triple.of(CHANNEL_IMG, "Image downloads",
NotificationManager.IMPORTANCE_LOW));
add(Triple.of(CHANNEL_COMMENT_CACHE, "Comment caching",
NotificationManager.IMPORTANCE_LOW));
add(Triple.of(CHANNEL_MAIL, "Reddit mail",
NotificationManager.IMPORTANCE_HIGH));
add(Triple.of(CHANNEL_MODMAIL, "Reddit modmail",
NotificationManager.IMPORTANCE_HIGH));
add(Triple.of(CHANNEL_SUBCHECKING, "Submission post checking",
NotificationManager.IMPORTANCE_LOW));
}};
NotificationManager notificationManager =
(NotificationManager) getSystemService(Context.NOTIFICATION_SERVICE);
for (Triple<String, String, Integer> notificationTriple : notificationTripleList) {
NotificationChannel notificationChannel =
new NotificationChannel(notificationTriple.getLeft(),
notificationTriple.getMiddle(), notificationTriple.getRight());
notificationChannel.enableLights(true);
notificationChannel.setShowBadge(
notificationTriple.getRight() == NotificationManager.IMPORTANCE_HIGH);
notificationChannel.setLightColor(
notificationTriple.getLeft().contains("MODMAIL") ? getResources().getColor(
R.color.md_red_500, null) : Palette.getColor(""));
if (notificationManager != null) {
notificationManager.createNotificationChannel(notificationChannel);
}
}
}
}
@Override
public TemplateRenderer buildRenderer(CodeTemplatePO templatePO) {
Triple<Configuration, Integer, String> triple = freeMarkerConfigFactory.getConfigurationTriple(templatePO);
FreeMarkerRenderer renderer = new FreeMarkerRenderer(triple.getLeft(), triple.getRight());
return renderer;
}
private void extractProperty(String schema, String table, String columnName, Integer columnType, String typeName, Map<String, PropertyType> columns, ListIterator<Triple<String, Integer, String>> metaDataIter) {
//check for ZONEDDATETIME, PERIOD, DURATION as they use more than one field to represent the type
PropertyType propertyType = null;
if (metaDataIter.hasNext()) {
Triple<String, Integer, String> column2MetaData = metaDataIter.next();
String column2Name = column2MetaData.getLeft();
String typeName2 = column2MetaData.getRight();
int column2Type = column2MetaData.getMiddle();
if (column2Name.startsWith(columnName + "~~~")) {
if (column2Type == Types.VARCHAR) {
propertyType = PropertyType.ZONEDDATETIME;
} else if ((column2Type == Types.ARRAY && this.sqlDialect.sqlArrayTypeNameToPropertyType(typeName2, this.sqlgGraph, schema, table, column2Name, metaDataIter) == PropertyType.STRING_ARRAY)) {
propertyType = PropertyType.ZONEDDATETIME_ARRAY;
} else {
if (metaDataIter.hasNext()) {
Triple<String, Integer, String> column3MetaData = metaDataIter.next();
String column3Name = column3MetaData.getLeft();
String typeName3 = column3MetaData.getRight();
int column3Type = column3MetaData.getMiddle();
if (column3Name.startsWith(columnName + "~~~")) {
if (column3Type == Types.ARRAY) {
Preconditions.checkState(sqlDialect.sqlArrayTypeNameToPropertyType(typeName3, this.sqlgGraph, schema, table, column3Name, metaDataIter) == PropertyType.INTEGER_ARRAY, "Only Period have a third column and it must be a Integer");
propertyType = PropertyType.PERIOD_ARRAY;
} else {
Preconditions.checkState(column3Type == Types.INTEGER, "Only Period have a third column and it must be a Integer");
propertyType = PropertyType.PERIOD;
}
} else {
metaDataIter.previous();
if (column2Type == Types.ARRAY) {
Preconditions.checkState(sqlDialect.sqlArrayTypeNameToPropertyType(typeName2, this.sqlgGraph, schema, table, column2Name, metaDataIter) == PropertyType.INTEGER_ARRAY, "Only Period have a third column and it must be a Integer");
propertyType = PropertyType.DURATION_ARRAY;
} else {
Preconditions.checkState(column2Type == Types.INTEGER, "Only Duration and Period have a second column and it must be a Integer");
propertyType = PropertyType.DURATION;
}
}
}
}
} else {
metaDataIter.previous();
}
}
if (propertyType == null) {
propertyType = this.sqlDialect.sqlTypeToPropertyType(this.sqlgGraph, schema, table, columnName, columnType, typeName, metaDataIter);
}
columns.put(columnName, propertyType);
}
/**
* Test that the tool sites of orientation bias that are manually picked out.
* Also tests scattering CollectF1R2Counts
*/
@Test(dataProvider = "scatterCounts")
public void testOnRealBam(final int scatterCount) throws IOException {
final File scatteredDir = createTempDir("scattered");
// Step 1: SplitIntervals
final File intervalDir = createTempDir("intervals");
final ArgumentsBuilder splitIntervalsArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addIntervals(new File(intervalList))
.addOutput(intervalDir)
.add(SplitIntervals.SCATTER_COUNT_SHORT_NAME, scatterCount);
runCommandLine(splitIntervalsArgs, SplitIntervals.class.getSimpleName());
// Step 2: CollectF1R2Counts
final File[] intervals = intervalDir.listFiles();
final List<File> extractedDirs = IntStream.range(0, intervals.length).mapToObj(i -> createTempDir("extracted_" + i)).collect(Collectors.toList());
final List<File> scatteredTarGzs = IntStream.range(0, intervals.length).mapToObj(i -> new File(scatteredDir, "scatter_" + i + ".tar.gz")).collect(Collectors.toList());
for (int i = 0; i < intervals.length; i++){
final ArgumentsBuilder collectF1R2CountsArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addIntervals(intervals[i])
.addOutput(scatteredTarGzs.get(i));
runCommandLine(collectF1R2CountsArgs, CollectF1R2Counts.class.getSimpleName());
IOUtils.extractTarGz(scatteredTarGzs.get(i).toPath(), extractedDirs.get(i).toPath());
final File refHist = F1R2CountsCollector.getRefHistogramsFromExtractedTar(extractedDirs.get(i)).get(0);
// Ensure that we print every bin, even when the count is 0
final int lineCount = (int) Files.lines(Paths.get(refHist.getAbsolutePath())).filter(l -> l.matches("^[0-9].+")).count();
Assert.assertEquals(lineCount, F1R2FilterConstants.DEFAULT_MAX_DEPTH);
}
// Step 3: LearnReadOrientationModel
final File priorTarGz = createTempFile("prior", ".tar.gz");
final ArgumentsBuilder args = new ArgumentsBuilder()
.addOutput(priorTarGz);
IntStream.range(0, intervals.length).forEach(n -> args.addInput(scatteredTarGzs.get(n)));
runCommandLine(args.getArgsList(), LearnReadOrientationModel.class.getSimpleName());
final File extractedPriorDir = createTempDir("extracted_priors");
IOUtils.extractTarGz(priorTarGz.toPath(), extractedPriorDir.toPath());
final ArtifactPriorCollection artifactPriorCollection = ArtifactPriorCollection.readArtifactPriors(extractedPriorDir.listFiles()[0]);
// Step 4: Mutect 2
final File unfilteredVcf = GATKBaseTest.createTempFile("unfiltered", ".vcf");
final File filteredVcf = GATKBaseTest.createTempFile("filtered", ".vcf");
final File bamout = GATKBaseTest.createTempFile("SM-CEMAH", ".bam");
final ArgumentsBuilder mutect2Args = new ArgumentsBuilder()
.addReference(b37Reference)
.addInput(new File(hapmapBamSnippet))
.addOutput(unfilteredVcf)
.add(AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, bamout);
runCommandLine(mutect2Args, Mutect2.class.getSimpleName());
final ArgumentsBuilder filterArgs = new ArgumentsBuilder()
.addReference(b37Reference)
.addVCF(unfilteredVcf)
.add(M2FiltersArgumentCollection.ARTIFACT_PRIOR_TABLE_NAME, priorTarGz)
.addOutput(filteredVcf);
runCommandLine(filterArgs, FilterMutectCalls.class.getSimpleName());
// These artifacts have been verified manually
// The pair is of type (Position, Expected Source of Prior Probability)
// Prior for e.g. TGA->A F2R1 should come from TCA->T F1R2
final List<Triple<Integer, ReadOrientation, ArtifactState>> knownArtifacts = Arrays.asList(
new ImmutableTriple<>(23421079, ReadOrientation.F2R1, ArtifactState.F2R1_G), // CAC->G F2R1
new ImmutableTriple<>(34144749, ReadOrientation.F2R1, ArtifactState.F2R1_A), // TGA->A F2R1, ref context is not canonical
new ImmutableTriple<>(62165528, ReadOrientation.F1R2, ArtifactState.F1R2_A)); // CGC->A F1R2
for (final Triple<Integer, ReadOrientation, ArtifactState> artifact : knownArtifacts) {
final int position = artifact.getLeft();
Optional<VariantContext> variant = StreamSupport.stream(new FeatureDataSource<VariantContext>(filteredVcf).spliterator(), false)
.filter(vc -> vc.getStart() == position).findFirst();
Assert.assertTrue(variant.isPresent());
// Check that the expected filters were applied
Assert.assertTrue(variant.get().getFilters().contains(GATKVCFConstants.READ_ORIENTATION_ARTIFACT_FILTER_NAME));
}
}