本文整理汇总了Java中com.google.genomics.v1.ReadGroupSet类的典型用法代码示例。如果您正苦于以下问题:Java ReadGroupSet类的具体用法?Java ReadGroupSet怎么用?Java ReadGroupSet使用的例子?那么, 这里精选的类代码示例或许可以为您提供帮助。
ReadGroupSet类属于com.google.genomics.v1包,在下文中一共展示了ReadGroupSet类的6个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: getReferences
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
private static List<ReferenceInfo> getReferences(Channel channel, ReadGroupSet readGroupSet) {
Set<String> referenceSetIds = Sets.newHashSet();
if (readGroupSet.getReferenceSetId() != null && !readGroupSet.getReferenceSetId().isEmpty()) {
LOG.fine("Found reference set from read group set " +
readGroupSet.getReferenceSetId());
referenceSetIds.add(readGroupSet.getReferenceSetId());
}
if (readGroupSet.getReadGroupsCount() > 0) {
LOG.fine("Found read groups");
for (ReadGroup readGroup : readGroupSet.getReadGroupsList()) {
if (readGroup.getReferenceSetId() != null && !readGroup.getReferenceSetId().isEmpty()) {
LOG.fine("Found reference set from read group: " +
readGroup.getReferenceSetId());
referenceSetIds.add(readGroup.getReferenceSetId());
}
}
}
ReferenceServiceV1BlockingStub referenceSetStub =
ReferenceServiceV1Grpc.newBlockingStub(channel);
List<ReferenceInfo> references = Lists.newArrayList();
for (String referenceSetId : referenceSetIds) {
LOG.fine("Getting reference set " + referenceSetId);
GetReferenceSetRequest getReferenceSetRequest = GetReferenceSetRequest
.newBuilder().setReferenceSetId(referenceSetId).build();
ReferenceSet referenceSet =
referenceSetStub.getReferenceSet(getReferenceSetRequest);
if (referenceSet == null || referenceSet.getReferenceIdsCount() == 0) {
continue;
}
for (String referenceId : referenceSet.getReferenceIdsList()) {
LOG.fine("Getting reference " + referenceId);
GetReferenceRequest getReferenceRequest = GetReferenceRequest
.newBuilder().setReferenceId(referenceId).build();
Reference reference = referenceSetStub.getReference(getReferenceRequest);
if (reference.getName() != null && !reference.getName().isEmpty()) {
references.add(new ReferenceInfo(reference, referenceSet));
LOG.fine("Adding reference " + reference.getName());
}
}
}
return references;
}
示例2: makeSAMRecord
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
public static final SAMRecord makeSAMRecord(Read read,
ReadGroupSet readGroupSet, List<Reference> references,
boolean forceSetMatePositionToThisPosition) {
return makeSAMRecord(read, makeSAMFileHeader(readGroupSet, references));
}
示例3: ReadIteratorResource
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
public ReadIteratorResource(ReadGroupSet readGroupSet, List<Reference> references,
UnmappedReads<Read> unmappedReads,
Iterable<Read> iterable) {
super(readGroupSet, references, unmappedReads, iterable,
new GenomicsConverter());
}
示例4: getReads
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
@Override
public ReadIteratorResource getReads(
String readsetId,
String sequenceName, int sequenceStart, int sequenceEnd)
throws IOException, GeneralSecurityException {
LOG.info("Getting readset from GRPC:" + readsetId + ", sequence " + sequenceName +
", start=" + sequenceStart + ", end=" + sequenceEnd);
final Channel channel = getChannel();
ReadServiceV1BlockingStub readStub = ReadServiceV1Grpc.newBlockingStub(channel);
GetReadGroupSetRequest getReadGroupSetRequest = GetReadGroupSetRequest
.newBuilder()
.setReadGroupSetId(readsetId)
.build();
ReadGroupSet readGroupSet = readStub.getReadGroupSet(getReadGroupSetRequest);
String datasetId = readGroupSet.getDatasetId();
LOG.info("Found readset " + readsetId + ", dataset " + datasetId);
final Map<String, Reference> references =
getReferences(readGroupSet);
final Reference reference = references.get(sequenceName);
if (reference != null) {
LOG.info("Reference for sequence name " + sequenceName + " is found, length="
+ String.valueOf(reference.getLength()));
} else {
LOG.warning("Reference for sequence name " + sequenceName + " not found");
}
LOG.info("Searching for reads in sequence " + sequenceName + " " +
String.valueOf(sequenceStart) + "-" + String.valueOf(sequenceEnd));
com.google.cloud.genomics.gatk.common.UnmappedReads<Read> unmappedReads = null;
if (sequenceName.isEmpty()) {
unmappedReads = getUnmappedMatesOfMappedReads(readsetId);
}
StreamingReadServiceBlockingStub streamingReadStub =
StreamingReadServiceGrpc.newBlockingStub(getChannel());
StreamReadsRequest.Builder streamReadsRequestBuilder = StreamReadsRequest.newBuilder()
.setReadGroupSetId(readsetId)
.setReferenceName(sequenceName);
if (sequenceStart != 0) {
streamReadsRequestBuilder.setStart(Long.valueOf(sequenceStart));
}
if (sequenceEnd != 0) {
streamReadsRequestBuilder.setEnd(Long.valueOf(sequenceEnd));
}
final StreamReadsRequest streamReadRequest = streamReadsRequestBuilder.build();
final Iterable<Read> reads = streamReadsResponseToReadsIterator(
streamingReadStub.streamReads(streamReadRequest), sequenceEnd);
return new ReadIteratorResource(readGroupSet,
Lists.newArrayList(references.values()), unmappedReads, reads);
}
示例5: getReferences
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
/**
* Collect a list of references mentioned in this Readgroupset and get their meta data.
* @throws GeneralSecurityException
* @throws IOException
*/
private Map<String, Reference> getReferences(ReadGroupSet readGroupSet)
throws IOException, GeneralSecurityException {
Set<String> referenceSetIds = Sets.newHashSet();
if (!Strings.isNullOrEmpty(readGroupSet.getReferenceSetId())) {
LOG.info("Found reference set from read group set " +
readGroupSet.getReferenceSetId());
referenceSetIds.add(readGroupSet.getReferenceSetId());
}
if (readGroupSet.getReadGroupsCount() > 0) {
LOG.info("Found read groups");
for (ReadGroup readGroup : readGroupSet.getReadGroupsList()) {
if (!Strings.isNullOrEmpty(readGroup.getReferenceSetId())) {
LOG.info("Found reference set from read group: " +
readGroup.getReferenceSetId());
referenceSetIds.add(readGroup.getReferenceSetId());
}
}
}
ReferenceServiceV1BlockingStub referenceSetStub =
ReferenceServiceV1Grpc.newBlockingStub(getChannel());
Map<String, Reference> references = Maps.newHashMap();
for (String referenceSetId : referenceSetIds) {
LOG.info("Getting reference set " + referenceSetId);
GetReferenceSetRequest getReferenceSetRequest = GetReferenceSetRequest
.newBuilder().setReferenceSetId(referenceSetId).build();
ReferenceSet referenceSet =
referenceSetStub.getReferenceSet(getReferenceSetRequest);
if (referenceSet == null || referenceSet.getReferenceIdsCount() == 0) {
continue;
}
for (String referenceId : referenceSet.getReferenceIdsList()) {
LOG.fine("Getting reference " + referenceId);
GetReferenceRequest getReferenceRequest = GetReferenceRequest
.newBuilder().setReferenceId(referenceId).build();
Reference reference = referenceSetStub.getReference(getReferenceRequest);
if (!Strings.isNullOrEmpty(reference.getName())) {
references.put(reference.getName(), reference);
LOG.fine("Adding reference " + reference.getName());
}
}
}
return references;
}
示例6: makeSAMFileHeader
import com.google.genomics.v1.ReadGroupSet; //导入依赖的package包/类
@Override
public SAMFileHeader makeSAMFileHeader(ReadGroupSet readGroupSet,
List<Reference> references) {
return ReadUtils.makeSAMFileHeader(readGroupSet, references);
}