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Searched refs:getReadName (Results 1 – 25 of 98) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/
H A DAbstractAlignmentMerger.java241 if (!rec.getReadName().equals(secondOfPair.getReadName())) in mergeAlignment()
242 …nd read from pair not found in unmapped bam: " + rec.getReadName() + ", " + secondOfPair.getReadNa… in mergeAlignment()
245 …throw new GATKException("First record in unmapped bam is not first of pair: " + rec.getReadName()); in mergeAlignment()
247 …KException("Second record in unmapped bam is not marked as paired: " + secondOfPair.getReadName()); in mergeAlignment()
249 …ATKException("Second record in unmapped bam is not second of pair: " + secondOfPair.getReadName()); in mergeAlignment()
255 if (nextAligned != null && rec.getReadName().equals(nextAligned.getReadName())) { in mergeAlignment()
336 … SAMRecordQueryNameComparator.compareReadNames(rec.getReadName(), nextAligned.getReadName()) > 0) { in mergeAlignment()
337 … throw new IllegalStateException("Aligned record iterator (" + nextAligned.getReadName() + in mergeAlignment()
338 ") is behind the unmapped reads (" + rec.getReadName() + ")"); in mergeAlignment()
352 …t(), () -> "Reads remaining on alignment iterator: " + alignedIterator.next().getReadName() + "!"); in mergeAlignment()
H A DSamAlignmentMerger.java226 final String readName = rec.getReadName();
284 … return (read1Iterator.peek().getReadName().compareTo(read2Iterator.peek().getReadName()) <= 0)
H A DHitsForInsert.java46 public String getReadName() { in getReadName() method in HitsForInsert
47 return getRepresentativeRead().getReadName(); in getReadName()
H A DMultiHitAlignedReadIterator.java91 final String readName = peekIterator.peek().getReadName(); in nextMaybeEmpty()
128 } while (peekIterator.hasNext() && peekIterator.peek().getReadName().equals(readName)); in nextMaybeEmpty()
/dports/biology/bamutil/bamUtil-1.0.15/src/
H A DBam2FastQ.cpp509 if(strcmp(prevRec->getReadName(), samRec.getReadName()) != 0) in handlePairedRN()
512 std::cerr << "Paired Read, " << prevRec->getReadName() in handlePairedRN()
531 std::cerr << "Both reads of " << samRec.getReadName() in handlePairedRN()
544 std::cerr << "Neither read of " << samRec.getReadName() in handlePairedRN()
589 std::cerr << "Paired Read, " << samRec.getReadName() in handlePairedCoord()
605 std::cerr << "Both reads of " << samRec.getReadName() in handlePairedCoord()
616 std::cerr << "Neither read of " << samRec.getReadName() in handlePairedCoord()
711 const char* readName = samRec.getReadName(); in writeFastQ()
787 std::cerr << "Paired Read, " << firstRec->getReadName() in cleanUpMateMap()
H A DMateMapByCoord.cpp37 const char* readName = record.getReadName(); in getMate()
65 if(strcmp(((*iter).second)->getReadName(), readName) == 0) in getMate()
H A DDiff.cpp476 (strcmp(rec1->getReadName(), in matchingRecs()
477 rec2->getReadName()) == 0)) in matchingRecs()
908 if(ifwrite(myDiffFile, record.getReadName(), nameLen) != nameLen) in writeReadName()
1005 (*mapPtr)[record.getReadName()] = myListUnmatched.insert(myListUnmatched.end(), &record); in addUnmatchedRecord()
1020 myUnmatchedFileIter = mapPtr->find(record.getReadName()); in removeFragmentMatch()
1053 mapPtr->erase(returnRec->getReadName()); in removeFirst()
H A DClipOverlap.cpp351 if(strcmp(samRecord->getReadName(), in handleSortedByReadName()
352 prevSamRecord->getReadName()) != 0) in handleSortedByReadName()
394 if(strcmp(samRecord->getReadName(), in handleSortedByReadName()
395 prevSamRecord->getReadName()) == 0) in handleSortedByReadName()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/validation/
H A DCompareBaseQualities.java151 if (!read1.getReadName().equals(read2.getReadName())){ in doWork()
153 read1.getReadName() + " vs " + read2.getReadName()); in doWork()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/exceptions/
H A DGATKException.java72 …In read %s @ %s attribute %s not of (or convertible to) type %s", read.getReadName(), "" + read.ge… in ReadAttributeTypeMismatch()
76 …of (or convertible to) type %s: class is '%s' and value is '%s'", read.getReadName(), "" + read.ge… in ReadAttributeTypeMismatch()
80 …In read %s @ %s attribute %s not of (or convertible to) type %s", read.getReadName(), "" + read.ge… in ReadAttributeTypeMismatch()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/
H A DSAMRecordComparator.java38 int cmp = pr1.sam.getReadName().compareTo(pr2.sam.getReadName()); in compare()
H A DSAMRecordList.java191 null : bamView.getHighlightSAMRecord().sam.getReadName()); in paintComponent()
198 if(highlightedSAMRecord != null && highlightedSAMRecord.equals(thisRead.getReadName())) in paintComponent()
206 thisRead.getReadName(), in paintComponent()
225 int thisWidth = thisRead.getReadName().length(); in getFormatString()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-sdk/ngs/inl/
H A DRead.hpp75 StringRef Read :: getReadName () const in getReadName() function in ngs::Read
77 { return StringRef ( self -> getReadName () ); } in getReadName()
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-sdk/ngs/inl/
H A DRead.hpp75 StringRef Read :: getReadName () const in getReadName() function in ngs::Read
77 { return StringRef ( self -> getReadName () ); } in getReadName()
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-sdk/ngs/inl/
H A DRead.hpp75 StringRef Read :: getReadName () const in getReadName() function in ngs::Read
77 { return StringRef ( self -> getReadName () ); } in getReadName()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DHeaderlessSAMRecordCoordinateComparator.java33 cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName()); in compare()
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/
H A DTestValidate.cpp103 assert(strcmp(samRecord.getReadName(), "1:1011:F:255+17M15D20M") == 0); in validateRead1()
223 assert(*varPtr == samRecord.getReadName()[i]); in validateRead1()
475 assert(*varPtr == samRecord.getReadName()[i]); in validateRead2()
625 assert(*varPtr == samRecord.getReadName()[i]); in validateRead3()
876 assert(*varPtr == samRecord.getReadName()[i]); in validateRead4()
1070 assert(*varPtr == samRecord.getReadName()[i]); in validateRead5()
1250 assert(*varPtr == samRecord.getReadName()[i]); in validateRead6()
1396 assert(*varPtr == samRecord.getReadName()[i]); in validateRead7()
1551 assert(*varPtr == samRecord.getReadName()[i]); in validateRead8()
1682 assert(*varPtr == samRecord.getReadName()[i]); in validateRead9()
[all …]
H A DValidationTest.cpp39 assert(strcmp(testRecord.getReadName(), "UNKNOWN") == 0); in testSamQNAME()
49 assert(strcmp(testRecord.getReadName(), qname) == 0); in testSamQNAME()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/align_worker_subtasks/
H A DBlastReadsSubTask.cpp149 taskLog.info(tr("%1 was skipped. No BLAST results.").arg(getReadName())); in onSubTaskFinished()
166 …Object.isNull(), setError(L10N::nullPointerError("MSA object for %1").arg(getReadName())), result); in onSubTaskFinished()
194 .arg(getReadName()) in onSubTaskFinished()
230 QString BlastAndSwReadTask::getReadName() const { in getReadName() function in U2::Workflow::BlastAndSwReadTask
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/htsjdk/samtools/
H A DSAMRecordSparkCodec.java113 alignment.getReadName() + "; read length: " + alignment.getReadLength() + in encode()
116 this.binaryCodec.writeString(alignment.getReadName(), false, true); in encode()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/
H A DAlignToReferenceBlastWorker.cpp189 readsNames.insert(read, getReadName(message)); in createTask()
239 QString AlignToReferenceBlastWorker::getReadName(const Message &message) const { in getReadName() function in U2::LocalWorkflow::AlignToReferenceBlastWorker
362 acceptedReads.append((QPair<QString, QPair<int, bool>>(subTask->getReadName(), pair))); in getAcceptedReads()
373 … discardedReads << QPair<QString, int>(subTask->getReadName(), subTask->getReadIdentity()); in getDiscardedReads()
/dports/biology/sra-tools/sra-tools-2.11.0/ngs/ngs-java/ngs/
H A DRead.java104 String getReadName () in getReadName() method
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-java/ngs/
H A DRead.java104 String getReadName () in getReadName() method
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-java/ngs/
H A DRead.java104 String getReadName () in getReadName() method
/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/
H A Dbam-priv.h116 static inline char const *getReadName(BAM_Alignment const *) __attribute__((always_inline));
187 static inline char const *getReadName(BAM_Alignment const *const self) { in getReadName() function

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