/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/ |
H A D | AbstractAlignmentMerger.java | 241 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 D | SamAlignmentMerger.java | 226 final String readName = rec.getReadName(); 284 … return (read1Iterator.peek().getReadName().compareTo(read2Iterator.peek().getReadName()) <= 0)
|
H A D | HitsForInsert.java | 46 public String getReadName() { in getReadName() method in HitsForInsert 47 return getRepresentativeRead().getReadName(); in getReadName()
|
H A D | MultiHitAlignedReadIterator.java | 91 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 D | Bam2FastQ.cpp | 509 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 D | MateMapByCoord.cpp | 37 const char* readName = record.getReadName(); in getMate() 65 if(strcmp(((*iter).second)->getReadName(), readName) == 0) in getMate()
|
H A D | Diff.cpp | 476 (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 D | ClipOverlap.cpp | 351 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 D | CompareBaseQualities.java | 151 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 D | GATKException.java | 72 …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 D | SAMRecordComparator.java | 38 int cmp = pr1.sam.getReadName().compareTo(pr2.sam.getReadName()); in compare()
|
H A D | SAMRecordList.java | 191 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 D | Read.hpp | 75 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 D | Read.hpp | 75 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 D | Read.hpp | 75 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 D | HeaderlessSAMRecordCoordinateComparator.java | 33 cmp = samRecord1.getReadName().compareTo(samRecord2.getReadName()); in compare()
|
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/ |
H A D | TestValidate.cpp | 103 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 D | ValidationTest.cpp | 39 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 D | BlastReadsSubTask.cpp | 149 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 D | SAMRecordSparkCodec.java | 113 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 D | AlignToReferenceBlastWorker.cpp | 189 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 D | Read.java | 104 String getReadName () in getReadName() method
|
/dports/biology/ncbi-vdb/ngs-2.11.0/ngs-java/ngs/ |
H A D | Read.java | 104 String getReadName () in getReadName() method
|
/dports/biology/ngs-sdk/ngs-2.11.1/ngs-java/ngs/ |
H A D | Read.java | 104 String getReadName () in getReadName() method
|
/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
H A D | bam-priv.h | 116 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
|