| /dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
| H A D | test_SubreadLengthQuery.cpp | 26 EXPECT_GE((r.QueryEnd() - r.QueryStart()), 500); in TEST()
38 EXPECT_GE((r.QueryEnd() - r.QueryStart()), 1000); in TEST()
50 EXPECT_GE((r.QueryEnd() - r.QueryStart()), 5000); in TEST()
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| H A D | test_BamRecordClipping.cpp | 776 EXPECT_EQ(prototype.QueryStart(), s0.QueryStart()); in TEST()
814 EXPECT_EQ(502, s1.QueryStart()); in TEST()
876 EXPECT_EQ(502, s2.QueryStart()); in TEST()
938 EXPECT_EQ(502, s3.QueryStart()); in TEST()
1130 EXPECT_EQ(prototype.QueryStart(), s0.QueryStart()); in TEST()
1230 EXPECT_EQ(504, s2.QueryStart()); in TEST()
1291 EXPECT_EQ(504, s3.QueryStart()); in TEST()
1382 EXPECT_EQ(clipStart, s3.QueryStart()); in TEST()
1441 EXPECT_EQ(502, s3.QueryStart()); in TEST()
1501 EXPECT_EQ(clipStart, s3.QueryStart()); in TEST()
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| H A D | test_BamRecordMapping.cpp | 96 EXPECT_EQ(qStart, s1.QueryStart()); in TEST()
128 EXPECT_EQ(qStart, s1_rev.QueryStart()); in TEST()
177 EXPECT_EQ(qStart, s2.QueryStart()); in TEST()
209 EXPECT_EQ(qStart, s2_rev.QueryStart()); in TEST()
258 EXPECT_EQ(qStart, s3.QueryStart()); in TEST()
290 EXPECT_EQ(qStart, s3_rev.QueryStart()); in TEST()
387 EXPECT_EQ(qStart, s1.QueryStart()); // 500 in TEST()
468 EXPECT_EQ(qStart, s2.QueryStart()); // 500 in TEST()
549 EXPECT_EQ(qStart, s3.QueryStart()); // 500 in TEST()
644 EXPECT_EQ(500, mapped.QueryStart()); // 500 in TEST()
[all …]
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| H A D | test_BamWriter.cpp | 86 EXPECT_EQ(0, record.QueryStart()); in TEST()
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| H A D | test_Compare.cpp | 532 std::sort(records.begin(), records.end(), Compare::QueryStart()); in TEST()
534 EXPECT_EQ(q4, records.at(0).QueryStart()); in TEST()
535 EXPECT_EQ(q2, records.at(1).QueryStart()); in TEST()
536 EXPECT_EQ(q1, records.at(2).QueryStart()); in TEST()
537 EXPECT_EQ(q3, records.at(3).QueryStart()); in TEST()
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| /dports/biology/pbbam/pbbam-0.18.0/src/ |
| H A D | VirtualZmwBamRecord.cpp | 30 return l1.QueryStart() < l2.QueryStart(); in __anon4a1db03e0102()
77 const auto stitchedSize = lastRecord.QueryEnd() - firstRecord.QueryStart(); in StitchSources()
154 virtualRegionsMap_[regionType].emplace_back(regionType, b.QueryStart(), b.QueryEnd()); in StitchSources()
165 virtualRegionsMap_[regionType].emplace_back(regionType, b.QueryStart(), b.QueryEnd(), in StitchSources()
195 this->QueryStart(firstRecord.QueryStart()); in StitchSources()
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| H A D | Validator.cpp | 198 const auto qStart = b.QueryStart(); in ValidateRecordCore()
225 const auto qStart = b.QueryStart(); in ValidateRecordRequiredTags()
259 (IsCcsOrTranscript(b.Type()) ? b.Sequence().size() : (b.QueryEnd() - b.QueryStart())); in ValidateRecordTagLengths()
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| H A D | AlignmentPrinter.cpp | 40 Position seqCoord = record.QueryStart(); in Print()
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| H A D | PbiRawData.cpp | 200 qStart_.push_back(b.QueryStart()); in AddRecord()
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| H A D | BamRecord.cpp | 493 const Position qStart = isCcsOrTranscript ? 0 : QueryStart(); in CalculateAlignedPositions()
670 const Position origQStart = isCcsOrTranscript ? 0 : QueryStart(); in ClipToQuery()
775 const Position origQStart = isCcsOrTranscript ? 0 : QueryStart(); in ClipToReferenceForward()
899 const Position origQStart = isCcsOrTranscript ? 0 : QueryStart(); in ClipToReferenceReverse()
1908 Position BamRecord::QueryStart() const in QueryStart() function in PacBio::BAM::BamRecord
1935 BamRecord& BamRecord::QueryStart(const Position pos) in QueryStart() function in PacBio::BAM::BamRecord
2146 newName += std::to_string(QueryStart()); in UpdateName()
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
| H A D | ensqcalignment.c | 459 pthis->QueryStart = qca->QueryStart; in ensQcalignmentNewCpy()
545 qca->QueryStart = qstart; in ensQcalignmentNewIni()
1337 qca->QueryStart = qstart; in ensQcalignmentSetQueryStart()
1641 indent, qca->QueryStart, in ensQcalignmentTrace()
1812 *Pstart = qca->QueryStart; in ensQcalignmentCalculateQueryCoordinates()
1818 *Pend = qca->QueryStart; in ensQcalignmentCalculateQueryCoordinates()
2594 start1 = qca1->QueryStart; in ensQcalignmentCalculateQueryCoverageQueryQuery()
2597 start2 = qca2->QueryStart; in ensQcalignmentCalculateQueryCoverageQueryQuery()
2604 start1 = qca1->QueryStart; in ensQcalignmentCalculateQueryCoverageQueryQuery()
4217 qca->QueryStart, in ensQcalignmentadaptorStore()
[all …]
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| H A D | ensqcvariation.c | 302 pthis->QueryStart = qcv->QueryStart; in ensQcvariationNewCpy()
397 qcv->QueryStart = qstart; in ensQcvariationNewIni()
733 return (qcv) ? qcv->QueryStart : 0U; in ensQcvariationGetQueryStart()
1153 qcv->QueryStart = qstart; in ensQcvariationSetQueryStart()
1426 indent, qcv->QueryStart, in ensQcvariationTrace()
2791 qcv->QueryStart, in ensQcvariationadaptorStore()
2894 qcv->QueryStart, in ensQcvariationadaptorUpdate()
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| H A D | ensqcsubmission.h | 99 ajuint QueryStart; member
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| H A D | ensqcvariation.h | 179 ajuint QueryStart; member
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| H A D | ensqcsubmission.c | 586 return (qcsb) ? qcsb->QueryStart : 0U; in ensQcsubmissionGetQueryStart()
930 qcsb->QueryStart = qstart; in ensQcsubmissionSetQueryStart()
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| H A D | ensqcalignment.h | 103 ajuint QueryStart; member
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| H A D | ensdatabaseentry.c | 1870 pthis->QueryStart = ir->QueryStart; in ensIdentityreferenceNewCpy()
1926 ir->QueryStart = qstart; in ensIdentityreferenceNewIni()
2171 return (ir) ? ir->QueryStart : 0; in ensIdentityreferenceGetQueryStart()
2433 ir->QueryStart = qstart; in ensIdentityreferenceSetQueryStart()
2609 indent, ir->QueryStart, in ensIdentityreferenceTrace()
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| H A D | ensdata.h | 1224 ajint QueryStart; member
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| /dports/biology/pbbam/pbbam-0.18.0/include/pbbam/ |
| H A D | Compare.h | 331 struct QueryStart : public MemberFunctionBase<Position, &BamRecord::QueryStart> struct
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| H A D | BamRecord.h | 114 Position QueryStart() const;
773 BamRecord& QueryStart(const PacBio::BAM::Position pos);
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| /dports/biology/diamond/diamond-2.0.13/src/output/ |
| H A D | clustering_variables.h | 49 class QueryStart: public Variable{
228 regMap[QueryStart::get_name()] = new QueryStart(); in StaticVariableRegistry()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/ngalign/ |
| H A D | banded_aligner.cpp | 321 TSeqPos QueryStart, in x_RunMMGlobal() argument
355 QueryStrandedStart = QueryStart; in x_RunMMGlobal()
359 QueryStrandedStop = ( (QueryVec.size()-1) - QueryStart); in x_RunMMGlobal()
404 ResultDenseg->OffsetRow(0, QueryStart); in x_RunMMGlobal()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/align/ngalign/ |
| H A D | banded_aligner.hpp | 131 TSeqPos QueryStart,
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| /dports/biology/pbbam/pbbam-0.18.0/tools/common/ |
| H A D | BamFileMerger.inl | 103 const auto lhsQStart = l.QueryStart();
104 const auto rhsQStart = r.QueryStart();
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| /dports/www/chromium-legacy/chromium-88.0.4324.182/chrome/browser/android/history_report/ |
| H A D | delta_file_backend_leveldb_unittest.cc | 109 TEST_F(DeltaFileBackendTest, QueryStart) { in TEST_F() argument
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