Home
last modified time | relevance | path

Searched refs:mapQual (Results 1 – 25 of 30) sorted by relevance

12

/dports/biology/pbbam/pbbam-0.18.0/tests/src/
H A Dtest_BamRecordMapping.cpp64 const uint8_t mapQual = 80; in TEST() local
94 EXPECT_EQ(mapQual, s1.MapQuality()); in TEST()
175 EXPECT_EQ(mapQual, s2.MapQuality()); in TEST()
256 EXPECT_EQ(mapQual, s3.MapQuality()); in TEST()
342 const uint8_t mapQual = 80; in TEST() local
385 EXPECT_EQ(mapQual, s1.MapQuality()); in TEST()
466 EXPECT_EQ(mapQual, s2.MapQuality()); in TEST()
547 EXPECT_EQ(mapQual, s3.MapQuality()); in TEST()
633 const uint8_t mapQual = 80; in TEST() local
642 EXPECT_EQ(mapQual, mapped.MapQuality()); in TEST()
[all …]
H A Dtest_BamRecordClipping.cpp140 const uint8_t mapQual = 80; in TEST() local
434 const uint8_t mapQual = 80; in TEST() local
711 const uint8_t mapQual = 80; in TEST() local
1010 const uint8_t mapQual = 80; in TEST() local
1355 const uint8_t mapQual = 80; in TEST() local
1420 const uint8_t mapQual = 80; in TEST() local
1474 const uint8_t mapQual = 80; in TEST() local
1539 const uint8_t mapQual = 80; in TEST() local
1596 const uint8_t mapQual = 80; in TEST() local
1617 const uint8_t mapQual = 80; in TEST() local
[all …]
H A Dtest_Compare.cpp69 const uint8_t mapQual = 80; in makeMappedRecords() local
82 s1.Map(0, 100, Strand::FORWARD, s1_cigar, mapQual); in makeMappedRecords()
83 s2.Map(0, 100, Strand::FORWARD, s2_cigar, mapQual); in makeMappedRecords()
84 s3.Map(0, 100, Strand::FORWARD, s3_cigar, mapQual); in makeMappedRecords()
85 s1_rev.Map(0, 100, Strand::REVERSE, s1_cigar, mapQual); in makeMappedRecords()
86 s2_rev.Map(0, 100, Strand::REVERSE, s2_cigar, mapQual); in makeMappedRecords()
87 s3_rev.Map(0, 100, Strand::REVERSE, s3_cigar, mapQual); in makeMappedRecords()
/dports/biology/bedtools/bedtools2-2.30.0/src/bedpeToBam/
H A DbedpeToBam.cpp40 void ProcessBedPE(BedFilePE *bedpe, GenomeFile *genome, int mapQual, bool uncompressedBam);
41 …dpe, BamAlignment &bam1,BamAlignment &bam2, map<string, int> &chromToId, int mapQual, int lineNum);
57 int mapQual = 255; in bedpetobam_main() local
97 mapQual = atoi(argv[i + 1]); in bedpetobam_main()
119 if (mapQual < 0 || mapQual > 255) { in bedpetobam_main()
129 ProcessBedPE(bedpe, genome, mapQual, uncompressedBam); in bedpetobam_main()
161 void ProcessBedPE(BedFilePE *bedpe, GenomeFile *genome, int mapQual, bool uncompressedBam) { in ProcessBedPE() argument
191 ConvertBedPEToBam(bedpeEntry, bamEntry1, bamEntry2, chromToId, mapQual, lineNum); in ProcessBedPE()
212 int mapQual, int lineNum) { in ConvertBedPEToBam() argument
236 bam1.MapQuality = mapQual; in ConvertBedPEToBam()
[all …]
/dports/biology/bedtools/bedtools2-2.30.0/src/bedToBam/
H A DbedToBam.cpp40 void ProcessBed(BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam);
41 … BED &bed, BamAlignment &bam, map<string, int> &chromToId, bool isBED12, int mapQual, int lineNum);
56 int mapQual = 255; in bedtobam_main() local
96 mapQual = atoi(argv[i + 1]); in bedtobam_main()
121 if (mapQual < 0 || mapQual > 255) { in bedtobam_main()
131 ProcessBed(bed, genome, isBED12, mapQual, uncompressedBam); in bedtobam_main()
167 void ProcessBed(BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam) { in ProcessBed() argument
193 ConvertBedToBam(bedEntry, bamEntry, chromToId, isBED12, mapQual, bed->_lineNum); in ProcessBed()
209 bool isBED12, int mapQual, int lineNum) { in ConvertBedToBam() argument
227 bam.MapQuality = mapQual; in ConvertBedToBam()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/
H A DAlignmentInterval.java68 public final int mapQual; field in AlignmentInterval
159 this.mapQual = mappingQuality; in AlignmentInterval()
191 .append(mapQual); in appendSATagString()
247 this.mapQual = samRecord.getMappingQuality(); in AlignmentInterval()
272 this.mapQual = read.getMappingQuality(); in AlignmentInterval()
321 this.mapQual = mapQual; in AlignmentInterval()
395 mapQual = input.readInt(); in AlignmentInterval()
409 output.writeInt(mapQual); in serialize()
464 if (mapQual != that.mapQual) return false; in equals()
479 result = 31 * result + mapQual; in hashCode()
[all …]
H A DAlignedContig.java199 …return (!alignmentIntervals.isEmpty()) && alignmentIntervals.get(0).mapQual > ALIGNMENT_MQ_THRESHO… in hasGoodMQ()
203 if ( alignment.mapQual > ALIGNMENT_MQ_THRESHOLD ) { in hasGoodMQ()
476 if ( alignment.mapQual >= mapQThresholdInclusive ) in removeDueToLowMQ()
724 || alignment.mapQual > ALIGNMENT_MQ_THRESHOLD_FOR_SPEED_BOOST; in heuristicSpeedUpWhenFacingManyMappings()
810 weight = alignmentInterval.mapQual / COVERAGE_MQ_NORMALIZATION_CONST; in computeTigExplainQualOfOneConfiguration()
812 weight = Math.max(alignmentInterval.mapQual / COVERAGE_MQ_NORMALIZATION_CONST, in computeTigExplainQualOfOneConfiguration()
842 ….filter(rep -> rep.getGoodMappings().stream().mapToInt(ai -> ai.mapQual).min().orElse(mqThreshold)… in filterSecondaryConfigurationsByMappingQualityThreshold()
H A DContigAlignmentsModifier.java49 …input.forwardStrand, input.mapQual, AlignmentInterval.NO_NM, AlignmentInterval.NO_AS, AlnModType.U… in clipAlignmentInterval()
350 new Cigar(alignmentElements), oneRegion.forwardStrand, oneRegion.mapQual, in grabCurrentInterval()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/
H A DSVMappingQualityFilter.java31 for (final String mapQual : mapQuals) { in test()
32 Integer integer = Integer.valueOf(mapQual); in test()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/
H A DAlignedAssemblyUnitTest.java44 final int[] mapQual = {0, 1, 10, 20, 30, 40, 50, 60}; in createInputsAndExpectedResults_Serialization() local
67 …strandedness[2*pair], mapQual[2*pair], mismatches[2*pair], 100, ContigAlignmentsModifier.AlnModTyp… in createInputsAndExpectedResults_Serialization()
72 …strandedness[2*pair+1], mapQual[2*pair+1], mismatches[2*pair+1], 100, ContigAlignmentsModifier.Aln… in createInputsAndExpectedResults_Serialization()
H A DAlignmentIntervalUnitTest.java200 …Assert.assertEquals(alignmentInterval.mapQual, Math.max(SAMRecord.NO_MAPPING_QUALITY,expectedMapQu… in testConstructionFromBwaMemAlignment()
216 …Assert.assertEquals(alignmentInterval.mapQual, Math.max(SAMRecord.NO_MAPPING_QUALITY,expectedMapQu… in testConstructionFromSAMRecord()
240 …Assert.assertEquals(alignmentInterval.mapQual, Math.max(SAMRecord.NO_MAPPING_QUALITY,expectedMapQu… in testConstructionFromStr()
257 …Assert.assertEquals(alignmentInterval.mapQual, Math.max(SAMRecord.NO_MAPPING_QUALITY,expectedMapQu… in testConstructionFromGATKRead()
303 Assert.assertEquals(fullInterval.mapQual, mq); in testAlignmentIntervalStrings()
314 Assert.assertEquals(basicInterval.mapQual, mq); in testAlignmentIntervalStrings()
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/internal/
H A DBamRecordBuilder.inl21 inline BamRecordBuilder& BamRecordBuilder::MapQuality(const uint8_t mapQual) argument
22 { core_.qual = mapQual; return *this; }
H A DBamRecordImpl.inl33 inline BamRecordImpl& BamRecordImpl::MapQuality(uint8_t mapQual) argument
34 { d_->core.qual = mapQual; return *this; }
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/
H A DTestUtilsForAssemblyBasedSVDiscovery.java81 final int mapQual = Integer.valueOf( fields[4] ); in fromSAMRecordString() local
97 mapQual, numMismatch, alignerScore, in fromSAMRecordString()
/dports/biology/pbbam/pbbam-0.18.0/include/pbbam/
H A DBamRecordBuilder.h118 BamRecordBuilder& MapQuality(const uint8_t mapQual);
H A DBamRecordImpl.h128 BamRecordImpl& MapQuality(uint8_t mapQual);
/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/
H A Dbam-alignment.h45 uint8_t mapQual; member
H A Dbam-priv.h160 return self->data->cooked.mapQual; in getMapQual()
H A Dsam.c558 RESULT_FIELD(mapQual) = 0; in DEF_PARSER_FUNCTION()
563 uint64_t value = RESULT_FIELD(mapQual); in DEF_PARSER_FUNCTION()
566 RESULT_FIELD(mapQual) = (uint8_t)value; in DEF_PARSER_FUNCTION()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/
H A DCpxVariantInterpreter.java310 …alueOf(Math.min(preprocessedTig.getHeadAlignment().mapQual, preprocessedTig.getTailAlignment().map… in toVariantContext()
H A DSimpleChimera.java111 …if (intervalOne.mapQual < SPLIT_PAIR_MIN_ALIGNMENT_MQ || intervalTwo.mapQual < SPLIT_PAIR_MIN_ALIG… in splitPairStrongEnoughEvidenceForCA()
H A DSimpleNovelAdjacencyAndChimericAlignmentEvidence.java265 minMQ = Math.min(simpleChimera.regionWithLowerCoordOnContig.mapQual, in ChimericContigAlignmentEvidenceAnnotations()
266 simpleChimera.regionWithHigherCoordOnContig.mapQual); in ChimericContigAlignmentEvidenceAnnotations()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/
H A DAlignedAssemblyOrExcuse.java192 final int mapQual = input.readInt(); in readAlignment() local
203 mapQual, nMismatches, alignerScore, suboptimalScore, in readAlignment()
/dports/biology/bamutil/bamUtil-1.0.15/test/
H A DtestDiff.sh29 ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --mapQual --mate --isiz…
79 ../bin/bam diff --in1 testFiles/testDiff1.sam --in2 testFiles/testDiff2.sam --mapQual --mate --isiz…
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/
H A DSVFastqUtilsUnitTest.java281 Assert.assertEquals(ai.mapQual, mappingQual[i]); in assertMappingIsAsExpected()
374 samRecord.setMappingQuality(primaryInterval.mapQual); in mappingFromGATKReadData()

12