| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AssemblyContigAlignmentsRDDProcessorUnitTest.java | 43 final AlignmentInterval intervalTwo = new AlignmentInterval( in forTestingNotDiscardForBadMQ() local
48 Arrays.asList(intervalOne, intervalTwo)); in forTestingNotDiscardForBadMQ()
139 AlignmentInterval intervalTwo = new AlignmentInterval( in forFilterSecondaryConfigurationsByMappingQualityThreshold() local
189 Arrays.asList(intervalOne, intervalTwo)); in forMiscFunctions()
194 … intervalTwo = new AlignmentInterval(new SimpleInterval("chr2_KI270774v1_alt", 105288, 105555), in forMiscFunctions()
197 Arrays.asList(intervalOne, intervalTwo)); in forMiscFunctions()
198 … data.add(new Object[]{contig, Arrays.asList(intervalTwo), Arrays.asList(intervalOne), 3, 1}); in forMiscFunctions()
202 intervalTwo = new AlignmentInterval(new SimpleInterval("chr21", 30375922, 30378473), in forMiscFunctions()
209 Arrays.asList(intervalOne, intervalTwo, intervalThree, intervalFour)); in forMiscFunctions()
215 … intervalTwo = new AlignmentInterval(new SimpleInterval("chrUn_JTFH01001804v1_decoy", 3674, 4300), in forMiscFunctions()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AlignedContig.java | 576 …thStichableAlignments( final AlignmentInterval intervalOne, final AlignmentInterval intervalTwo ) { in simpleChimeraWithStichableAlignments() argument
577 if ( intervalOne.startInAssembledContig > intervalTwo.startInAssembledContig ) in simpleChimeraWithStichableAlignments()
579 intervalOne.toPackedString() + "\tSecond: " + intervalTwo.toPackedString()); in simpleChimeraWithStichableAlignments()
580 if ( !intervalOne.referenceSpan.getContig().equals(intervalTwo.referenceSpan.getContig()) ) in simpleChimeraWithStichableAlignments()
582 if ( intervalOne.forwardStrand != intervalTwo.forwardStrand ) in simpleChimeraWithStichableAlignments()
584 if ( intervalOne.containsOnRead(intervalTwo) || intervalTwo.containsOnRead(intervalOne) ) in simpleChimeraWithStichableAlignments()
586 if ( intervalOne.containsOnRef(intervalTwo) || intervalTwo.containsOnRef(intervalOne) ) in simpleChimeraWithStichableAlignments()
591 final int overlapOnContig = AlignmentInterval.overlapOnContig(intervalOne, intervalTwo); in simpleChimeraWithStichableAlignments()
592 final int overlapOnRefSpan = AlignmentInterval.overlapOnRefSpan(intervalOne, intervalTwo); in simpleChimeraWithStichableAlignments()
594 …final boolean canBeStitched = intervalTwo.referenceSpan.getStart() - intervalOne.referenceSpan.get… in simpleChimeraWithStichableAlignments()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ |
| H A D | SimpleChimeraUnitTest.java | 69 final AlignmentInterval intervalTwo, in testSplitPairStrongEnoughEvidenceForCA() argument
71 … Assert.assertEquals(SimpleChimera.splitPairStrongEnoughEvidenceForCA(intervalOne, intervalTwo), in testSplitPairStrongEnoughEvidenceForCA()
147 …AlignmentInterval intervalTwo = new AlignmentInterval(new SimpleInterval("chr21:25625379-25625595"… in casesForInvertedDuplication() local
148 result.add(new TestData(intervalOne, intervalTwo, bareBoneHg38SAMSeqDict, null, in casesForInvertedDuplication()
153 …intervalTwo = new AlignmentInterval(new SimpleInterval("chr20", 48513297, 48513578), 84, 365, Text… in casesForInvertedDuplication()
154 …result.add(new TestData(intervalOne, intervalTwo, TestUtilsForAssemblyBasedSVDiscovery.bareBoneHg3… in casesForInvertedDuplication()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/ |
| H A D | SimpleChimera.java | 109 final AlignmentInterval intervalTwo) { in splitPairStrongEnoughEvidenceForCA() argument
111 …if (intervalOne.mapQual < SPLIT_PAIR_MIN_ALIGNMENT_MQ || intervalTwo.mapQual < SPLIT_PAIR_MIN_ALIG… in splitPairStrongEnoughEvidenceForCA()
117 …return Math.min(intervalOne.getSizeOnRead(), intervalTwo.getSizeOnRead()) >= SPLIT_PAIR_MIN_ALIGNM… in splitPairStrongEnoughEvidenceForCA()
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| H A D | SegmentedCpxVariantSimpleVariantExtractor.java | 363 … final SVInterval intervalTwo = new SVInterval(dummyChr, missing.getStart() - 1, missing.getEnd());
367 …if( 2 >= Math.abs( Math.min(missing.size(), deletedRange.size()) - intervalTwo.overlapLen(interval…
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| /dports/emulators/nestopia/nestopia-1.51.1/source/win32/ |
| H A D | NstDirect2D.hpp | 116 bool intervalTwo; member
338 uchar intervalTwo; member in Nestopia::DirectX::Direct2D::Device
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| H A D | NstDirect2D.cpp | 646 adapter.intervalTwo = caps.PresentationIntervals & D3DPRESENT_INTERVAL_TWO; in EnumerateAdapters()
662 …<< "Direct3D: vsync on every second refresh: " << (adapter.intervalTwo ? "supported\r\n" : "unsupp… in EnumerateAdapters()
775 intervalTwo = adapter.intervalTwo; in Create()
947 else if (timing.frameRate * 2 == rate && intervalTwo) in GetDesiredPresentationInterval()
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