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Searched refs:overlapFraction (Results 1 – 25 of 27) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/
H A DSvDiscoveryUtils.java58 final float falsePos = 1.f - narlyBreakpoints.overlapFraction(trueBreakpoints); in evaluateNarlsAgainstTruth()
61 final float falseNeg = 1.f - trueBreakpoints.overlapFraction(narlyBreakpoints); in evaluateNarlsAgainstTruth()
74 final float falsePos = 1.f - intervals.overlapFraction(trueBreakpoints); in evaluateIntervalsAgainstTruth()
76 final float falseNeg = 1.f - trueBreakpoints.overlapFraction(intervals); in evaluateIntervalsAgainstTruth()
/dports/biology/bedtools/bedtools2-2.30.0/src/tagBam/
H A DtagBamMain.cpp33 float overlapFraction = 1E-9; in tagbam_main() local
125 overlapFraction = atof(argv[i + 1]); in tagbam_main()
179 if (haveFraction && overlapFraction == 0.0) { in tagbam_main()
189 overlapFraction); in tagbam_main()
H A DtagBam.cpp19 bool sameStrand, bool diffStrand, float overlapFraction): in TagBam() argument
30 _overlapFraction(overlapFraction) in TagBam()
H A DtagBam.h44 bool diffStrand, float overlapFraction);
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/
H A DSVIntervalTreeTest.java230 Assert.assertEquals(tree1.overlapFraction(tree2), Float.NaN); in overlapFractionTest()
232 Assert.assertEquals(tree1.overlapFraction(tree2), 0.f); in overlapFractionTest()
234 Assert.assertEquals(tree1.overlapFraction(tree2), 0.f); in overlapFractionTest()
236 Assert.assertEquals(tree1.overlapFraction(tree2), 1.f); in overlapFractionTest()
239 Assert.assertEquals(tree1.overlapFraction(tree2), 1.f); in overlapFractionTest()
241 Assert.assertEquals(tree1.overlapFraction(tree2), 0.5f); in overlapFractionTest()
/dports/biology/bedtools/bedtools2-2.30.0/src/multiBamCov/
H A DmultiBamCovMain.cpp46 float overlapFraction = 1E-9; in multibamcov_main() local
96 overlapFraction = atof(argv[i + 1]); in multibamcov_main()
136 diffStrand, overlapFraction, in multibamcov_main()
H A DmultiBamCov.cpp24 bool diffStrand, float overlapFraction, in MultiCovBam() argument
36 _overlapFraction(overlapFraction), in MultiCovBam()
H A DmultiBamCov.h38 bool diffStrand, float overlapFraction,
/dports/biology/bedtools/bedtools2-2.30.0/src/pairToPair/
H A DpairToPairMain.cpp36 float overlapFraction = 1E-9; in pairtopair_main() local
92 overlapFraction = atof(argv[i + 1]); in pairtopair_main()
137 PairToPair *bi = new PairToPair(bedAFile, bedBFile, overlapFraction, searchType, in pairtopair_main()
H A DpairToPair.h33 PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction,
H A DpairToPair.cpp19 PairToPair::PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction, in PairToPair() argument
24 _overlapFraction = overlapFraction; in PairToPair()
/dports/biology/bedtools/bedtools2-2.30.0/src/pairToBed/
H A DpairToBedMain.cpp36 float overlapFraction = 1E-9; in pairtobed_main() local
109 overlapFraction = atof(argv[i + 1]); in pairtobed_main()
159 BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction, in pairtobed_main()
H A DpairToBed.h45 BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
H A DpairToBed.cpp36 BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction, in BedIntersectPE() argument
42 _overlapFraction = overlapFraction; in BedIntersectPE()
/dports/biology/bedtools/bedtools2-2.30.0/src/shuffleBed/
H A DshuffleBedMain.cpp43 float overlapFraction = 1E-9; in shuffle_main() local
112 overlapFraction = atof(argv[i + 1]); in shuffle_main()
147 overlapFraction, seed, in shuffle_main()
H A DshuffleBed.h40 float overlapFraction, int seed,
H A DshuffleBed.cpp21 float overlapFraction, int seed, in BedShuffle() argument
33 _overlapFraction = overlapFraction; in BedShuffle()
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/chromsweep/
H A Dchromsweep.cpp23 float overlapFraction, bool reciprocal, in ChromSweep() argument
29 , _overlapFraction(overlapFraction) in ChromSweep()
H A Dchromsweep.h36 float overlapFraction = 0.0, bool reciprocal = false,
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/bedFile/
H A DbedFile.cpp340 bool diffStrand, float overlapFraction, in allHits() argument
369 (float) aLength >= overlapFraction) in allHits()
386 else if (bOverlap >= overlapFraction) in allHits()
399 bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal) { in anyHits() argument
427 (float) aLength >= overlapFraction) in anyHits()
444 else if (bOverlap >= overlapFraction) in anyHits()
H A DbedFile.h447 float overlapFraction, bool reciprocal);
451 bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal);
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/
H A DGenomeLocUnitTest.java163 double overlapFraction; field in GenomeLocUnitTest.ReciprocalOverlapProvider
177 this.overlapFraction = Math.min((1.0*shared)/gl1.size(), (1.0*shared)/gl2.size()); in ReciprocalOverlapProvider()
178 …at("%d-%d / %d-%d overlap=%d / %.2f", start1, stop1, start2, stop2, overlapSize, overlapFraction)); in ReciprocalOverlapProvider()
210 Assert.assertEquals(cfg.gl1.reciprocialOverlapFraction(cfg.gl2), cfg.overlapFraction); in testReciprocalOverlapProvider()
/dports/games/cultivation/Cultivation_8_UnixSource/game2/gameSource/
H A DGardenerAI2.cpp334 double overlapFraction = overlapAreaSum / ourPlotArea; in passTime() local
335 if( overlapFraction > 1 ) { in passTime()
336 overlapFraction = 1; in passTime()
342 if( overlapFraction >= threshold ) { in passTime()
353 ( overlapFraction - threshold ) / range; in passTime()
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/bedFilePE/
H A DbedFilePE.h79 vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames);
H A DbedFilePE.cpp409 … vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames) { in FindOverlapsPerBin() argument
442 if ( (overlap / size) >= overlapFraction ) { in FindOverlapsPerBin()

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