/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/ |
H A D | SvDiscoveryUtils.java | 58 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 D | tagBamMain.cpp | 33 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 D | tagBam.cpp | 19 bool sameStrand, bool diffStrand, float overlapFraction): in TagBam() argument 30 _overlapFraction(overlapFraction) in TagBam()
|
H A D | tagBam.h | 44 bool diffStrand, float overlapFraction);
|
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/ |
H A D | SVIntervalTreeTest.java | 230 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 D | multiBamCovMain.cpp | 46 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 D | multiBamCov.cpp | 24 bool diffStrand, float overlapFraction, in MultiCovBam() argument 36 _overlapFraction(overlapFraction), in MultiCovBam()
|
H A D | multiBamCov.h | 38 bool diffStrand, float overlapFraction,
|
/dports/biology/bedtools/bedtools2-2.30.0/src/pairToPair/ |
H A D | pairToPairMain.cpp | 36 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 D | pairToPair.h | 33 PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction,
|
H A D | pairToPair.cpp | 19 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 D | pairToBedMain.cpp | 36 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 D | pairToBed.h | 45 BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
|
H A D | pairToBed.cpp | 36 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 D | shuffleBedMain.cpp | 43 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 D | shuffleBed.h | 40 float overlapFraction, int seed,
|
H A D | shuffleBed.cpp | 21 float overlapFraction, int seed, in BedShuffle() argument 33 _overlapFraction = overlapFraction; in BedShuffle()
|
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/chromsweep/ |
H A D | chromsweep.cpp | 23 float overlapFraction, bool reciprocal, in ChromSweep() argument 29 , _overlapFraction(overlapFraction) in ChromSweep()
|
H A D | chromsweep.h | 36 float overlapFraction = 0.0, bool reciprocal = false,
|
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/bedFile/ |
H A D | bedFile.cpp | 340 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 D | bedFile.h | 447 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 D | GenomeLocUnitTest.java | 163 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 D | GardenerAI2.cpp | 334 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 D | bedFilePE.h | 79 vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames);
|
H A D | bedFilePE.cpp | 409 … vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames) { in FindOverlapsPerBin() argument 442 if ( (overlap / size) >= overlapFraction ) { in FindOverlapsPerBin()
|