コード例 #1
0
  @Test
  public void testReduce_homdel_100() throws Exception {
    double[] y = NODEL_ISIZES;

    ReadGroupInfo readGroupInfo = new ReadGroupInfo();
    readGroupInfo.isize = 100;
    readGroupInfo.isizeSD = 15;

    List<ReadPairInfo> rpis = new ArrayList<ReadPairInfo>();
    for (int i = 0; i < y.length; i++) {
      double isize = y[i];
      ReadPairInfo rpi = new ReadPairInfo();
      rpi.insertSize = (int) isize;
      rpi.readGroupId = 0;
      rpis.add(rpi);
    }

    Map<Short, ReadGroupInfo> rgis = new HashMap<Short, ReadGroupInfo>();
    rgis.put((short) 0, readGroupInfo);
    GMMScorerResults results =
        scorer.reduceReadPairInfos(rpis.iterator(), rgis, new GenomicLocationWithQuality());

    assertEquals(0, results.w0, 0.0001);
  }
コード例 #2
0
  @Test
  public void testReduce_2_16168700() throws Exception {
    double[] y =
        new double[] {
          492, 549, 558, 517, 562, 523, 533, 537, 544, 546, 540, 506, 516, 519, 560, 515, 498, 546,
          493, 518, 520, 517, 153, 164, 189, 208, 154, 203, 540, 194, 497, 566, 551, 555, 139, 491,
          510, 229, 199, 190, 213, 190, 151, 210, 218, 226, 186, 173, 171, 226, 212, 181, 216, 146,
          171, 184, 214, 199, 192, 184, 136, 208, 214, 226, 203, 200, 217, 176, 174, 222, 182, 186,
          188, 202, 211, 190, 216, 163, 201, 244, 241, 216, 254, 189, 189, 158, 213, 240, 203, 238,
          241, 178, 195, 196, 213, 225, 187, 239, 219, 171, 235, 227, 216, 163, 214, 220, 195, 180,
          189, 206, 211, 178, 206, 207, 201, 205, 203, 197, 221, 215, 215, 161, 199, 136, 203, 212,
          172, 211, 222, 180, 157, 207, 187, 202, 188, 191, 180, 197, 197, 199, 209, 237, 255, 174,
          187, 212, 215, 218, 142, 201, 150, 155, 206, 192, 182, 156, 201, 248, 195, 206, 165, 178,
          217, 184, 178, 164, 167, 130, 196, 195, 139, 211, 191, 176, 212, 195, 149, 226, 199, 247,
          168, 223, 176, 198, 196, 226, 144, 196, 213, 191, 203, 173, 188, 186, 265, 222, 219, 209,
          218, 206, 226, 208, 188, 240, 172, 210, 198, 155, 206, 163, 183, 165, 197, 168, 135, 225,
          226, 190, 222, 189, 152, 245, 212, 231, 193, 150, 162, 210, 185, 217, 244, 233, 167, 100,
          169, 187, 203, 141, 189, 214, 158, 154, 164, 210, 220, 176, 208, 184, 218, 157, 171, 184,
          203, 200, 189, 187, 223, 199, 174, 194, 210, 155, 145, 189, 250, 209, 174, 196, 165, 262,
          219, 182, 196, 206, 201, 180, 168, 212, 187, 215, 207, 243, 170, 195, 210, 146, 244, 271,
          134, 147, 220, 206, 206, 214, 167, 192, 173, 181, 185, 234, 189, 207, 218, 185, 221, 165,
          244, 247, 251, 195, 170, 204, 183, 183, 201, 202, 169, 183, 243, 186, 202, 207, 195, 134,
          146, 165, 214, 217, 180, 187, 166, 219, 179, 204, 190, 172, 204, 159, 247, 217, 234, 215,
          196, 216, 178, 235, 190, 225, 181, 228, 243, 201, 215, 239, 231, 232, 215, 150, 224, 189,
          212, 192, 208, 237, 189, 155, 279, 182, 214, 200, 176, 211, 236, 231, 208, 177, 235, 207,
          221, 189, 222, 209, 241, 191, 226, 232, 217, 179, 208, 193, 217, 164, 218, 192, 186, 147,
          190, 255, 203, 187, 197, 159, 179, 217, 214, 191, 187, 210, 194, 205, 161, 188, 147, 204,
          165, 170, 191, 170, 254, 170, 187, 149, 206, 209, 180, 172, 277, 219, 245, 198, 206, 181,
          115, 235, 188, 146, 219, 251, 176, 196, 221, 252, 238, 217, 164, 220, 213, 183, 200, 169,
          140, 182, 201, 259, 175, 179, 245, 173, 208, 184, 171, 210, 161, 185, 197, 225, 229, 162,
          228, 239, 151, 176, 175, 191, 185, 172, 210, 222, 196, 244, 155, 210, 226, 206, 202, 226,
          182, 203, 211, 54, 183, 162, 218, 178, 222, 186, 175, 185, 206
        };

    double[] q =
        new double[] {
          -2.1696611175533603E-10,
          -6.785146088283706E-8,
          -8.024704012413976E-8,
          -1.7379881135464118E-4,
          -0.6931471805599502,
          -0.693147180559951,
          -0.6931471805678728,
          -0.693147180572517,
          -0.6931471805725841,
          -0.6931471805798182,
          -0.6931471805997381,
          -0.693147180622788,
          -0.6931471806495079,
          -0.6931471807594544,
          -0.6931471845248532,
          -0.6931475377340768,
          -0.6931503533452836,
          -0.6931512316685288,
          -0.6931840359492512,
          -0.693305956786865,
          -0.6937753785184062,
          -5.64897333105462,
          -7.084857412316782,
          -7.354808352597096,
          -7.359377330663584,
          -7.872364521913692,
          -8.04267742026059,
          -8.669566545094245,
          -8.969160504596012,
          -9.221512806273967,
          -9.443121607473534,
          -9.662320273839363,
          -9.89927891367327,
          -9.899475907902985,
          -10.088747376089458,
          -10.136296317056333,
          -10.390994468392968,
          -10.466896786383858,
          -10.54685718548888,
          -10.563884362458577,
          -10.581221493505096,
          -10.62770119673156,
          -10.63334549133029,
          -10.646393514132974,
          -10.657253069096956,
          -10.663702915211145,
          -10.676735018643225,
          -10.681529869083171,
          -10.686913818512526,
          -10.699011191869902,
          -10.712076390390033,
          -10.71494371186775,
          -10.7264211634449,
          -10.740214964542467,
          -10.749791882491355,
          -10.750311639419573,
          -10.754497756231224,
          -10.756823839754684,
          -10.761609867517738,
          -10.766403150113543,
          -10.771343223309085,
          -10.775062291368782,
          -10.77835101998959,
          -10.78197573924654,
          -10.790276905621603,
          -10.795256866828304,
          -10.80181701129367,
          -10.803087896128151,
          -10.80314009117173,
          -10.80380175386974,
          -10.814394966508459,
          -10.81537122505761,
          -10.817492173087448,
          -10.827675844546354,
          -10.829443481011559,
          -10.830179309986828,
          -10.838212544645792,
          -10.844131294622137,
          -10.848542068923848,
          -10.853854857544324,
          -10.856020915168198,
          -10.859558263487916,
          -10.860158700196953,
          -10.880641680567678,
          -10.888588199397667,
          -10.88874066031219,
          -10.91229133295613,
          -10.924107483771525,
          -10.928346113518579,
          -10.92964687162989,
          -10.932350396150245,
          -10.947241656379116,
          -10.960930793781891,
          -10.968987987336805,
          -10.97537609031065,
          -10.97888333176698,
          -10.983714693620161,
          -10.98396459725721,
          -10.988026161635448,
          -11.000349775425226,
          -11.005190098864151,
          -11.008058181344321,
          -11.019278024115216,
          -11.021291910823129,
          -11.028322692242273,
          -11.029149326715867,
          -11.061707802901795,
          -11.068395939657464,
          -11.069852995949653,
          -11.069933889625611,
          -11.076805056632331,
          -11.083382084815497,
          -11.08509571105233,
          -11.089824851323177,
          -11.089885487887706,
          -11.094113103444364,
          -11.100555423526552,
          -11.10133122503366,
          -11.113614986629823,
          -11.120602422354539,
          -11.145674693493445,
          -11.155171514432995,
          -11.155584476787158,
          -11.16235322235817,
          -11.1743979194754,
          -11.179930631664496,
          -11.18119861073529,
          -11.186147109040785,
          -11.186253203506407,
          -11.194110915846878,
          -11.199850352222427,
          -11.205512744495765,
          -11.206608319859358,
          -11.208810637615429,
          -11.208935886080297,
          -11.212548365317536,
          -11.21424709756695,
          -11.23214588034072,
          -11.23570216013649,
          -11.241624346768159,
          -11.244808957153834,
          -11.266084963986366,
          -11.268474719034423,
          -11.274459210338485,
          -11.277656936264519,
          -11.287998772134518,
          -11.29176173512852,
          -11.32731360798145,
          -11.3311640427555,
          -11.333039066255113,
          -11.337135957453896,
          -11.358383144232379,
          -11.366000617155429,
          -11.36659303658937,
          -11.384491692834233,
          -11.393971852444107,
          -11.397996304813965,
          -11.398666888576694,
          -11.402682214394648,
          -11.405528284621504,
          -11.407568257147572,
          -11.407675455579561,
          -11.41065714680622,
          -11.413605020736467,
          -11.4148346590077,
          -11.415836742763219,
          -11.420320556150081,
          -11.428985678366118,
          -11.433031937419411,
          -11.434169066321804,
          -11.435919487005071,
          -11.440941652690302,
          -11.448930587418992,
          -11.452612464056163,
          -11.453244486778988,
          -11.456067248558421,
          -11.459937035668403,
          -11.465816007733807,
          -11.4667715838359,
          -11.469548419058178,
          -11.506416283676629,
          -11.507980892477075,
          -11.508295681284594,
          -11.510764489174388,
          -11.521049706794319,
          -11.534339191667677,
          -11.554287990779184,
          -11.554403010730585,
          -11.557098234728846,
          -11.558454457201158,
          -11.558527724793233,
          -11.56231529416586,
          -11.571770761162302,
          -11.571770950887338,
          -11.607173819094001,
          -11.607813409351401,
          -11.609557604640045,
          -11.612361592929172,
          -11.616746254410995,
          -11.617624768597299,
          -11.619735777410394,
          -11.627618299073958,
          -11.62944394218113,
          -11.632677032446942,
          -11.633634976353044,
          -11.656295440568524,
          -11.67754449036551,
          -11.679715107322874,
          -11.681644956169858,
          -11.683492771248496,
          -11.684179635522574,
          -11.688069451670032,
          -11.69307353975453,
          -11.705608623096106,
          -11.718261062653541,
          -11.721859752278295,
          -11.725105691811862,
          -11.74293467318785,
          -11.74604369023696,
          -11.750169688924437,
          -11.755383243031819,
          -11.75838466961116,
          -11.760354632643484,
          -11.765392247336596,
          -11.773565769921127,
          -11.795011574718444,
          -11.798918108029099,
          -11.80044509306538,
          -11.802451468952714,
          -11.802870247278562,
          -11.808387690341426,
          -11.811275898644656,
          -11.81515379404222,
          -11.823109810566377,
          -11.830430003357971,
          -11.831698794922358,
          -11.833383051107955,
          -11.845948060608585,
          -11.857525221947936,
          -11.872834546949225,
          -11.884868237981923,
          -11.892365054656624,
          -11.89518643359543,
          -11.906122690678668,
          -11.907464313404134,
          -11.919426054164733,
          -11.936547937965024,
          -11.948251494311359,
          -11.960643538424119,
          -11.964765517009852,
          -11.971871206040912,
          -11.979188840635903,
          -11.979872541286628,
          -11.980059958768567,
          -11.983324560267182,
          -11.989347998124508,
          -11.990776747102908,
          -11.99889265952341,
          -12.008243796387097,
          -12.023278749706506,
          -12.031611349208564,
          -12.033054852806274,
          -12.049962180295484,
          -12.051187384115412,
          -12.05373847617144,
          -12.059378026508043,
          -12.061165014529005,
          -12.08425921677133,
          -12.09290153858423,
          -12.096657564011192,
          -12.104708475256558,
          -12.105411877986661,
          -12.120906812725586,
          -12.125078259994385,
          -12.128819793798097,
          -12.131577706216952,
          -12.137083478593583,
          -12.139965138023623,
          -12.144840271962934,
          -12.16647882827111,
          -12.176385324600925,
          -12.19331777410186,
          -12.206280608871772,
          -12.206368172521795,
          -12.21221581648059,
          -12.213997443665919,
          -12.217147145466207,
          -12.223044019810153,
          -12.227008013842497,
          -12.240297236766862,
          -12.246202784275956,
          -12.247633359841192,
          -12.249949482076318,
          -12.252280350545725,
          -12.259958059662193,
          -12.269491325434306,
          -12.271041060855865,
          -12.271560124839013,
          -12.278694185360683,
          -12.27872132138998,
          -12.281563915928338,
          -12.28822897720492,
          -12.296341433158773,
          -12.308269982919533,
          -12.327691266877867,
          -12.336869339082376,
          -12.341056064100963,
          -12.356900031894881,
          -12.376800778971106,
          -12.380930491424309,
          -12.399361188991575,
          -12.400429215097255,
          -12.400505214268058,
          -12.415877378043504,
          -12.418190646488394,
          -12.428500964237001,
          -12.434414081290308,
          -12.454876625161518,
          -12.456919070770772,
          -12.469664441900012,
          -12.493521693362812,
          -12.494697985905036,
          -12.504294353427472,
          -12.520024626960016,
          -12.535297564869646,
          -12.539342819183414,
          -12.540348346241775,
          -12.554023456234265,
          -12.559622674013278,
          -12.571204825571195,
          -12.574741730551908,
          -12.583825658741782,
          -12.626304184802747,
          -12.627749295535345,
          -12.637190715097805,
          -12.647945005733536,
          -12.669042955168685,
          -12.675206250932629,
          -12.681832925909207,
          -12.687801255687505,
          -12.691598881155024,
          -12.711106689629208,
          -12.73904118528932,
          -12.742302306626886,
          -12.74955717594839,
          -12.765080380251657,
          -12.768093773024798,
          -12.775903088506945,
          -12.823522421893,
          -12.826894576679015,
          -12.827617882552838,
          -12.831061272166139,
          -12.831646753233883,
          -12.843083873122257,
          -12.86085924799955,
          -12.903402521217178,
          -12.906104025278378,
          -12.906447168159744,
          -12.910875138821364,
          -12.91455067260042,
          -12.934919274290205,
          -12.956163559665734,
          -12.963918515173502,
          -12.97051594259994,
          -12.9753163463167,
          -12.984005448337019,
          -12.999829630789407,
          -13.045536310822637,
          -13.048772683530792,
          -13.052781597159033,
          -13.085228846958847,
          -13.08691508819893,
          -13.093911862249723,
          -13.142853842381857,
          -13.152551785535437,
          -13.154477154375927,
          -13.161777998003828,
          -13.167025161781197,
          -13.169691464089375,
          -13.181291817433694,
          -13.182216311875594,
          -13.219039826262367,
          -13.219499341503145,
          -13.227825837956352,
          -13.232727488905265,
          -13.252450113577616,
          -13.25439216258476,
          -13.264044774348491,
          -13.287510294333067,
          -13.297580706956184,
          -13.323571082504627,
          -13.334592054896639,
          -13.360688679044983,
          -13.376950374813497,
          -13.385030581320638,
          -13.400183248891341,
          -13.445952135319157,
          -13.449928892501957,
          -13.451586983108424,
          -13.469723421966817,
          -13.522936682874917,
          -13.551028122190452,
          -13.557758633290474,
          -13.57476024509103,
          -13.605446257818688,
          -13.606780427143324,
          -13.629226177962948,
          -13.637966053406343,
          -13.66253085031366,
          -13.712552861438235,
          -13.741313735475032,
          -13.791349633886988,
          -13.800682412370243,
          -13.802428810557252,
          -13.825743843031923,
          -13.83659679813952,
          -13.844631092429726,
          -13.846398874836751,
          -13.8602601997209,
          -13.861075786933808,
          -13.873522177022677,
          -13.8830254730683,
          -13.954565735702303,
          -13.962626346683482,
          -14.011017965921496,
          -14.021602339057813,
          -14.061349097166467,
          -14.1346480370544,
          -14.18642244862005,
          -14.264723939869263,
          -14.27575260774345,
          -14.292091994883386,
          -14.317414739954774,
          -14.32918558019255,
          -14.3363631404843,
          -14.40035941836633,
          -14.435348487784918,
          -14.443018727672229,
          -14.472990208844504,
          -14.500717254745936,
          -14.610011834805242,
          -14.616852240862958,
          -14.666163986368062,
          -14.684036947144627,
          -14.73093485648133,
          -14.735052619883703,
          -14.760689339795253,
          -14.763644797399394,
          -14.82090441612769,
          -14.848015393628826,
          -14.949915735929597,
          -15.004929672272947,
          -15.029480148258049,
          -15.032346096384781,
          -15.075222638833846,
          -15.080903343346119,
          -15.097314551862558,
          -15.115440735308157,
          -15.131922627917003,
          -15.226072618784602,
          -15.22890069250707,
          -15.233054064019132,
          -15.269549783702754,
          -15.303170788599967,
          -15.303788808882992,
          -15.416808319958273,
          -15.56464735941875,
          -15.796329199467257,
          -15.846777242562403,
          -16.005857824831633,
          -16.12351236735087,
          -16.150061512413757,
          -16.247090127882622,
          -16.278741427053546,
          -16.31169763271048,
          -16.416623168840637,
          -16.532872414202522,
          -16.684488046806592,
          -16.713654174537385,
          -16.87719518865177,
          -17.008598037470506,
          -17.10448955459016,
          -17.123895973086224,
          -17.25176272912007,
          -17.29356856286769,
          -17.409667809368557,
          -17.928570585634525,
          -17.960983028162417,
          -18.418115592931766,
          -18.420680743952364,
          -18.420680743952364,
          -18.420680743952364,
          -18.420680743952364,
          -18.45900866840194,
          -18.607842667340645,
          -19.147320224015054,
          -19.35446227099996,
          -19.538798616221108,
          -19.600596948545835
        };

    ReadGroupInfo readGroupInfo = new ReadGroupInfo();
    readGroupInfo.isize = 200;
    readGroupInfo.isizeSD = 30;

    List<ReadPairInfo> rpis = new ArrayList<ReadPairInfo>();
    for (int i = 0; i < y.length; i++) {
      double isize = y[i];
      ReadPairInfo rpi = new ReadPairInfo();
      rpi.insertSize = (int) isize;
      rpi.readGroupId = 0;
      rpi.pMappingCorrect = q[i];
      rpis.add(rpi);
    }

    scorer.setMaxLogMapqDiff(5);
    scorer.setMinCoverage(3);

    Map<Short, ReadGroupInfo> rgis = new HashMap<Short, ReadGroupInfo>();
    rgis.put((short) 0, readGroupInfo);
    GMMScorerResults results =
        scorer.reduceReadPairInfos(rpis.iterator(), rgis, new GenomicLocationWithQuality());

    assertEquals(0, results.w0, 0.0001);
  }