474b9ac55dcb8e3c4cc56b00d52bd210b7989038 markd Thu Mar 7 22:59:45 2024 -0800 create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209 diff --git src/utils/bamToPsl/tests/expected/test2.psl src/utils/bamToPsl/tests/expected/test2.psl index cc89eec..b51dcea 100644 --- src/utils/bamToPsl/tests/expected/test2.psl +++ src/utils/bamToPsl/tests/expected/test2.psl @@ -1,14 +1,14 @@ 79822 0 0 0 55 585 34 128 + NOTCH2-201 158114 77707 158114 4386 858037 524795 604745 90 1015,4,3,6,1170,340,2332,2205,1239,708,1287,1,3,515,3170,1075,1483,4473,1274,2114,843,11,171,791,14,1356,540,42,3035,322,1747,1981,1451,359,133,166,1452,36,293,439,1744,50,190,2073,923,1318,5,1968,46,1301,424,1631,913,821,1078,753,853,490,1723,82,274,405,178,2605,751,154,3571,2508,263,660,886,59,201,132,3101,51,96,899,149,92,1337,96,161,383,419,232,1654,293,177,50, 77707,79115,79120,79124,79133,80304,80649,82981,85190,86433,87144,88461,88463,88469,88984,92155,93230,94716,99193,100473,102587,103432,103443,103614,104406,104420,105778,106320,106362,109397,109721,111469,113450,114905,115268,115403,115570,117026,117063,117357,117798,119543,119595,119788,121862,122795,124113,124118,126088,126134,127435,127859,129492,130410,131235,132314,133067,133920,134410,136133,136215,136490,136895,137073,139706,140458,140613,144184,146694,146957,147618,148504,148565,148770,148902,152003,152056,152152,153054,153204,153296,154634,154730,154891,155274,155693,155928,157582,157884,158064, 524795,525810,525814,525817,525823,526993,527333,529669,531874,533113,533821,535108,535109,535112,535637,538807,539885,541368,545841,547115,549230,550073,550093,550265,551056,551071,552427,552967,553010,556046,556368,558115,560102,561553,561912,562045,562211,563663,563699,563992,564431,566175,566225,566415,568488,569411,570730,570736,572704,572751,574054,574479,576110,577023,577844,578922,579678,580535,581028,582752,582838,583112,583526,583705,586310,587061,587215,590787,593295,593561,594221,595108,595167,595368,595522,598627,598678,598778,599677,599826,599919,601256,601353,601515,601899,602319,602551,604225,604518,604695, 79821 0 0 0 47 586 42 155 - NOTCH2-201 158114 77707 158114 5806 416233 308369 388345 89 44,169,12,268,1681,232,796,158,104,2477,100,46,3106,392,879,664,271,2509,3569,155,732,2620,163,424,274,68,1734,476,1613,1085,806,42,29,832,31,1615,440,1302,45,76,1890,1314,914,2092,196,55,1741,434,292,44,1447,156,149,278,80,1442,1990,1748,3343,54,542,1349,12,793,751,282,2100,1283,3043,1433,1476,1079,3158,519,9,2,1284,711,1254,2186,2329,1454,6,7,5,2,7,12,1035, 0,47,222,237,505,2189,2421,3217,3375,3480,5957,6059,6105,9211,9603,10484,11148,11421,13930,17500,17656,18416,21036,21199,21624,21898,21966,23700,24176,25789,26878,27689,27731,27760,28592,28623,30238,30678,31980,32027,32103,33993,35308,36223,38318,38516,38572,40315,40750,41043,41091,42539,42697,42850,43128,43212,44654,46645,48395,51738,51794,52338,53687,53700,54493,55244,55526,57630,58917,61960,63396,64872,65952,69110,69636,69664,69667,70954,71668,72926,75132,77466,79331,79337,79344,79349,79353,79360,79372, 308369,308413,308582,308594,308882,310563,310796,311593,311752,311856,314337,314437,314487,317617,318010,318889,319556,319827,322337,325906,326061,326793,329414,329589,330013,330289,330359,332096,332581,334196,335281,336087,336130,336160,337015,337047,338665,339107,340411,340456,340533,342424,343738,344652,346744,346940,346995,348736,349170,349462,349506,350953,351109,351258,351537,351617,353064,355054,356802,360146,360200,360742,362092,362104,362898,363650,363933,366033,367316,370360,371793,373270,374349,377508,378027,378036,378038,379322,380033,381287,383473,385802,387259,387268,387278,387284,387286,387297,387310, 79814 0 0 0 51 593 43 147 - NOTCH2-201 158114 77707 158114 6068 456676 278040 358001 94 109,395,1681,232,796,160,102,1417,1059,100,46,3106,130,258,879,665,271,2509,3569,155,732,2622,163,424,258,84,1734,476,2698,806,926,1614,440,1302,45,1968,1312,905,2093,196,55,1741,325,109,292,44,130,1317,156,150,1804,1564,426,1441,307,3343,54,542,1349,12,793,160,591,282,2100,1282,3043,1433,1476,1079,1170,1471,517,515,3,7,2,1296,692,1253,2157,39,2331,333,4,4,1109,6,7,5,2,7,12,1035, 0,110,505,2189,2421,3217,3377,3480,4898,5957,6059,6105,9211,9345,9603,10483,11148,11421,13930,17500,17656,18414,21036,21199,21624,21882,21966,23700,24176,26878,27689,28624,30238,30678,31980,32027,33995,35317,36222,38318,38516,38572,40315,40640,40750,41043,41091,41221,42539,42696,42850,44654,46218,46645,48086,48395,51738,51794,52338,53687,53700,54493,54653,55244,55526,57631,58917,61960,63396,64872,65952,67122,68593,69110,69632,69638,69672,69675,70974,71669,72926,75085,75130,77466,77801,77806,77811,79331,79337,79344,79349,79353,79360,79372, 278040,278149,278564,280245,280478,281275,281436,281538,282955,284018,284118,284168,287290,287420,287679,288558,289226,289497,292007,295576,295731,296463,299086,299269,299693,299953,300039,301776,302260,304958,305764,306690,308305,308747,310051,310096,312066,313378,314290,316383,316579,316634,318375,318701,318810,319102,319146,319277,320594,320750,320900,322709,324274,324700,326142,326449,329794,329848,330390,331740,331752,332546,332713,333305,333588,335688,336970,340014,341447,342925,344004,345175,346647,347167,347682,347685,347692,347694,348990,349682,350935,353092,353131,355462,355795,355799,355803,356915,356924,356934,356940,356942,356953,356966, -950 0 0 0 16 293 15 27781 - NOTCH2-201 1243 0 1243 7504 319192 255199 283930 31 8,49,5,48,18,2,10,5,6,8,3,13,130,167,8,112,7,21,4,8,90,34,4,27,13,22,12,4,3,51,58, 0,271,320,326,375,395,400,413,419,429,438,447,460,590,757,765,877,885,906,910,918,1009,1044,1048,1075,1088,1111,1123,1129,1134,1185, 255199,276515,276565,276570,276618,276636,276638,276648,276653,276659,276667,276670,278555,278871,283432,283442,283555,283562,283585,283590,283599,283689,283723,283730,283762,283776,283798,283813,283817,283820,283872, -1340 0 0 0 36 2568 42 422450 + NOTCH2-201 3908 0 3908 6028 1102654 392548 816338 76 101,5,54,6,31,5,2,1,3,20,6,264,18,9,4,4,16,67,54,9,51,125,5,6,2,6,3,11,3,3,6,10,8,2,2,4,6,7,3,2,6,6,17,17,2,3,6,10,7,3,15,7,3,8,7,24,7,2,4,6,7,7,1,2,6,4,7,16,4,5,7,37,8,19,83,23, 0,101,106,161,167,205,213,217,219,225,752,758,1022,1040,1049,1053,1057,1075,1142,1197,1206,1257,1385,1390,1397,1399,1406,1410,1421,1425,1435,1455,1468,1476,1480,1482,1486,1493,1502,1505,1508,1514,1521,1539,1556,1558,1561,1567,1584,1594,1598,1615,1625,1628,1636,1643,1667,1674,1676,1680,1686,1693,1704,1705,1707,1713,1718,1731,2082,2087,2092,3726,3763,3771,3795,3885, 392548,392653,392659,392713,392724,392755,392760,392762,392763,392766,486667,486674,486939,515916,552330,552335,552340,552356,552425,552479,625751,625803,625928,669185,669191,669194,669200,669203,669215,669218,669221,669227,669237,669248,669250,669253,669259,669265,669272,669276,669278,669289,669295,669312,669332,669335,669339,669346,669356,669363,669366,669381,669388,669393,669404,669412,669437,669446,669450,669455,669463,669471,669478,669480,669483,669490,669494,669501,799219,799223,799231,816160,816203,816213,816232,816315, +950 0 0 0 16 293 15 27781 - NOTCH2-201 158114 26648 27891 7504 319192 255199 283930 31 8,49,5,48,18,2,10,5,6,8,3,13,130,167,8,112,7,21,4,8,90,34,4,27,13,22,12,4,3,51,58, 130223,130494,130543,130549,130598,130618,130623,130636,130642,130652,130661,130670,130683,130813,130980,130988,131100,131108,131129,131133,131141,131232,131267,131271,131298,131311,131334,131346,131352,131357,131408, 255199,276515,276565,276570,276618,276636,276638,276648,276653,276659,276667,276670,278555,278871,283432,283442,283555,283562,283585,283590,283599,283689,283723,283730,283762,283776,283798,283813,283817,283820,283872, +1340 0 0 0 36 2568 42 422450 + NOTCH2-201 158114 18186 22094 6028 1102654 392548 816338 76 101,5,54,6,31,5,2,1,3,20,6,264,18,9,4,4,16,67,54,9,51,125,5,6,2,6,3,11,3,3,6,10,8,2,2,4,6,7,3,2,6,6,17,17,2,3,6,10,7,3,15,7,3,8,7,24,7,2,4,6,7,7,1,2,6,4,7,16,4,5,7,37,8,19,83,23, 18186,18287,18292,18347,18353,18391,18399,18403,18405,18411,18938,18944,19208,19226,19235,19239,19243,19261,19328,19383,19392,19443,19571,19576,19583,19585,19592,19596,19607,19611,19621,19641,19654,19662,19666,19668,19672,19679,19688,19691,19694,19700,19707,19725,19742,19744,19747,19753,19770,19780,19784,19801,19811,19814,19822,19829,19853,19860,19862,19866,19872,19879,19890,19891,19893,19899,19904,19917,20268,20273,20278,21912,21949,21957,21981,22071, 392548,392653,392659,392713,392724,392755,392760,392762,392763,392766,486667,486674,486939,515916,552330,552335,552340,552356,552425,552479,625751,625803,625928,669185,669191,669194,669200,669203,669215,669218,669221,669227,669237,669248,669250,669253,669259,669265,669272,669276,669278,669289,669295,669312,669332,669335,669339,669346,669356,669363,669366,669381,669388,669393,669404,669412,669437,669446,669450,669455,669463,669471,669478,669480,669483,669490,669494,669501,799219,799223,799231,816160,816203,816213,816232,816315, 1376 0 0 0 40 581 41 202198 - NOTCH2-201 158114 18101 20058 120 1393864 594111 797685 82 7,1,8,89,72,13,121,5,3,13,4,3,130,4,6,4,139,8,7,10,5,1,8,5,4,1,1,7,6,4,17,17,4,5,7,2,6,4,3,2,12,5,12,6,13,3,8,3,7,13,2,7,3,4,3,8,16,17,21,1,2,82,5,3,2,2,5,1,9,58,2,4,1,93,91,4,10,26,40,2,2,12, 138056,138542,138543,138551,138640,138716,138729,138850,138855,138858,138873,138879,138883,139017,139021,139027,139031,139170,139178,139185,139195,139200,139201,139213,139219,139226,139231,139236,139244,139250,139254,139271,139291,139297,139306,139320,139324,139330,139334,139339,139342,139355,139363,139375,139382,139399,139405,139413,139417,139426,139441,139444,139453,139456,139462,139467,139475,139491,139511,139532,139533,139538,139620,139625,139628,139630,139632,139637,139638,139648,139714,139719,139724,139728,139821,139915,139919,139929,139955,139997,139999,140001, 594111,594118,662683,662692,662784,662856,777094,777216,777223,777230,777243,777247,777250,777380,777385,777392,777398,777543,777558,777566,777577,778873,778875,778883,778888,778892,778893,778894,778901,778908,778913,778932,778949,778953,778958,778965,778967,778974,778979,778982,778984,778996,779001,779022,779028,779041,779044,779055,779058,779065,779078,779080,779087,779091,779095,779098,779112,797152,797169,797192,797194,797196,797283,797291,797296,797299,797304,797315,797317,797326,797384,797386,797390,797391,797486,797577,797584,797598,797625,797665,797668,797673, -453 0 0 0 8 971 5 14425 - NOTCH2-201 1424 0 1424 4008 854445 681194 696072 13 7,17,3,7,2,4,159,135,49,2,8,9,51, 0,964,984,988,995,997,1001,1161,1301,1352,1355,1364,1373, 681194,695614,695631,695634,695643,695647,695655,695814,695949,695998,696000,696008,696021, +453 0 0 0 8 971 5 14425 - NOTCH2-201 158114 40699 42123 4008 854445 681194 696072 13 7,17,3,7,2,4,159,135,49,2,8,9,51, 115991,116955,116975,116979,116986,116988,116992,117152,117292,117343,117346,117355,117364, 681194,695614,695631,695634,695643,695647,695655,695814,695949,695998,696000,696008,696021, 734 0 0 0 12 342 11 1490 + NOTCH2-201 158114 40699 41775 4234 1362281 881146 883370 23 54,15,2,29,4,7,47,131,4,48,66,6,6,34,58,13,2,45,19,3,81,30,30, 40699,40753,40769,40773,40807,40815,40824,40871,41009,41013,41061,41127,41133,41139,41483,41543,41558,41560,41605,41624,41631,41714,41745, 881146,881202,881217,881219,881248,881252,881259,881307,881438,881444,881493,881560,881567,881576,883084,883142,883155,883159,883206,883226,883229,883310,883340, -751 0 0 0 17 2232 10 51257 + NOTCH2-201 2983 0 2983 6548 185744 21727 73735 26 8,5,4,62,1,17,1,3,1,18,4,6,239,2,61,4,2,29,122,45,1,40,17,29,4,26, 0,1892,1897,1902,1964,1965,1983,1985,1995,1999,2019,2024,2032,2271,2274,2335,2340,2344,2691,2813,2858,2861,2903,2922,2951,2957, 21727,38051,38059,38063,38127,38129,38146,38147,38150,38151,38169,38173,38179,38420,38422,38486,38490,38492,73448,73571,73617,73618,73658,73675,73705,73709, -944 0 0 0 43 5081 18 342350 - NOTCH2-201 6025 0 6025 4026 1754125 1004160 1347454 59 8,7,7,8,3,31,28,81,2,17,66,66,3,3,3,1,1,6,1,8,5,1,2,3,15,6,5,4,4,2,11,16,2,6,6,3,12,4,6,9,2,24,3,4,2,10,27,7,69,35,2,114,2,69,47,11,6,18,20, 0,1288,2328,3876,4965,4968,5000,5030,5115,5117,5134,5202,5269,5274,5278,5281,5286,5292,5300,5304,5312,5320,5322,5325,5329,5344,5353,5363,5370,5374,5376,5388,5408,5411,5419,5426,5438,5457,5467,5475,5525,5528,5553,5559,5563,5565,5576,5603,5613,5682,5719,5721,5844,5847,5921,5968,5980,5986,6005, 1004160,1013041,1077122,1178002,1178010,1238950,1238981,1239009,1239090,1239096,1239115,1239181,1239247,1239250,1239253,1239257,1239258,1239259,1239265,1239266,1239276,1239281,1239282,1239284,1239287,1346862,1346868,1346873,1346877,1346882,1346888,1346899,1346915,1346917,1346923,1346929,1346932,1346944,1346948,1346954,1346963,1346965,1346989,1346992,1346998,1347002,1347012,1347042,1347049,1347119,1347154,1347158,1347272,1347274,1347343,1347395,1347406,1347416,1347434, +751 0 0 0 17 2232 10 51257 + NOTCH2-201 158114 38792 41775 6548 185744 21727 73735 26 8,5,4,62,1,17,1,3,1,18,4,6,239,2,61,4,2,29,122,45,1,40,17,29,4,26, 38792,40684,40689,40694,40756,40757,40775,40777,40787,40791,40811,40816,40824,41063,41066,41127,41132,41136,41483,41605,41650,41653,41695,41714,41743,41749, 21727,38051,38059,38063,38127,38129,38146,38147,38150,38151,38169,38173,38179,38420,38422,38486,38490,38492,73448,73571,73617,73618,73658,73675,73705,73709, +944 0 0 0 43 5081 18 342350 - NOTCH2-201 158114 40718 46743 4026 1754125 1004160 1347454 59 8,7,7,8,3,31,28,81,2,17,66,66,3,3,3,1,1,6,1,8,5,1,2,3,15,6,5,4,4,2,11,16,2,6,6,3,12,4,6,9,2,24,3,4,2,10,27,7,69,35,2,114,2,69,47,11,6,18,20, 111371,112659,113699,115247,116336,116339,116371,116401,116486,116488,116505,116573,116640,116645,116649,116652,116657,116663,116671,116675,116683,116691,116693,116696,116700,116715,116724,116734,116741,116745,116747,116759,116779,116782,116790,116797,116809,116828,116838,116846,116896,116899,116924,116930,116934,116936,116947,116974,116984,117053,117090,117092,117215,117218,117292,117339,117351,117357,117376, 1004160,1013041,1077122,1178002,1178010,1238950,1238981,1239009,1239090,1239096,1239115,1239181,1239247,1239250,1239253,1239257,1239258,1239259,1239265,1239266,1239276,1239281,1239282,1239284,1239287,1346862,1346868,1346873,1346877,1346882,1346888,1346899,1346915,1346917,1346923,1346929,1346932,1346944,1346948,1346954,1346963,1346965,1346989,1346992,1346998,1347002,1347012,1347042,1347049,1347119,1347154,1347158,1347272,1347274,1347343,1347395,1347406,1347416,1347434, 478 0 0 0 12 1945 6 16363 - NOTCH2-201 158114 38792 41215 8926 721618 147211 164052 18 13,4,60,2,1,63,3,239,5,5,18,1,3,1,17,1,24,18, 116899,116914,116918,116980,116983,116984,117048,117051,117292,117298,117305,117332,117334,117338,117340,117357,117358,119304, 147211,147224,147229,147289,147291,147295,147358,147363,147602,147607,147612,147630,147631,147634,147635,147653,147656,164034, -745 0 0 0 9 6055 15 322549 - NOTCH2-201 6800 0 6800 6866 519917 75932 399226 22 20,43,15,2,58,2,7,111,7,28,7,4,8,5,219,20,53,3,102,21,1,9, 0,20,63,79,81,141,144,151,262,270,298,305,3277,5127,5132,6588,6608,6661,6666,6769,6790,6791, 75932,75953,75998,76013,76016,76074,76076,76086,76198,76205,76235,77616,262197,398372,398378,399012,399033,399088,399091,399193,399215,399217, -433 0 0 0 7 2846 13 58582 + NOTCH2-201 3279 0 3279 7542 170510 20502 79517 19 7,7,4,4,6,6,27,2,61,18,21,12,29,4,5,1,115,9,95, 0,1234,2853,2857,2862,2871,2877,2904,2907,2968,2987,3008,3020,3049,3054,3059,3060,3175,3184, 20502,23589,79082,79087,79091,79097,79106,79134,79136,79198,79216,79238,79251,79282,79286,79292,79294,79410,79422, -274 0 0 0 4 3525 4 153039 + NOTCH2-201 3799 0 3799 866 1781753 575630 728943 7 117,22,3,108,3,6,15, 0,117,139,144,253,2724,3784, 575630,575748,575772,575775,575883,725690,728928, +745 0 0 0 9 6055 15 322549 - NOTCH2-201 158114 31332 38132 6866 519917 75932 399226 22 20,43,15,2,58,2,7,111,7,28,7,4,8,5,219,20,53,3,102,21,1,9, 119982,120002,120045,120061,120063,120123,120126,120133,120244,120252,120280,120287,123259,125109,125114,126570,126590,126643,126648,126751,126772,126773, 75932,75953,75998,76013,76016,76074,76076,76086,76198,76205,76235,77616,262197,398372,398378,399012,399033,399088,399091,399193,399215,399217, +433 0 0 0 7 2846 13 58582 + NOTCH2-201 158114 23795 27074 7542 170510 20502 79517 19 7,7,4,4,6,6,27,2,61,18,21,12,29,4,5,1,115,9,95, 23795,25029,26648,26652,26657,26666,26672,26699,26702,26763,26782,26803,26815,26844,26849,26854,26855,26970,26979, 20502,23589,79082,79087,79091,79097,79106,79134,79136,79198,79216,79238,79251,79282,79286,79292,79294,79410,79422, +274 0 0 0 4 3525 4 153039 + NOTCH2-201 158114 20764 24563 866 1781753 575630 728943 7 117,22,3,108,3,6,15, 20764,20881,20903,20908,21017,23488,24548, 575630,575748,575772,575775,575883,725690,728928,