674696c75bd0ccdbdc2ca7a1c2bb3068545e7236 kent Tue Mar 19 13:09:53 2013 -0700 Making C version of genePredToBed so as to have somewhat better error reporting. diff --git src/hg/genePredToBed/expected.bed src/hg/genePredToBed/expected.bed new file mode 100644 index 0000000..b644b89 --- /dev/null +++ src/hg/genePredToBed/expected.bed @@ -0,0 +1,100 @@ +chr6 46517444 46620523 uc011dwa.1 0 - 46518102 46620319 0 12 730,88,89,96,134,91,108,94,150,115,136,381, 0,4059,37369,38326,46279,75710,81255,86681,88121,89786,92455,102698, +chr13 108439708 108487799 uc001vqm.3 0 - 108439708 108439708 0 2 1750,50, 0,48041, +chr18 14089933 14091018 uc002kss.3 0 + 14089933 14089933 0 1 1085, 0, +chr3 142720380 142779567 uc003evk.1 0 + 142720470 142775292 0 28 135,45,132,99,115,134,68,95,33,83,166,212,44,105,67,164,163,80,88,123,157,96,67,160,111,119,177,4414, 0,9276,10683,12772,14718,15303,18430,19060,19811,19934,20958,21314,22436,25610,26801,26944,31245,31732,33349,34443,35640,36569,37355,41578,49400,52137,53404,54773, +chr14 88882269 88904804 uc001xwt.3 0 + 88883134 88904766 0 8 919,473,67,116,54,78,55,623, 0,10306,11704,13422,15246,17209,21617,21912, +chr6 33849611 33849646 uc003ofz.3 0 - 33849611 33849611 0 1 35, 0, +chr5 178029664 178054054 uc011dgg.1 0 - 178030846 178050417 0 10 1094,59,95,167,117,67,91,223,161,108, 0,1180,10132,10809,11063,14218,14680,15892,20592,24282, +chr1 9656916 9674935 uc021ofz.1 0 + 9658554 9673141 0 8 195,177,350,204,233,300,138,1892, 0,1590,4246,5210,10698,13647,14894,16127, +chr1 146032541 146068252 uc001eoy.3 0 - 146034391 146057327 0 23 1867,109,169,52,173,52,173,52,164,52,206,73,215,103,210,212,73,215,210,148,124,142,99, 0,2497,3320,4147,4908,5677,6448,7254,8348,12407,13748,14418,15527,16575,18456,20010,20684,21757,24733,25045,33025,33573,35612, +chr21 46934628 46962385 uc010gpz.2 0 - 46935571 46951888 0 6 1426,142,202,760,242,104, 0,11102,16055,16674,23052,27653, +chr13 24844856 24881212 uc010tdb.2 0 + 24844995 24876911 0 9 194,137,180,180,233,130,373,75,4477, 0,13416,15495,18280,19933,24020,26644,29682,31879, +chr2 212240441 213403352 uc002veh.1 0 - 212248339 213403254 0 27 8344,298,171,98,147,76,156,186,99,123,133,75,155,94,133,200,91,74,127,114,142,119,66,135,187,152,180, 0,11136,44724,46290,48438,52691,55228,186186,243460,248205,254745,282037,289606,297447,303335,326250,328387,329601,336333,337818,346676,349359,374922,412308,571713,749035,1162731, +chr8 17154305 17271040 uc003wxm.3 0 - 17157370 17270801 0 14 3428,127,141,201,50,126,110,133,135,129,158,163,123,263, 0,5357,7582,8960,12480,14714,16495,34353,44566,52156,64320,74240,76321,116472, +chr17 43180318 43181690 uc010dad.1 0 + 43180345 43181460 0 2 171,614, 0,758, +chr7 1626206 1629259 uc021zys.1 0 + 1626842 1627634 0 1 3053, 0, +chrY 15434947 15592550 uc022cnl.1 0 - 15435228 15591545 0 20 323,206,106,130,773,396,96,93,90,220,127,94,35,55,121,59,50,109,64,1157, 0,487,1533,3153,12495,31935,32855,34809,35396,36699,43199,46188,70791,73850,87925,91667,125949,147053,156186,156446, +chr20 1876084 1920540 uc002wft.3 0 + 1876093 1918214 0 8 88,357,318,333,114,25,52,2575, 0,19660,25956,26874,29325,32436,39276,41881, +chr4 37828281 37864559 uc011byb.1 0 + 37828354 37863233 0 14 154,168,107,85,84,194,190,98,181,94,130,190,134,1429, 0,3304,7958,10869,13188,13406,17703,18972,20270,20541,21861,23523,28947,34849, +chr6_apd_hap1 873546 904496 uc011eih.2 0 - 874861 903697 0 23 1489,144,129,128,94,108,117,133,151,78,64,243,192,66,102,171,135,161,21,186,204,85,335, 0,2266,2632,3341,4163,4670,4875,6374,7002,8697,10324,11016,18861,19512,19864,21065,21650,25251,26852,28223,29161,30066,30615, +chr3 46477495 46526724 uc003cpr.3 0 - 46477685 46509745 0 20 225,190,185,68,142,156,54,91,155,175,179,56,148,183,109,164,68,149,106,249, 0,1935,3291,5411,7436,9276,10435,11303,12858,13848,14489,18299,19289,19790,20284,23650,32246,33441,34355,48980, +chr4 22388998 22457457 uc010ieo.1 0 - 22389327 22457454 0 17 1572,96,146,124,125,209,160,204,162,156,202,165,214,161,72,72,26, 0,1712,5169,14055,15299,25806,26225,33510,36815,47935,49064,50880,55274,57597,60064,67490,68433, +chr2 87011727 87018837 uc002sru.3 0 - 87013042 87017948 0 5 1367,31,111,354,938, 0,3925,5035,5723,6172, +chr16 3019341 3023485 uc002csk.4 0 + 3019675 3021949 0 3 500,105,1970, 0,1933,2174, +chr11 111322063 111327330 uc001pli.1 0 + 111322131 111327264 0 6 71,175,122,126,122,91, 0,2070,2897,3624,4418,5176, +chr1 98157272 98386615 uc010oub.1 0 - 98157272 98157272 0 7 82,197,113,162,88,83,176, 0,7634,8473,29793,48675,136397,229167, +chr16 55836763 55867075 uc002eim.3 0 - 55836960 55866967 0 14 381,73,132,148,84,141,39,105,108,154,134,145,205,160, 0,677,3481,7665,8075,10051,14072,16683,17520,18516,20698,23299,25915,30152, +chr10 47083533 47088320 uc001jee.3 0 + 47086783 47087911 0 3 204,156,1596, 0,2000,3191, +chrX 64770501 64772301 uc022bye.1 0 - 64771062 64772172 0 1 1800, 0, +chr15 31361592 31393929 uc001zfn.4 0 - 31362035 31369124 0 3 837,80,70, 0,7515,32267, +chr6_ssto_hap7 2701358 2716888 uc021zwf.1 0 + 2712338 2714006 0 6 980,255,288,279,136,302, 0,10759,11288,12163,12541,15228, +chr15 89859535 89878026 uc002bns.4 0 - 89859981 89876985 0 23 523,161,209,169,123,247,136,118,54,161,108,87,121,237,127,152,183,80,147,168,196,818,123, 0,1071,2236,2626,2923,4461,4820,5431,5657,6437,7099,7510,7802,9145,10307,10607,10862,12151,12380,12638,13776,16791,18368, +chr1 155658881 155708800 uc010pgl.2 0 + 155679570 155708033 0 12 84,52,102,109,93,131,81,159,60,90,118,853, 0,20682,32426,36291,36836,38517,39951,40117,42265,42853,47855,49066, +chr1 213165523 213189168 uc001hka.3 0 - 213168382 213181686 0 8 3011,164,58,127,422,70,257,214, 0,4973,8144,8604,12851,14947,16028,23431, +chr1 117602948 117645491 uc001egy.3 0 + 117602968 117644146 0 23 48,103,87,67,990,115,183,128,82,120,151,106,182,154,92,83,134,171,59,151,83,75,1490, 0,128,2060,13334,14543,15853,16314,17589,19241,21501,23691,26090,28474,29728,30205,31001,31490,32404,34982,35822,37024,38506,41053, +chr5 90076897 90460033 uc003kjw.3 0 + 90077181 90459717 0 26 498,202,220,240,150,474,144,175,136,1106,118,172,243,408,185,250,140,161,101,117,179,158,122,192,178,435, 0,2043,2757,6990,8621,9792,21658,24203,26521,29152,34538,42344,47863,59497,67556,72203,72981,74660,82676,184334,204263,291366,321138,368949,372140,382701, +chr16 86508130 86542466 uc021tmg.1 0 - 86508130 86508130 0 4 2675,166,52,206, 0,3361,4180,34130, +chr6_dbb_hap3 3892030 3893069 uc011gka.2 0 + 3892030 3892030 0 2 175,705, 0,334, +chr6 32150344 32152099 uc011dpq.2 0 - 32150555 32152092 0 6 456,88,113,196,107,152, 0,546,708,987,1313,1603, +chr4 13527942 13533041 uc010idp.1 0 - 13527942 13527942 0 4 1575,96,181,270, 0,1832,2603,4829, +chr7 91712483 91719937 uc003ulk.3 0 + 91712498 91719007 0 6 486,64,122,192,189,1239, 0,1470,1649,2325,3058,6215, +chr3 133502876 133540336 uc003epx.2 0 + 133524692 133538610 0 8 112,327,95,78,83,137,55,1940, 0,21643,22576,23713,27084,31557,32845,35520, +chr12 55688071 55689016 uc010sph.2 0 - 55688071 55689016 0 1 945, 0, +chr5 56469774 56560506 uc003jri.4 0 + 56542161 56558579 0 11 264,953,124,224,67,185,141,168,188,103,2086, 0,1500,56898,57150,62018,72352,73127,75461,77006,87232,88646, +chr2 202004997 202037411 uc002uxg.3 0 + 202014500 202028696 0 6 165,55,50,82,511,8854, 0,5103,8728,9479,20157,23560, +chr22 47070504 47075688 uc003bhy.3 0 + 47070600 47073148 0 4 143,85,69,2645, 0,860,1992,2539, +chr2 227833704 227833838 uc021vxp.1 0 - 227833704 227833704 0 1 134, 0, +chr2 191334217 191367041 uc010zge.1 0 + 191334565 191364944 0 6 158,98,162,99,281,2301, 0,266,19165,20276,27947,30523, +chr19 44084789 44088114 uc002owv.1 0 + 44085440 44085896 0 3 32,153,2400, 0,574,925, +chr2 128712559 128785633 uc002tpq.1 0 - 128712560 128783866 0 16 359,105,178,303,122,142,105,91,145,125,125,112,159,236,118,120, 0,22999,31799,34578,38201,41364,44755,45070,45321,55283,58044,59817,61403,62694,71195,72954, +chr3 52350334 52434513 uc011bef.2 0 + 52356458 52434462 0 78 227,367,73,175,157,133,162,253,158,212,299,151,194,226,120,83,142,156,199,254,213,165,122,106,180,141,164,114,189,106,114,150,87,187,92,155,178,195,120,159,108,141,161,158,174,39,179,231,197,136,209,172,192,111,186,192,168,192,132,126,120,150,161,226,196,152,197,145,159,132,171,180,177,171,131,352,235,173, 0,6090,7489,9821,10416,11563,14829,15823,28171,29176,30153,31505,32569,32876,33670,34189,35643,36233,36784,37061,38524,40295,41295,41579,42239,42927,43597,43992,44845,45342,46069,46676,48319,48514,50138,50414,52422,53506,53791,54158,54399,55627,55908,56577,58921,59636,62283,63586,65321,66001,67067,67541,68467,69018,69841,70343,71848,72099,72487,73142,74616,74860,75124,76145,76511,77015,78146,78596,78989,79228,80049,80299,80549,81388,81713,82531,83226,84006, +chr17 45401326 45518677 uc002iln.3 0 + 45405719 45518080 0 25 114,70,162,115,161,112,131,83,144,144,72,495,138,72,144,75,144,72,144,72,45,144,72,144,881, 0,493,2265,4308,11235,17960,20201,21055,23847,37417,46476,50511,53805,55221,67476,70064,71873,78171,79917,80601,85686,88812,90887,105857,116470, +chr12 17141680 17143562 uc021qvt.1 0 + 17141948 17142548 0 1 1882, 0, +chr11 33724555 33744273 uc001mus.4 0 - 33731671 33743991 0 3 7334,102,349, 0,14360,19369, +chr5 160060261 160112267 uc003lyo.2 0 - 160061151 160112227 0 7 1352,128,132,107,86,205,426, 0,2927,7206,10883,15916,37208,51580, +chr17 18325494 18328647 uc002gtv.3 0 + 18325582 18326029 0 1 3153, 0, +chr19_gl000209_random 149188 153112 uc002qup.1 0 + 149293 153110 0 3 286,300,295, 0,1750,3629, +chr17 34261522 34266560 uc002hkj.2 0 - 34261799 34266360 0 4 347,79,159,339, 0,2236,3239,4699, +chr6 157802556 158094977 uc003qqt.3 0 + 157803053 158094154 0 9 742,161,159,138,49,103,110,103,1222, 0,161060,211463,246824,251309,264212,265734,272000,291199, +chr6 44107444 44123256 uc010jyz.3 0 + 44107444 44107444 0 16 52,109,71,81,124,134,138,154,107,87,66,163,106,168,81,828, 0,544,1320,7139,7669,8544,8805,9084,10151,10516,10856,12138,12885,13968,14657,14984, +chr4 78079449 78091213 uc003hkp.4 0 + 78079685 78087077 0 7 374,138,251,79,99,206,4260, 0,1070,2424,3183,3352,5977,7504, +chr3 38589552 38691164 uc021wvt.1 0 - 38597226 38674798 0 28 3497,175,101,138,54,282,123,174,155,121,159,441,351,174,239,133,372,180,198,142,64,231,92,129,90,119,325,143, 0,6313,7594,8379,9169,12085,14353,18347,27235,28599,31272,32869,37629,39338,49667,50856,55650,56667,57889,58607,60089,61672,65913,72781,74338,82249,84973,101469, +chr1 228395860 228548951 uc001hsn.3 0 + 228399484 228548456 0 81 26,1006,270,261,309,267,282,276,276,276,276,276,276,276,276,276,276,279,267,270,267,267,113,154,105,267,270,267,267,267,273,267,267,273,267,267,264,264,264,264,264,264,264,267,267,273,273,197,76,273,276,288,282,371,871,279,79,125,198,33,99,219,61,71,123,140,201,83,174,157,117,165,159,178,114,168,103,130,112,43,1654, 0,3606,5281,6014,6630,7403,8261,8853,16299,35023,36136,37253,38368,41805,48491,55956,60370,65610,66018,66412,67600,68290,68770,69000,69594,70529,71015,71661,72019,72370,73773,74858,75343,77918,78613,79534,79901,80465,83738,84363,85193,85992,86620,98212,98741,99099,99951,100939,101324,107687,108549,109304,109732,110724,113184,115168,124700,125039,125423,126352,126655,126920,127631,128040,128844,129084,129784,130130,130693,131785,132346,132564,132935,133277,133959,141730,142681,143161,144791,147991,151437, +chr1 114437370 114447741 uc010owp.2 0 - 114437686 114445300 0 11 744,282,208,104,84,497,148,131,97,189,178, 0,1008,1509,3091,3969,5155,6487,7006,7889,9856,10193, +chr5 68660569 68662644 uc003jwc.1 0 - 68660769 68661564 0 2 1012,315, 0,1760, +chr19 3880617 3928080 uc002lyy.4 0 + 3885765 3924590 0 13 389,118,59,222,186,103,132,87,99,36,72,33,3500, 0,5107,21867,24814,27114,27648,28866,30183,33138,37122,38186,40146,43963, +chr6 37273649 37300746 uc003onp.3 0 + 37280737 37298948 0 6 284,107,76,128,96,1927, 0,7044,7942,10829,11237,25170, +chr17 10616638 10633646 uc002gmx.3 0 - 10618769 10633168 0 6 2267,60,124,61,30,550, 0,9948,11689,12882,15709,16458, +chr2 234627437 234681951 uc002vux.3 0 + 234627466 234681205 0 5 896,132,88,220,1044, 0,48242,49057,49428,53470, +chr6_mcf_hap5 4745788 4755906 uc011idk.2 0 - 4745788 4755560 0 5 371,399,261,171,383, 0,721,8947,9424,9735, +chr1 144160410 144201052 uc021otk.1 0 + 144163792 144201051 0 22 177,52,173,109,173,52,173,52,173,109,173,52,173,52,173,109,173,52,173,52,173,60, 0,886,1590,2477,3216,4108,19063,19945,20653,21540,22285,27941,28601,29483,30171,35820,36565,37457,38109,38991,39695,40582, +chr5 87491022 87516536 uc011ctx.2 0 - 87492027 87502897 0 8 1283,97,94,114,141,61,114,157, 0,2463,3770,7756,10608,11233,11823,25357, +chr6 101846860 102517958 uc010kcw.3 0 + 101847153 102513788 0 17 408,168,258,182,54,174,144,108,114,207,224,119,218,226,251,132,1737, 0,222963,227394,277637,283567,287194,400662,403345,419384,460301,490654,525615,529429,636355,656344,666811,669361, +chr14 31803517 31926680 uc010tpk.1 0 - 31803606 31872181 0 25 145,139,170,190,160,191,106,176,164,110,100,153,112,251,156,256,161,175,150,109,212,200,45,70,192, 0,3164,9584,10775,13436,15477,16300,24325,24582,29877,37498,40504,46155,49209,52108,52808,54533,59740,60887,64361,65989,68538,93832,118963,122971, +chr18 19408964 19409049 uc021uic.1 0 - 19408964 19408964 0 1 85, 0, +chr15 85115422 85123412 uc002bko.2 0 + 85115422 85115422 0 3 148,230,2234, 0,830,5756, +chr11 94501507 94609918 uc001pfc.3 0 + 94501677 94603960 0 12 219,922,292,145,90,146,150,191,126,227,276,6065, 0,31048,53188,61708,63110,81771,85590,91182,96392,97599,100855,102346, +chrX 78426468 78427726 uc004edg.1 0 + 78426504 78427506 0 1 1258, 0, +chr11 61595712 61631693 uc001nsk.3 0 + 61595862 61631262 0 10 357,111,198,102,126,61,77,98,97,515, 0,9537,12093,12383,19918,28770,29213,34731,35041,35466, +chr3 128628708 128712919 uc003elg.1 0 - 128629141 128712147 0 8 468,147,125,88,141,214,191,1034, 0,61421,65913,67113,68179,77750,78862,83177, +chr2 36779403 36825332 uc002rph.2 0 - 36780305 36825285 0 8 919,66,76,269,142,117,109,313, 0,3422,6177,26336,29029,31092,38642,45616, +chr6_apd_hap1 3447095 3451054 uc011epm.1 0 + 3448683 3450474 0 9 79,129,123,110,96,171,80,154,627, 0,1560,1920,2123,2332,2509,2772,2925,3332, +chr1 144480744 144521009 uc001ela.4 0 - 144480744 144480744 0 2 1021,236, 0,40029, +chr1 6161846 6191808 uc001alz.2 0 - 6165427 6189087 0 21 3641,54,164,196,133,109,138,90,133,80,160,145,134,89,93,175,173,111,232,181,118, 0,4447,4829,8008,8607,9988,10353,11122,19318,19707,22161,22730,23313,23737,23979,24785,26259,26712,27051,28361,29844, +chr13 64560503 64650144 uc001vii.1 0 - 64560503 64560503 0 6 669,105,25,118,191,770, 0,3725,16014,16977,47976,88871, +chr1 218715031 218715241 uc021pjc.1 0 - 218715031 218715031 0 1 210, 0, +chr17 28268622 28435470 uc002het.3 0 + 28268814 28435042 0 23 234,63,85,577,157,49,71,156,100,894,78,93,215,157,290,170,229,153,104,254,287,97,619, 0,635,1960,27186,51560,54707,58301,92625,109513,111650,114283,114459,116071,117940,136610,138467,139148,141286,145458,148816,150266,151235,166229, +chr5 180688222 180699308 uc003mnq.3 0 + 180688222 180688222 0 3 163,117,392, 0,10351,10694, +chr19 48711342 48752925 uc021uwq.1 0 - 48714966 48737735 0 10 3890,45,142,126,260,230,151,141,102,146, 0,7254,10785,13644,22352,22691,23574,26317,32876,41437, +chr11 86013252 86056985 uc001pbu.3 0 + 86013490 86056680 0 5 268,238,152,119,360, 0,4034,35168,42392,43373, +chr6_mann_hap4 991939 1007473 uc011gpx.1 0 + 991939 991939 0 7 270,259,276,117,122,156,1068, 0,532,1373,1789,3227,12761,14466, +chr19 35306897 35306939 uc002nwi.3 0 - 35306897 35306897 0 1 42, 0, +chr6_cox_hap2 3170147 3180755 uc011fgh.2 0 - 3170315 3178386 0 6 398,74,86,87,57,211, 0,607,4195,8191,9321,10397, +chr8 71485452 71520694 uc003xyo.2 0 - 71487166 71520434 0 11 1788,161,144,105,71,85,59,117,122,64,383, 0,9946,10432,13677,13888,21288,23045,24677,24916,26801,34859, +chr2 62839006 62889763 uc002sbw.1 0 - 62839006 62839006 0 8 352,76,97,59,124,164,39,21, 0,444,1734,13081,17481,19530,50023,50736, +chr6_mann_hap4 2430964 2456237 uc011gvx.2 0 + 2445776 2456077 0 6 61,164,77,30,124,452, 0,10843,14748,23610,23836,24821, +chr3 118930588 118959752 uc003eci.3 0 - 118931395 118948946 0 8 940,105,123,188,233,398,218,56, 0,4498,6908,12316,15067,18105,25111,29108, +chr20 49202646 49307916 uc010zyt.2 0 - 49203768 49307665 0 22 1223,91,84,203,162,162,136,124,131,573,130,146,126,44,64,150,54,24,79,147,119,254, 0,1692,3576,6234,6925,8443,9259,10030,11470,15962,18535,22279,22503,22802,23183,23463,24743,25071,29892,33876,44628,105016, +chr19 58867504 58869001 uc021vcw.1 0 - 58867504 58869001 0 1 1497, 0, +chr12 10460416 10469850 uc009zhh.3 0 + 10460676 10467392 0 5 267,93,152,104,2579, 0,1570,3646,5592,6855, +chr5 304291 438405 uc003jaw.3 0 + 304334 434949 0 11 45,72,182,107,90,130,137,200,62,142,4438, 0,39716,49553,72433,109167,118552,119664,123630,128286,128629,129676,