root/galaxy-central/test-data/sort_out2.bed

chr6    108298214       108386086       NM_007214       0       -       108299600       108385906       0       21      1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304,   0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
chr6    108593954       108616704       NM_003269       0       +       108594662       108615360       0       9       733,146,88,236,147,97,150,106,1507,     0,5400,8778,10445,12037,14265,14749,15488,21243,
chr6    108639410       108689143       NM_152827       0       -       108640045       108688818       0       3       741,125,487,    0,2984,49246,
chr6    108722790       108950942       NM_145315       0       +       108722976       108950321       0       13      325,224,52,102,131,100,59,83,71,101,141,114,750,        0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
chr7    113320332       113924911       AK131266        0       +       113862563       113893433       0       20      285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124,        0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
chr7    116511232       116557294       NM_003391       0       -       116512159       116556994       0       5       1157,265,278,227,383,   0,20384,37843,43339,45679,
chr7    116713967       116902666       NM_000492       0       +       116714099       116901113       0       27      185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754,  0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
chr7    116944658       117107512       AF377960        0       -       116945541       116979926       0       23      1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173,      0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
chr2    118288484       118306183       NM_006773       0       +       118288583       118304530       0       14      184,285,144,136,101,200,115,140,162,153,114,57,178,1796,        0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
chr2    118389378       118390700       BC005078        0       -       118390395       118390500       0       1       1322,   0,
chr8    118880786       119193239       NM_000127       0       -       118881131       119192466       0       11      531,172,161,90,96,119,133,120,108,94,1735,      0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
chrX    122719582       122773357       NM_001167       0       +       122745047       122766566       0       7       96,909,100,79,43,201,6985,      0,25433,28421,31040,32533,40295,46790,
chr9    128763240       128783870       NM_174933       0       +       128764156       128783586       0       12      261,118,74,159,76,48,56,63,129,117,127,370,     0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
chr9    128787362       128789566       NM_014908       0       -       128787519       128789136       0       1       2204,   0,
chr9    128789530       128848928       NM_015354       0       +       128789552       128848511       0       44      54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594,   0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
chr9    128849867       128870133       NM_020145       0       -       128850516       128869987       0       11      757,241,101,90,24,63,93,134,129,142,209,        0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
chr5    131170738       131357870       AF099740        0       -       131311206       131357817       0       31      112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248,    0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
chr5    131424245       131426795       NM_000588       0       +       131424298       131426383       0       5       215,42,90,42,535,       0,313,1658,1872,2015,
chr5    131556201       131590458       NM_004199       0       -       131556601       131582218       0       15      471,97,69,66,54,100,71,177,194,240,138,152,97,100,170,  0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
chr5    131621285       131637046       NM_003687       0       +       131621326       131635821       0       7       134,152,82,179,164,118,1430,    0,4915,8770,13221,13609,14097,14331,
chr1    147962006       147975713       NM_005997       0       -       147962192       147975670       0       6       574,145,177,115,153,160,        0,1543,7859,9048,9340,13547,
chr1    147984101       148035079       BC007833        0       +       147984545       148033414       0       14      529,32,81,131,118,153,300,206,84,49,85,130,46,1668,     0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
chr1    148077485       148111797       NM_002651       0       -       148078400       148111728       0       12      1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
chr1    148185113       148187485       NM_002796       0       +       148185136       148187378       0       7       163,207,147,82,117,89,120,      0,416,877,1199,1674,1977,2252,
chrX    152648233       152662158       NM_000425       0       -       152648964       152662138       0       28      963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100,    0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
chrX    152691216       152693487       NM_000054       0       +       152691446       152693029       0       3       255,885,664,    0,616,1607,
chrX    152693677       152712545       NM_001666       0       -       152694029       152712503       0       22      586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109,       0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
chr2    220108603       220116964       NM_001927       0       +       220108689       220116217       0       9       664,61,96,162,126,221,44,83,789,        0,1718,1874,2118,2451,2963,5400,7286,7572,
chr2    220229182       220233943       NM_024536       0       -       220229609       220233765       0       4       1687,180,574,492,       0,1990,2660,4269,