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from pathlib import Path
DATA_PATH = Path("../../data")
#TEST_SAMPLES = DATA_PATH / 'test_samples_with_flag.tsv'
#READS = DATA_PATH / 'SLX-11873.D707_D502.HFNWFBBXX.s_5.GRCh37.bwa2.bamdownsample001.sorted.bam'
# GENOME = DATA_PATH / 'Homo_sapiens.GRCh37.87.gff3.gz'
GH38_GENOME = DATA_PATH / 'Homo_sapiens.GRCh38.109.gff3.gz'
GH38_REGULATION = DATA_PATH / 'homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20221007.gff.gz'
#CLASSIFICATIONS_DB = DATA_PATH / 'classifications_db.npy'
#REGULATIONS_DB = DATA_PATH / 'regulations_db.npy'
SEGWAY_ENCYCLOPEDIA_37 = DATA_PATH / 'segway_encyclopedia.bed.gz'
SEGWAY_ENCYCLOPEDIA_38 = DATA_PATH / 'segway_encyclopedia_with_header_hg38.bed.gz'
CHROMOSOME_TO_INT_GH37 = {'10': 10, '11': 11, '12': 12, '13': 13, '14': 14, '15': 15, '16': 16, '17': 17, '18': 18,
'19': 19, '1': 1, '20': 20, '21': 21, '22': 22, '2': 2, '3': 3, '4': 4, '5': 5, '6': 6,
'7': 7, '8': 8, '9': 9, 'MT': 23, 'X': 24, 'Y': 25, "GL000192.1": 26, "GL000225.1": 27,
"GL000194.1": 28, "GL000193.1": 29, "GL000200.1": 30, "GL000222.1": 31, "GL000212.1": 32,
"GL000195.1": 33, "GL000223.1": 34, "GL000224.1": 35, "GL000219.1": 36, "GL000205.1": 37,
"GL000215.1": 38, "GL000216.1": 39, "GL000217.1": 40, "GL000199.1": 41, "GL000211.1": 42,
"GL000213.1": 43, "GL000220.1": 44, "GL000218.1": 45, "GL000209.1": 46, "GL000221.1": 47,
"GL000214.1": 48, "GL000228.1": 49, "GL000227.1": 50, "GL000191.1": 51, "GL000208.1": 52,
"GL000198.1": 53, "GL000204.1": 54, "GL000233.1": 55, "GL000237.1": 56, "GL000230.1": 57,
"GL000242.1": 58, "GL000243.1": 59, "GL000241.1": 60, "GL000236.1": 61, "GL000240.1": 62,
"GL000206.1": 63, "GL000232.1": 64, "GL000234.1": 65, "GL000202.1": 66, "GL000238.1": 67,
"GL000244.1": 68, "GL000248.1": 69, "GL000196.1": 70, "GL000249.1": 71, "GL000246.1": 72,
"GL000203.1": 73, "GL000197.1": 74, "GL000245.1": 75, "GL000247.1": 76, "GL000201.1": 77,
"GL000235.1": 78, "GL000239.1": 79, "GL000210.1": 80, "GL000231.1": 81, "GL000229.1": 82,
"GL000226.1": 83, "GL000207.1": 84}
CHROMOSOME_TO_INT_GH38 = {'1': 1, '2': 2, '3': 3, '4': 4, '5': 5, '6': 6, '7': 7, '8': 8, '9': 9, '10': 10, '11': 11,
'12': 12, '13': 13, '14': 14, '15': 15, '16': 16, '17': 17, '18': 18, '19': 19, '20': 20,
'21': 21, '22': 22, 'X': 23, 'Y': 24, 'MT': 25, 'GL000008.2': 26, 'GL000009.2': 27,
'GL000194.1': 28, 'GL000195.1': 29, 'GL000205.2': 30, 'GL000208.1': 31, 'GL000213.1': 32,
'GL000214.1': 33, 'GL000216.2': 34, 'GL000218.1': 35, 'GL000219.1': 36, 'GL000220.1': 37,
'GL000221.1': 38, 'GL000224.1': 39, 'GL000225.1': 40, 'GL000226.1': 41, 'KI270302.1': 42,
'KI270303.1': 43, 'KI270304.1': 44, 'KI270305.1': 45, 'KI270310.1': 46, 'KI270311.1': 47,
'KI270312.1': 48, 'KI270315.1': 49, 'KI270316.1': 50, 'KI270317.1': 51, 'KI270320.1': 52,
'KI270322.1': 53, 'KI270329.1': 54, 'KI270330.1': 55, 'KI270333.1': 56, 'KI270334.1': 57,
'KI270335.1': 58, 'KI270336.1': 59, 'KI270337.1': 60, 'KI270338.1': 61, 'KI270340.1': 62,
'KI270362.1': 63, 'KI270363.1': 64, 'KI270364.1': 65, 'KI270366.1': 66, 'KI270371.1': 67,
'KI270372.1': 68, 'KI270373.1': 69, 'KI270374.1': 70, 'KI270375.1': 71, 'KI270376.1': 72,
'KI270378.1': 73, 'KI270379.1': 74, 'KI270381.1': 75, 'KI270382.1': 76, 'KI270383.1': 77,
'KI270384.1': 78, 'KI270385.1': 79, 'KI270386.1': 80, 'KI270387.1': 81, 'KI270388.1': 82,
'KI270389.1': 83, 'KI270390.1': 84, 'KI270391.1': 85, 'KI270392.1': 86, 'KI270393.1': 87,
'KI270394.1': 88, 'KI270395.1': 89, 'KI270396.1': 90, 'KI270411.1': 91, 'KI270412.1': 92,
'KI270414.1': 93, 'KI270417.1': 94, 'KI270418.1': 95, 'KI270419.1': 96, 'KI270420.1': 97,
'KI270422.1': 98, 'KI270423.1': 99, 'KI270424.1': 100, 'KI270425.1': 101, 'KI270429.1': 102,
'KI270435.1': 103, 'KI270438.1': 104, 'KI270442.1': 105, 'KI270448.1': 106, 'KI270465.1': 107,
'KI270466.1': 108, 'KI270467.1': 109, 'KI270468.1': 110, 'KI270507.1': 111, 'KI270508.1': 112,
'KI270509.1': 113, 'KI270510.1': 114, 'KI270511.1': 115, 'KI270512.1': 116, 'KI270515.1': 117,
'KI270516.1': 118, 'KI270517.1': 119, 'KI270518.1': 120, 'KI270519.1': 121, 'KI270521.1': 122,
'KI270522.1': 123, 'KI270528.1': 124, 'KI270529.1': 125, 'KI270530.1': 126, 'KI270538.1': 127,
'KI270539.1': 128, 'KI270544.1': 129, 'KI270548.1': 130, 'KI270579.1': 131, 'KI270580.1': 132,
'KI270581.1': 133, 'KI270582.1': 134, 'KI270583.1': 135, 'KI270584.1': 136, 'KI270587.1': 137,
'KI270588.1': 138, 'KI270589.1': 139, 'KI270590.1': 140, 'KI270591.1': 141, 'KI270593.1': 142,
'KI270706.1': 143, 'KI270707.1': 144, 'KI270708.1': 145, 'KI270709.1': 146, 'KI270710.1': 147,
'KI270711.1': 148, 'KI270712.1': 149, 'KI270713.1': 150, 'KI270714.1': 151, 'KI270715.1': 152,
'KI270716.1': 153, 'KI270717.1': 154, 'KI270718.1': 155, 'KI270719.1': 156, 'KI270720.1': 157,
'KI270721.1': 158, 'KI270722.1': 159, 'KI270723.1': 160, 'KI270724.1': 161, 'KI270725.1': 162,
'KI270726.1': 163, 'KI270727.1': 164, 'KI270728.1': 165, 'KI270729.1': 166, 'KI270730.1': 167,
'KI270731.1': 168, 'KI270732.1': 169, 'KI270733.1': 170, 'KI270734.1': 171, 'KI270735.1': 172,
'KI270736.1': 173, 'KI270737.1': 174, 'KI270738.1': 175, 'KI270739.1': 176, 'KI270740.1': 177,
'KI270741.1': 178, 'KI270742.1': 179, 'KI270743.1': 180, 'KI270744.1': 181, 'KI270745.1': 182,
'KI270746.1': 183, 'KI270747.1': 184, 'KI270748.1': 185, 'KI270749.1': 186, 'KI270750.1': 187,
'KI270751.1': 188, 'KI270752.1': 189, 'KI270753.1': 190, 'KI270754.1': 191, 'KI270755.1': 192,
'KI270756.1': 193, 'KI270757.1': 194}
CLASSIFICATIONS_ORDER_GH37 = {'RNA': 31, 'snoRNA_gene': 30, 'lincRNA': 29, 'VD_gene_segment': 28, 'NMD_transcript_variant': 27,
'exon': 26, 'miRNA': 25, 'biological_region': 24, 'mRNA': 23, 'snRNA': 22, 'rRNA_gene': 21,
'miRNA_gene': 20, 'gene': 19, 'rRNA': 18, 'nc_primary_transcript': 17, 'CDS': 16, 'snoRNA': 15,
'processed_pseudogene': 14, 'V_gene_segment': 13, 'three_prime_UTR': 12, 'mt_gene': 11,
'processed_transcript': 10, 'pseudogene': 9, 'snRNA_gene': 8, 'lincRNA_gene': 7,
'pseudogenic_transcript': 6, 'J_gene_segment': 5, 'supercontig': 4, 'C_gene_segment': 3,
'aberrant_processed_transcript': 2, 'transcript': 1, 'five_prime_UTR': 0}
CLASSIFICATIONS_ORDER_GH38 = {'scaffold': 24, 'pseudogene': 23, 'lnc_RNA': 22, 'ncRNA': 21,
'unconfirmed_transcript': 20, 'V_gene_segment': 19, 'biological_region': 18, 'snRNA': 17,
'D_gene_segment': 16, 'five_prime_UTR': 15, 'pseudogenic_transcript': 14, 'gene': 13,
'mRNA': 12, 'scRNA': 11, 'snoRNA': 10, 'tRNA': 9, 'J_gene_segment': 8, 'ncRNA_gene': 7,
'exon': 6, 'rRNA': 5, 'miRNA': 4, 'three_prime_UTR': 3, 'transcript': 2,
'C_gene_segment': 1, 'CDS': 0}
REGULATORY_REGIONS_ORDER37 = {'enhancer': 5, 'TF_binding_site': 4, 'promoter_flanking_region': 3, 'promoter': 2,
'open_chromatin_region': 1, 'CTCF_binding_site': 0}
REGULATORY_REGIONS_ORDER38 = {'CTCF_binding_site': 4, 'promoter': 3, 'open_chromatin_region': 2,
'TF_binding_site':1, 'enhancer':0}
CELL_TYPES_LABELS = {'Promoter': 9, 'Enhancer': 8, 'Transcribed': 7, 'Bivalent':6, 'RegPermissive': 5, 'ConstitutiveHet': 4,
'FacultativeHet': 3, 'LowConfidence': 2, 'Quiescent': 1}
CHROMOSOMES_LENGTHS_GH37 ={1: 249250621, 10: 135534747, 11: 135006516, 12: 133851895, 13: 115169878, 14: 107349540, 15: 102531392,
16: 90354753, 17: 81195210, 18: 78077248, 19: 59128983, 2: 243199373, 20: 63025520, 21: 48129895,
22: 51304566, 3: 198022430, 4: 191154276, 5: 180915260, 6: 171115067, 7: 159138663,
8: 146364022, 9: 141213431, 23: 16569, 24: 155270560, 25: 59373566, 26: 547496, 27: 211173, 28: 191469,
29: 189789, 30: 187035, 31: 186861, 32: 186858, 33: 182896, 34: 180455, 35: 179693, 36: 179198,
37: 174588, 38: 172545, 39: 172294, 40: 172149, 41: 169874, 42: 166566, 43: 164239, 44: 161802,
45: 161147, 46: 159169, 47: 155397, 48: 137718, 49: 129120, 50: 128374, 51: 106433, 52: 92689,
53: 90085, 54: 81310, 55: 45941, 56: 45867, 57: 43691, 58: 43523, 59: 43341, 60: 42152, 61: 41934,
62: 41933, 63: 41001, 64: 40652, 65: 40531, 66: 40103, 67: 39939, 68: 39929, 69: 39786, 70: 38914,
71: 38502, 72: 38154, 73: 37498, 74: 37175, 75: 36651, 76: 36422, 77: 36148, 78: 34474, 79: 33824,
80: 27682, 81: 27386, 82: 19913, 83: 15008, 84: 4262}
CHROMOSOMES_LENGTHS_GH38 = {1: 248956422, 2: 242193529, 3: 198295559, 4: 190214555, 5: 181538259, 6: 170805979,
7: 159345973, 8: 145138636, 9: 138394717, 10: 133797422, 11: 135086622, 12: 133275309,
13: 114364328, 14: 107043718, 15: 101991189, 16: 90338345, 17: 83257441, 18: 80373285,
19: 58617616, 20: 64444167, 21: 46709983, 22: 50818468, 23: 156040895, 24: 56887902,
25: 16569, 26: 209709, 27: 201709, 28: 191469, 29: 182896, 30: 185591, 31: 92689,
32: 164239, 33: 137718, 34: 176608, 35: 161147, 36: 179198, 37: 161802, 38: 155397,
39: 179693, 40: 211173, 41: 15008, 42: 2274, 43: 1942, 44: 2165, 45: 1472, 46: 1201,
47: 12399, 48: 998, 49: 2276, 50: 1444, 51: 37690, 52: 4416, 53: 21476, 54: 1040,
55: 1652, 56: 2699, 57: 1368, 58: 1048, 59: 1026, 60: 1121, 61: 1428, 62: 1428,
63: 3530, 64: 1803, 65: 2855, 66: 8320, 67: 2805, 68: 1650, 69: 1451, 70: 2656,
71: 2378, 72: 1136, 73: 1048, 74: 1045, 75: 1930, 76: 4215, 77: 1750, 78: 1658,
79: 990, 80: 1788, 81: 1537, 82: 1216, 83: 1298, 84: 2387, 85: 1484, 86: 971,
87: 1308, 88: 970, 89: 1143, 90: 1880, 91: 2646, 92: 1179, 93: 2489, 94: 2043,
95: 2145, 96: 1029, 97: 2321, 98: 1445, 99: 981, 100: 2140, 101: 1884, 102: 1361,
103: 92983, 104: 112505, 105: 392061, 106: 7992, 107: 1774, 108: 1233, 109: 3920,
110: 4055, 111: 5353, 112: 1951, 113: 2318, 114: 2415, 115: 8127, 116: 22689,
117: 6361, 118: 1300, 119: 3253, 120: 2186, 121: 138126, 122: 7642, 123: 5674,
124: 2983, 125: 1899, 126: 2168, 127: 91309, 128: 993, 129: 1202, 130: 1599,
131: 31033, 132: 1553, 133: 7046, 134: 6504, 135: 1400, 136: 4513, 137: 2969,
138: 6158, 139: 44474, 140: 4685, 141: 5796, 142: 3041, 143: 175055, 144: 32032,
145: 127682, 146: 66860, 147: 40176, 148: 42210, 149: 176043, 150: 40745, 151: 41717,
152: 161471, 153: 153799, 154: 40062, 155: 38054, 156: 176845, 157: 39050, 158: 100316,
159: 194050, 160: 38115, 161: 39555, 162: 172810, 163: 43739, 164: 448248, 165: 1872759,
166: 280839, 167: 112551, 168: 150754, 169: 41543, 170: 179772, 171: 165050, 172: 42811,
173: 181920, 174: 103838, 175: 99375, 176: 73985, 177: 37240, 178: 157432, 179: 186739,
180: 210658, 181: 168472, 182: 41891, 183: 66486, 184: 198735, 185: 93321, 186: 158759,
187: 148850, 188: 150742, 189: 27745, 190: 62944, 191: 40191, 192: 36723, 193: 79590,
194: 71251}
PARTIAL_SUMS_GH37 = [0, 249250621, 492449994, 690472424, 881626700, 1062541960, 1233657027, 1392795690, 1539159712, 1680373143,
1815907890, 1950914406, 2084766301, 2199936179, 2307285719, 2409817111, 2500171864, 2581367074, 2659444322,
2718573305, 2781598825, 2829728720, 2881033286, 2881049855, 3036320415, 3095693981, 3096241477, 3096452650,
3096644119, 3096833908, 3097020943, 3097207804, 3097394662, 3097577558, 3097758013, 3097937706, 3098116904,
3098291492, 3098464037, 3098636331, 3098808480, 3098978354, 3099144920, 3099309159, 3099470961, 3099632108,
3099791277, 3099946674, 3100084392, 3100213512, 3100341886, 3100448319, 3100541008, 3100631093, 3100712403,
3100758344, 3100804211, 3100847902, 3100891425, 3100934766, 3100976918, 3101018852, 3101060785, 3101101786,
3101142438, 3101182969, 3101223072, 3101263011, 3101302940, 3101342726, 3101381640, 3101420142, 3101458296,
3101495794, 3101532969, 3101569620, 3101606042, 3101642190, 3101676664, 3101710488, 3101738170, 3101765556,
3101785469, 3101800477, 3101804739, 3351055360, 3594254733, 3792277163, 3983431439, 4164346699, 4335461766,
4494600429, 4640964451, 4782177882, 4917712629, 5052719145, 5186571040, 5301740918, 5409090458, 5511621850,
5601976603, 5683171813, 5761249061, 5820378044, 5883403564, 5931533459, 5982838025, 5982854594, 6138125154,
6197498720, 6198046216, 6198257389, 6198448858, 6198638647, 6198825682, 6199012543, 6199199401, 6199382297,
6199562752, 6199742445, 6199921643, 6200096231, 6200268776, 6200441070, 6200613219, 6200783093, 6200949659,
6201113898, 6201275700, 6201436847, 6201596016, 6201751413, 6201889131, 6202018251, 6202146625, 6202253058,
6202345747, 6202435832, 6202517142, 6202563083, 6202608950, 6202652641, 6202696164, 6202739505, 6202781657,
6202823591, 6202865524, 6202906525, 6202947177, 6202987708, 6203027811, 6203067750, 6203107679, 6203147465,
6203186379, 6203224881, 6203263035, 6203300533, 6203337708, 6203374359, 6203410781, 6203446929, 6203481403,
6203515227, 6203542909, 6203570295, 6203590208, 6203605216, 6203609478]
PARTIAL_SUMS_GH38 = [0, 248956422, 491149951, 689445510, 879660065, 1061198324, 1232004303, 1391350276, 1536488912,
1674883629, 1808681051, 1943767673, 2077042982, 2191407310, 2298451028, 2400442217, 2490780562,
2574038003, 2654411288, 2713028904, 2777473071, 2824183054, 2875001522, 3031042417, 3087930319,
3087946888, 3088156597, 3088358306, 3088549775, 3088732671, 3088918262, 3089010951, 3089175190,
3089312908, 3089489516, 3089650663, 3089829861, 3089991663, 3090147060, 3090326753, 3090537926,
3090552934, 3090555208, 3090557150, 3090559315, 3090560787, 3090561988, 3090574387, 3090575385,
3090577661, 3090579105, 3090616795, 3090621211, 3090642687, 3090643727, 3090645379, 3090648078,
3090649446, 3090650494, 3090651520, 3090652641, 3090654069, 3090655497, 3090659027, 3090660830,
3090663685, 3090672005, 3090674810, 3090676460, 3090677911, 3090680567, 3090682945, 3090684081,
3090685129, 3090686174, 3090688104, 3090692319, 3090694069, 3090695727, 3090696717, 3090698505,
3090700042, 3090701258, 3090702556, 3090704943, 3090706427, 3090707398, 3090708706, 3090709676,
3090710819, 3090712699, 3090715345, 3090716524, 3090719013, 3090721056, 3090723201, 3090724230,
3090726551, 3090727996, 3090728977, 3090731117, 3090733001, 3090734362, 3090827345, 3090939850,
3091331911, 3091339903, 3091341677, 3091342910, 3091346830, 3091350885, 3091356238, 3091358189,
3091360507, 3091362922, 3091371049, 3091393738, 3091400099, 3091401399, 3091404652, 3091406838,
3091544964, 3091552606, 3091558280, 3091561263, 3091563162, 3091565330, 3091656639, 3091657632,
3091658834, 3091660433, 3091691466, 3091693019, 3091700065, 3091706569, 3091707969, 3091712482,
3091715451, 3091721609, 3091766083, 3091770768, 3091776564, 3091779605, 3091954660, 3091986692,
3092114374, 3092181234, 3092221410, 3092263620, 3092439663, 3092480408, 3092522125, 3092683596,
3092837395, 3092877457, 3092915511, 3093092356, 3093131406, 3093231722, 3093425772, 3093463887,
3093503442, 3093676252, 3093719991, 3094168239, 3096040998, 3096321837, 3096434388, 3096585142,
3096626685, 3096806457, 3096971507, 3097014318, 3097196238, 3097300076, 3097399451, 3097473436,
3097510676, 3097668108, 3097854847, 3098065505, 3098233977, 3098275868, 3098342354, 3098541089,
3098634410, 3098793169, 3098942019, 3099092761, 3099120506, 3099183450, 3099223641, 3099260364,
3099339954, 3099411205, 3348367627, 3590561156, 3788856715, 3979071270, 4160609529, 4331415508,
4490761481, 4635900117, 4774294834, 4908092256, 5043178878, 5176454187, 5290818515, 5397862233,
5499853422, 5590191767, 5673449208, 5753822493, 5812440109, 5876884276, 5923594259, 5974412727,
6130453622, 6187341524, 6187358093, 6187567802, 6187769511, 6187960980, 6188143876, 6188329467,
6188422156, 6188586395, 6188724113, 6188900721, 6189061868, 6189241066, 6189402868, 6189558265,
6189737958, 6189949131, 6189964139, 6189966413, 6189968355, 6189970520, 6189971992, 6189973193,
6189985592, 6189986590, 6189988866, 6189990310, 6190028000, 6190032416, 6190053892, 6190054932,
6190056584, 6190059283, 6190060651, 6190061699, 6190062725, 6190063846, 6190065274, 6190066702,
6190070232, 6190072035, 6190074890, 6190083210, 6190086015, 6190087665, 6190089116, 6190091772,
6190094150, 6190095286, 6190096334, 6190097379, 6190099309, 6190103524, 6190105274, 6190106932,
6190107922, 6190109710, 6190111247, 6190112463, 6190113761, 6190116148, 6190117632, 6190118603,
6190119911, 6190120881, 6190122024, 6190123904, 6190126550, 6190127729, 6190130218, 6190132261,
6190134406, 6190135435, 6190137756, 6190139201, 6190140182, 6190142322, 6190144206, 6190145567,
6190238550, 6190351055, 6190743116, 6190751108, 6190752882, 6190754115, 6190758035, 6190762090,
6190767443, 6190769394, 6190771712, 6190774127, 6190782254, 6190804943, 6190811304, 6190812604,
6190815857, 6190818043, 6190956169, 6190963811, 6190969485, 6190972468, 6190974367, 6190976535,
6191067844, 6191068837, 6191070039, 6191071638, 6191102671, 6191104224, 6191111270, 6191117774,
6191119174, 6191123687, 6191126656, 6191132814, 6191177288, 6191181973, 6191187769, 6191190810,
6191365865, 6191397897, 6191525579, 6191592439, 6191632615, 6191674825, 6191850868, 6191891613,
6191933330, 6192094801, 6192248600, 6192288662, 6192326716, 6192503561, 6192542611, 6192642927,
6192836977, 6192875092, 6192914647, 6193087457, 6193131196, 6193579444, 6195452203, 6195733042,
6195845593, 6195996347, 6196037890, 6196217662, 6196382712, 6196425523, 6196607443, 6196711281,
6196810656, 6196884641, 6196921881, 6197079313, 6197266052, 6197476710, 6197645182, 6197687073,
6197753559, 6197952294, 6198045615, 6198204374, 6198353224, 6198503966, 6198531711, 6198594655,
6198634846, 6198671569, 6198751159, 6198822410]
### Match gene Runtimes
BEDTOOLS_TIMES = [29.757471561431885, 30.437360048294067, 43.943015813827515, 106.90546178817749, 1528.7368199825287]
MY_ALGORITHM_TIMES = [0.000926971435546875, 0.0010945796966552734, 0.002707958221435547, 0.02183985710144043,
0.16087698936462402]