PyPI - RefgenDetector - Versions diffs - 3.0.0__py3-none-any.whl - Mend

RefgenDetector 3.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (13) hide show

refgenDetector/__init__.py +0 -0
refgenDetector/aligment_files.py +272 -0
refgenDetector/chromosomes_dict.py +34 -0
refgenDetector/ref_manager.py +240 -0
refgenDetector/reference_genome_dictionaries.py +820 -0
refgenDetector/refgenDetector_main.py +114 -0
refgenDetector/variant_files.py +363 -0
refgendetector-3.0.0.dist-info/METADATA +300 -0
refgendetector-3.0.0.dist-info/RECORD +13 -0
refgendetector-3.0.0.dist-info/WHEEL +5 -0
refgendetector-3.0.0.dist-info/entry_points.txt +2 -0
refgendetector-3.0.0.dist-info/licenses/LICENSE +3 -0
refgendetector-3.0.0.dist-info/top_level.txt +1 -0

refgenDetector/reference_genome_dictionaries.py ADDED Viewed

@@ -0,0 +1,820 @@
+#!/usr/bin/env python
+""" reference_genome_dictionaries.py: repository with the unique contigs for each reference genome to be inferred"""
+import json
+from pathlib import Path
+__author__ = "Mireia Marin Ginestar"
+__version__ = "2.0"
+__maintainer__ = "Mireia Marin Ginestar"
+__email__ = "mireia.marin@crg.eu"
+__status__ = "Developement"
+# MAJOR RELEASES
+hg16={
+    "chr1": 246127941,
+    "chr2": 243615958,
+    "chr3": 199344050,
+    "chr4": 191731959,
+    "chr5": 181034922,
+    "chr6": 170914576,
+    "chr7": 158545518,
+    "chr8": 146308819,
+    "chr9": 136372045,
+    "chrX": 153692391,
+    "chrY": 50286555,
+    "chr10": 135037215,
+    "chr11": 134482954,
+    "chr12": 132078379,
+    "chr13": 113042980,
+    "chr14": 105311216,
+    "chr15": 100256656,
+    "chr16": 90041932,
+    "chr17": 81860266,
+    "chr18": 76115139,
+    "chr19": 63811651,
+    "chr20": 63741868,
+    "chr21": 46976097,
+    "chr22": 49396972
+}
+hg17={
+    "chr10": 135413628,
+    "chr11": 134452384,
+    "chr12": 132449811,
+    "chr13": 114142980,
+    "chr14": 106368585,
+    "chr15": 100338915,
+    "chr16": 88827254,
+    "chr17": 78774742,
+    "chr18": 76117153,
+    "chr19": 63811651,
+    "chr1": 245522847,
+    "chr20": 62435964,
+    "chr21": 46944323,
+    "chr22": 49554710,
+    "chr2": 243018229,
+    "chr3": 199505740,
+    "chr4": 191411218,
+    "chr5": 180857866,
+    "chr6": 170975699,
+    "chr7": 158628139,
+    "chr8": 146274826,
+    "chr9": 138429268,
+    "chrX": 154824264,
+    "chrY": 57701691
+}
+hg18={
+    "chr1": 247249719,
+    "chr10": 135374737,
+    "chr11": 134452384,
+    "chr12": 132349534,
+    "chr13": 114142980,
+    "chr14": 106368585,
+    "chr15": 100338915,
+    "chr16": 88827254,
+    "chr17": 78774742,
+    "chr18": 76117153,
+    "chr19": 63811651,
+    "chr2": 242951149,
+    "chr20": 62435964,
+    "chr21": 46944323,
+    "chr22": 49691432,
+    "chr3": 199501827,
+    "chr4": 191273063,
+    "chr5": 180857866,
+    "chr6": 170899992,
+    "chr7": 158821424,
+    "chr8": 146274826,
+    "chr9": 140273252,
+    "chrX": 154913754,
+    "chrY": 57772954
+}
+GRCh37={
+    "chr1": 249250621,
+    "chr2": 243199373,
+    "chr3": 198022430,
+    "chr4": 191154276,
+    "chr5": 180915260,
+    "chr6": 171115067,
+    "chr7": 159138663,
+    "chr8": 146364022,
+    "chr9": 141213431,
+    "chr10": 135534747,
+    "chr11": 135006516,
+    "chr12": 133851895,
+    "chr13": 115169878,
+    "chr14": 107349540,
+    "chr15": 102531392,
+    "chr16": 90354753,
+    "chr17": 81195210,
+    "chr18": 78077248,
+    "chr19": 59128983,
+    "chr20": 63025520,
+    "chr21": 48129895,
+    "chr22": 51304566,
+    "chrX": 155270560,
+    "chrY": 59373566
+}
+GRCh38={
+    "chr1": 248956422,
+    "chr2": 242193529,
+    "chr3": 198295559,
+    "chr4": 190214555,
+    "chr5": 181538259,
+    "chr6": 170805979,
+    "chr7": 159345973,
+    "chr8": 145138636,
+    "chr9": 138394717,
+    "chr10": 133797422,
+    "chr11": 135086622,
+    "chr12": 133275309,
+    "chr13": 114364328,
+    "chr14": 107043718,
+    "chr15": 101991189,
+    "chr16": 90338345,
+    "chr17": 83257441,
+    "chr18": 80373285,
+    "chr19": 58617616,
+    "chr20": 64444167,
+    "chr21": 46709983,
+    "chr22": 50818468,
+    "chrX": 156040895,
+    "chrY": 57227415
+}
+T2T={
+    "1": 248387328,
+    "2": 242696752,
+    "3": 201105948,
+    "4": 193574945,
+    "5": 182045439,
+    "6": 172126628,
+    "7": 160567428,
+    "8": 146259331,
+    "9": 150617247,
+    "10": 134758134,
+    "11": 135127769,
+    "12": 133324548,
+    "13": 113566686,
+    "14": 101161492,
+    "15": 99753195,
+    "16": 96330374,
+    "17": 84276897,
+    "18": 80542538,
+    "19": 61707364,
+    "20": 66210255,
+    "21": 45090682,
+    "22": 51324926,
+    "X": 154259566,
+    "Y": 62460029
+}
+# GRCh37 FLAVORS
+hs37d5={"hs37d5":35477943, "NC_007605":171823}
+b37={"NC_007605":171823} # this contig is also present in hs37d5, but b37 doesn't include hs37d5 contig
+hg19={"ChrM":16571} # chrM it is shared with hg16, hg17 and hg18
+# GRCh38 FLAVORS
+verily_difGRCh38={"chrUn_KN707606v1_decoy": 2200, "chrUn_KN707607v1_decoy": 3033, "chrUn_KN707608v1_decoy": 3112, "chrUn_KN707609v1_decoy": 1642, "chrUn_KN707610v1_decoy": 1393, "chrUn_KN707611v1_decoy": 1103, "chrUn_KN707612v1_decoy": 1039, "chrUn_KN707613v1_decoy": 1619, "chrUn_KN707614v1_decoy": 3122, "chrUn_KN707615v1_decoy": 1934, "chrUn_KN707616v1_decoy": 3111, "chrUn_KN707617v1_decoy": 2545, "chrUn_KN707618v1_decoy": 2295, "chrUn_KN707619v1_decoy": 1551, "chrUn_KN707620v1_decoy": 2046, "chrUn_KN707621v1_decoy": 1222, "chrUn_KN707622v1_decoy": 1535, "chrUn_KN707623v1_decoy": 3784, "chrUn_KN707624v1_decoy": 1329, "chrUn_KN707625v1_decoy": 1238, "chrUn_KN707626v1_decoy": 5623, "chrUn_KN707627v1_decoy": 5821, "chrUn_KN707628v1_decoy": 2960, "chrUn_KN707629v1_decoy": 1848, "chrUn_KN707630v1_decoy": 2315, "chrUn_KN707631v1_decoy": 1945, "chrUn_KN707632v1_decoy": 1424, "chrUn_KN707633v1_decoy": 1274, "chrUn_KN707634v1_decoy": 1007, "chrUn_KN707635v1_decoy": 1414, "chrUn_KN707636v1_decoy": 1725, "chrUn_KN707637v1_decoy": 5354, "chrUn_KN707638v1_decoy": 2189, "chrUn_KN707639v1_decoy": 1294, "chrUn_KN707640v1_decoy": 1831, "chrUn_KN707641v1_decoy": 1647, "chrUn_KN707642v1_decoy": 2943, "chrUn_KN707643v1_decoy": 2857, "chrUn_KN707644v1_decoy": 1030, "chrUn_KN707645v1_decoy": 1070, "chrUn_KN707646v1_decoy": 1735, "chrUn_KN707647v1_decoy": 1982, "chrUn_KN707648v1_decoy": 1564, "chrUn_KN707649v1_decoy": 1775, "chrUn_KN707650v1_decoy": 1540, "chrUn_KN707651v1_decoy": 2013, "chrUn_KN707652v1_decoy": 1176, "chrUn_KN707653v1_decoy": 1890, "chrUn_KN707654v1_decoy": 3644, "chrUn_KN707655v1_decoy": 2785, "chrUn_KN707656v1_decoy": 1017, "chrUn_KN707657v1_decoy": 1068, "chrUn_KN707658v1_decoy": 1007, "chrUn_KN707659v1_decoy": 2605, "chrUn_KN707660v1_decoy": 8410, "chrUn_KN707661v1_decoy": 5534, "chrUn_KN707662v1_decoy": 2173, "chrUn_KN707663v1_decoy": 1065, "chrUn_KN707664v1_decoy": 8683, "chrUn_KN707665v1_decoy": 2670, "chrUn_KN707666v1_decoy": 2420, "chrUn_KN707667v1_decoy": 2189, "chrUn_KN707668v1_decoy": 2093, "chrUn_KN707669v1_decoy": 1184, "chrUn_KN707670v1_decoy": 1205, "chrUn_KN707671v1_decoy": 2786, "chrUn_KN707672v1_decoy": 2794, "chrUn_KN707673v1_decoy": 19544, "chrUn_KN707674v1_decoy": 2848, "chrUn_KN707675v1_decoy": 10556, "chrUn_KN707676v1_decoy": 9066, "chrUn_KN707677v1_decoy": 7267, "chrUn_KN707678v1_decoy": 2462, "chrUn_KN707680v1_decoy": 1297, "chrUn_KN707681v1_decoy": 4379, "chrUn_KN707682v1_decoy": 4208, "chrUn_KN707683v1_decoy": 4068, "chrUn_KN707684v1_decoy": 2940, "chrUn_KN707685v1_decoy": 3938, "chrUn_KN707686v1_decoy": 2072, "chrUn_KN707688v1_decoy": 4248, "chrUn_KN707689v1_decoy": 5823, "chrUn_KN707690v1_decoy": 3715, "chrUn_KN707691v1_decoy": 4885, "chrUn_KN707692v1_decoy": 4813, "chrUn_KN707693v1_decoy": 2899, "chrUn_KN707694v1_decoy": 1228, "chrUn_KN707695v1_decoy": 3119, "chrUn_KN707696v1_decoy": 3828, "chrUn_KN707697v1_decoy": 1186, "chrUn_KN707698v1_decoy": 1908, "chrUn_KN707699v1_decoy": 2795, "chrUn_KN707700v1_decoy": 3703, "chrUn_KN707701v1_decoy": 6722, "chrUn_KN707702v1_decoy": 6466, "chrUn_KN707703v1_decoy": 2235, "chrUn_KN707704v1_decoy": 2871, "chrUn_KN707705v1_decoy": 4632, "chrUn_KN707706v1_decoy": 4225, "chrUn_KN707707v1_decoy": 4339, "chrUn_KN707708v1_decoy": 2305, "chrUn_KN707709v1_decoy": 3273, "chrUn_KN707710v1_decoy": 5701, "chrUn_KN707711v1_decoy": 4154, "chrUn_KN707712v1_decoy": 1243, "chrUn_KN707714v1_decoy": 2922, "chrUn_KN707715v1_decoy": 3044, "chrUn_KN707716v1_decoy": 2888, "chrUn_KN707717v1_decoy": 1742, "chrUn_KN707718v1_decoy": 4969, "chrUn_KN707719v1_decoy": 3270, "chrUn_KN707720v1_decoy": 6028, "chrUn_KN707721v1_decoy": 1105, "chrUn_KN707722v1_decoy": 2884, "chrUn_KN707723v1_decoy": 1124, "chrUn_KN707724v1_decoy": 1454, "chrUn_KN707725v1_decoy": 2565, "chrUn_KN707726v1_decoy": 2149, "chrUn_KN707727v1_decoy": 2630, "chrUn_KN707728v1_decoy": 14625, "chrUn_KN707729v1_decoy": 7431, "chrUn_KN707730v1_decoy": 5776, "chrUn_KN707731v1_decoy": 4820, "chrUn_KN707732v1_decoy": 1227, "chrUn_KN707733v1_decoy": 7503, "chrUn_KN707734v1_decoy": 9652, "chrUn_KN707735v1_decoy": 1091, "chrUn_KN707736v1_decoy": 2467, "chrUn_KN707737v1_decoy": 1270, "chrUn_KN707738v1_decoy": 4365, "chrUn_KN707739v1_decoy": 4284, "chrUn_KN707740v1_decoy": 10282, "chrUn_KN707741v1_decoy": 5601, "chrUn_KN707742v1_decoy": 4758, "chrUn_KN707743v1_decoy": 1624, "chrUn_KN707744v1_decoy": 4024, "chrUn_KN707745v1_decoy": 1276, "chrUn_KN707746v1_decoy": 5083, "chrUn_KN707747v1_decoy": 2075, "chrUn_KN707748v1_decoy": 3553, "chrUn_KN707749v1_decoy": 7010, "chrUn_KN707750v1_decoy": 4718, "chrUn_KN707751v1_decoy": 3546, "chrUn_KN707752v1_decoy": 2873, "chrUn_KN707753v1_decoy": 2144, "chrUn_KN707754v1_decoy": 2243, "chrUn_KN707755v1_decoy": 5343, "chrUn_KN707756v1_decoy": 4877, "chrUn_KN707757v1_decoy": 3034, "chrUn_KN707758v1_decoy": 2826, "chrUn_KN707759v1_decoy": 1221, "chrUn_KN707760v1_decoy": 1169, "chrUn_KN707761v1_decoy": 2319, "chrUn_KN707762v1_decoy": 3450, "chrUn_KN707763v1_decoy": 2674, "chrUn_KN707764v1_decoy": 3912, "chrUn_KN707765v1_decoy": 6020, "chrUn_KN707766v1_decoy": 2303, "chrUn_KN707767v1_decoy": 2552, "chrUn_KN707768v1_decoy": 3656, "chrUn_KN707769v1_decoy": 1591, "chrUn_KN707770v1_decoy": 1209, "chrUn_KN707771v1_decoy": 3176, "chrUn_KN707772v1_decoy": 8915, "chrUn_KN707773v1_decoy": 4902, "chrUn_KN707774v1_decoy": 3324, "chrUn_KN707775v1_decoy": 5997, "chrUn_KN707776v1_decoy": 2618, "chrUn_KN707777v1_decoy": 10311, "chrUn_KN707778v1_decoy": 2440, "chrUn_KN707779v1_decoy": 12444, "chrUn_KN707780v1_decoy": 5691, "chrUn_KN707781v1_decoy": 2717, "chrUn_KN707782v1_decoy": 5277, "chrUn_KN707783v1_decoy": 4373, "chrUn_KN707784v1_decoy": 3224, "chrUn_KN707785v1_decoy": 2631, "chrUn_KN707786v1_decoy": 5385, "chrUn_KN707787v1_decoy": 3678, "chrUn_KN707788v1_decoy": 1412, "chrUn_KN707789v1_decoy": 1443, "chrUn_KN707790v1_decoy": 1098, "chrUn_KN707791v1_decoy": 3240, "chrUn_KN707792v1_decoy": 1915, "chrUn_KN707793v1_decoy": 4667, "chrUn_KN707794v1_decoy": 7219, "chrUn_KN707795v1_decoy": 3277, "chrUn_KN707796v1_decoy": 3473, "chrUn_KN707797v1_decoy": 4243, "chrUn_KN707798v1_decoy": 17599, "chrUn_KN707799v1_decoy": 5095, "chrUn_KN707800v1_decoy": 2237, "chrUn_KN707801v1_decoy": 2901, "chrUn_KN707802v1_decoy": 2666, "chrUn_KN707803v1_decoy": 5336, "chrUn_KN707804v1_decoy": 4383, "chrUn_KN707805v1_decoy": 5446, "chrUn_KN707806v1_decoy": 6252, "chrUn_KN707807v1_decoy": 4616, "chrUn_KN707808v1_decoy": 3021, "chrUn_KN707809v1_decoy": 3667, "chrUn_KN707810v1_decoy": 4563, "chrUn_KN707811v1_decoy": 1120, "chrUn_KN707812v1_decoy": 3845, "chrUn_KN707813v1_decoy": 2272, "chrUn_KN707814v1_decoy": 4764, "chrUn_KN707815v1_decoy": 5410, "chrUn_KN707816v1_decoy": 7150, "chrUn_KN707817v1_decoy": 1762, "chrUn_KN707818v1_decoy": 1207, "chrUn_KN707819v1_decoy": 1331, "chrUn_KN707820v1_decoy": 8307, "chrUn_KN707822v1_decoy": 2575, "chrUn_KN707823v1_decoy": 3970, "chrUn_KN707824v1_decoy": 1352, "chrUn_KN707825v1_decoy": 3040, "chrUn_KN707826v1_decoy": 2070, "chrUn_KN707827v1_decoy": 2913, "chrUn_KN707828v1_decoy": 2389, "chrUn_KN707829v1_decoy": 1835, "chrUn_KN707830v1_decoy": 4807, "chrUn_KN707831v1_decoy": 2201, "chrUn_KN707832v1_decoy": 1265, "chrUn_KN707833v1_decoy": 1961, "chrUn_KN707834v1_decoy": 1064, "chrUn_KN707835v1_decoy": 1932, "chrUn_KN707836v1_decoy": 3213, "chrUn_KN707837v1_decoy": 1178, "chrUn_KN707838v1_decoy": 2926, "chrUn_KN707839v1_decoy": 1038, "chrUn_KN707840v1_decoy": 3298, "chrUn_KN707841v1_decoy": 8992, "chrUn_KN707842v1_decoy": 6698, "chrUn_KN707843v1_decoy": 4880, "chrUn_KN707844v1_decoy": 1766, "chrUn_KN707845v1_decoy": 3532, "chrUn_KN707846v1_decoy": 2297, "chrUn_KN707847v1_decoy": 1234, "chrUn_KN707848v1_decoy": 1205, "chrUn_KN707849v1_decoy": 2790, "chrUn_KN707850v1_decoy": 2006, "chrUn_KN707851v1_decoy": 4593, "chrUn_KN707852v1_decoy": 1579, "chrUn_KN707853v1_decoy": 9597, "chrUn_KN707854v1_decoy": 10451, "chrUn_KN707855v1_decoy": 3219, "chrUn_KN707856v1_decoy": 2300, 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"chrUn_JTFH01001782v1_decoy": 5375, "chrUn_JTFH01001783v1_decoy": 5300, "chrUn_JTFH01001784v1_decoy": 5255, "chrUn_JTFH01001785v1_decoy": 5157, "chrUn_JTFH01001786v1_decoy": 5130, "chrUn_JTFH01001787v1_decoy": 4978, "chrUn_JTFH01001788v1_decoy": 4957, "chrUn_JTFH01001789v1_decoy": 4947, "chrUn_JTFH01001790v1_decoy": 4897, "chrUn_JTFH01001791v1_decoy": 4867, "chrUn_JTFH01001792v1_decoy": 4845, "chrUn_JTFH01001793v1_decoy": 4678, "chrUn_JTFH01001794v1_decoy": 4641, "chrUn_JTFH01001795v1_decoy": 4592, "chrUn_JTFH01001796v1_decoy": 4543, "chrUn_JTFH01001797v1_decoy": 4532, "chrUn_JTFH01001798v1_decoy": 4503, "chrUn_JTFH01001799v1_decoy": 4495, "chrUn_JTFH01001800v1_decoy": 4444, "chrUn_JTFH01001801v1_decoy": 4414, "chrUn_JTFH01001802v1_decoy": 4409, "chrUn_JTFH01001803v1_decoy": 4302, "chrUn_JTFH01001804v1_decoy": 4300, "chrUn_JTFH01001805v1_decoy": 4277, "chrUn_JTFH01001806v1_decoy": 4173, "chrUn_JTFH01001807v1_decoy": 4169, "chrUn_JTFH01001808v1_decoy": 4136, "chrUn_JTFH01001809v1_decoy": 4101, "chrUn_JTFH01001810v1_decoy": 4089, "chrUn_JTFH01001811v1_decoy": 4015, "chrUn_JTFH01001812v1_decoy": 4000, "chrUn_JTFH01001813v1_decoy": 3973, "chrUn_JTFH01001814v1_decoy": 3732, "chrUn_JTFH01001815v1_decoy": 3709, "chrUn_JTFH01001816v1_decoy": 3686, "chrUn_JTFH01001817v1_decoy": 3676, "chrUn_JTFH01001818v1_decoy": 3673, "chrUn_JTFH01001819v1_decoy": 3672, "chrUn_JTFH01001820v1_decoy": 3633, "chrUn_JTFH01001821v1_decoy": 3633, "chrUn_JTFH01001822v1_decoy": 3613, "chrUn_JTFH01001823v1_decoy": 3605, "chrUn_JTFH01001824v1_decoy": 3592, "chrUn_JTFH01001825v1_decoy": 3586, "chrUn_JTFH01001826v1_decoy": 3584, "chrUn_JTFH01001827v1_decoy": 3577, "chrUn_JTFH01001828v1_decoy": 3537, "chrUn_JTFH01001829v1_decoy": 3510, "chrUn_JTFH01001830v1_decoy": 3509, "chrUn_JTFH01001831v1_decoy": 3488, "chrUn_JTFH01001832v1_decoy": 3473, "chrUn_JTFH01001833v1_decoy": 3445, "chrUn_JTFH01001834v1_decoy": 3427, "chrUn_JTFH01001835v1_decoy": 3395, "chrUn_JTFH01001836v1_decoy": 3367, "chrUn_JTFH01001837v1_decoy": 3337, "chrUn_JTFH01001838v1_decoy": 3324, "chrUn_JTFH01001839v1_decoy": 3315, "chrUn_JTFH01001840v1_decoy": 3313, "chrUn_JTFH01001841v1_decoy": 3283, "chrUn_JTFH01001842v1_decoy": 3250, "chrUn_JTFH01001843v1_decoy": 3247, "chrUn_JTFH01001844v1_decoy": 3237, "chrUn_JTFH01001845v1_decoy": 3235, "chrUn_JTFH01001846v1_decoy": 3200, "chrUn_JTFH01001847v1_decoy": 3195, "chrUn_JTFH01001848v1_decoy": 3175, "chrUn_JTFH01001849v1_decoy": 3158, "chrUn_JTFH01001850v1_decoy": 3143, "chrUn_JTFH01001851v1_decoy": 3139, "chrUn_JTFH01001852v1_decoy": 3138, "chrUn_JTFH01001853v1_decoy": 3136, "chrUn_JTFH01001854v1_decoy": 3132, "chrUn_JTFH01001855v1_decoy": 3132, "chrUn_JTFH01001856v1_decoy": 3095, "chrUn_JTFH01001857v1_decoy": 3094, "chrUn_JTFH01001858v1_decoy": 3093, "chrUn_JTFH01001859v1_decoy": 3059, "chrUn_JTFH01001860v1_decoy": 2985, "chrUn_JTFH01001861v1_decoy": 2975, "chrUn_JTFH01001862v1_decoy": 2967, "chrUn_JTFH01001863v1_decoy": 2961, "chrUn_JTFH01001864v1_decoy": 2955, "chrUn_JTFH01001865v1_decoy": 2935, "chrUn_JTFH01001866v1_decoy": 2933, "chrUn_JTFH01001867v1_decoy": 2909, "chrUn_JTFH01001868v1_decoy": 2904, "chrUn_JTFH01001869v1_decoy": 2892, "chrUn_JTFH01001870v1_decoy": 2886, "chrUn_JTFH01001871v1_decoy": 2885, "chrUn_JTFH01001872v1_decoy": 2878, "chrUn_JTFH01001873v1_decoy": 2875, "chrUn_JTFH01001874v1_decoy": 2861, "chrUn_JTFH01001875v1_decoy": 2856, "chrUn_JTFH01001876v1_decoy": 2838, "chrUn_JTFH01001877v1_decoy": 2801, "chrUn_JTFH01001878v1_decoy": 2797, "chrUn_JTFH01001879v1_decoy": 2788, "chrUn_JTFH01001880v1_decoy": 2773, "chrUn_JTFH01001881v1_decoy": 2755, "chrUn_JTFH01001882v1_decoy": 2754, "chrUn_JTFH01001883v1_decoy": 2743, "chrUn_JTFH01001884v1_decoy": 2725, "chrUn_JTFH01001885v1_decoy": 2722, "chrUn_JTFH01001886v1_decoy": 2682, "chrUn_JTFH01001887v1_decoy": 2669, "chrUn_JTFH01001888v1_decoy": 2663, "chrUn_JTFH01001889v1_decoy": 2652, "chrUn_JTFH01001890v1_decoy": 2647, "chrUn_JTFH01001891v1_decoy": 2635, "chrUn_JTFH01001892v1_decoy": 2633, "chrUn_JTFH01001893v1_decoy": 2629, "chrUn_JTFH01001894v1_decoy": 2612, "chrUn_JTFH01001895v1_decoy": 2599, "chrUn_JTFH01001896v1_decoy": 2566, "chrUn_JTFH01001897v1_decoy": 2556, "chrUn_JTFH01001898v1_decoy": 2551, "chrUn_JTFH01001899v1_decoy": 2551, "chrUn_JTFH01001900v1_decoy": 2538, "chrUn_JTFH01001901v1_decoy": 2538, "chrUn_JTFH01001902v1_decoy": 2525, "chrUn_JTFH01001903v1_decoy": 2498, "chrUn_JTFH01001904v1_decoy": 2496, "chrUn_JTFH01001905v1_decoy": 2483, "chrUn_JTFH01001906v1_decoy": 2475, "chrUn_JTFH01001907v1_decoy": 2469, "chrUn_JTFH01001908v1_decoy": 2455, "chrUn_JTFH01001909v1_decoy": 2444, "chrUn_JTFH01001910v1_decoy": 2437, "chrUn_JTFH01001911v1_decoy": 2435, "chrUn_JTFH01001912v1_decoy": 2427, "chrUn_JTFH01001913v1_decoy": 2419, "chrUn_JTFH01001914v1_decoy": 2413, "chrUn_JTFH01001915v1_decoy": 2412, "chrUn_JTFH01001916v1_decoy": 2400, "chrUn_JTFH01001917v1_decoy": 2399, "chrUn_JTFH01001918v1_decoy": 2396, "chrUn_JTFH01001919v1_decoy": 2393, "chrUn_JTFH01001920v1_decoy": 2386, "chrUn_JTFH01001921v1_decoy": 2384, "chrUn_JTFH01001922v1_decoy": 2382, "chrUn_JTFH01001923v1_decoy": 2382, "chrUn_JTFH01001924v1_decoy": 2367, "chrUn_JTFH01001925v1_decoy": 2366, "chrUn_JTFH01001926v1_decoy": 2362, "chrUn_JTFH01001927v1_decoy": 2361, "chrUn_JTFH01001928v1_decoy": 2353, "chrUn_JTFH01001929v1_decoy": 2349, "chrUn_JTFH01001930v1_decoy": 2348, "chrUn_JTFH01001931v1_decoy": 2340, "chrUn_JTFH01001932v1_decoy": 2339, "chrUn_JTFH01001933v1_decoy": 2336, "chrUn_JTFH01001934v1_decoy": 2333, "chrUn_JTFH01001935v1_decoy": 2330, "chrUn_JTFH01001936v1_decoy": 2327, "chrUn_JTFH01001938v1_decoy": 2293, "chrUn_JTFH01001939v1_decoy": 2292, "chrUn_JTFH01001940v1_decoy": 2287, "chrUn_JTFH01001943v1_decoy": 2267, "chrUn_JTFH01001944v1_decoy": 2260, "chrUn_JTFH01001945v1_decoy": 2257, "chrUn_JTFH01001946v1_decoy": 2240, "chrUn_JTFH01001947v1_decoy": 2239, "chrUn_JTFH01001948v1_decoy": 2232, "chrUn_JTFH01001949v1_decoy": 2230, "chrUn_JTFH01001950v1_decoy": 2230, "chrUn_JTFH01001951v1_decoy": 2222, "chrUn_JTFH01001952v1_decoy": 2216, "chrUn_JTFH01001953v1_decoy": 2214, "chrUn_JTFH01001954v1_decoy": 2210, "chrUn_JTFH01001955v1_decoy": 2203, "chrUn_JTFH01001956v1_decoy": 2197, "chrUn_JTFH01001957v1_decoy": 2196, "chrUn_JTFH01001958v1_decoy": 2196, "chrUn_JTFH01001959v1_decoy": 2179, "chrUn_JTFH01001960v1_decoy": 2178, "chrUn_JTFH01001961v1_decoy": 2178, "chrUn_JTFH01001962v1_decoy": 2172, "chrUn_JTFH01001963v1_decoy": 2170, "chrUn_JTFH01001964v1_decoy": 2167, "chrUn_JTFH01001965v1_decoy": 2167, "chrUn_JTFH01001966v1_decoy": 2157, "chrUn_JTFH01001967v1_decoy": 2153, "chrUn_JTFH01001968v1_decoy": 2151, "chrUn_JTFH01001969v1_decoy": 2147, "chrUn_JTFH01001971v1_decoy": 2142, "chrUn_JTFH01001972v1_decoy": 2142, "chrUn_JTFH01001973v1_decoy": 2136, "chrUn_JTFH01001974v1_decoy": 2130, "chrUn_JTFH01001975v1_decoy": 2128, "chrUn_JTFH01001976v1_decoy": 2126, "chrUn_JTFH01001977v1_decoy": 2126, "chrUn_JTFH01001978v1_decoy": 2119, "chrUn_JTFH01001979v1_decoy": 2107, "chrUn_JTFH01001980v1_decoy": 2091, "chrUn_JTFH01001981v1_decoy": 2087, "chrUn_JTFH01001982v1_decoy": 2086, "chrUn_JTFH01001983v1_decoy": 2083, "chrUn_JTFH01001984v1_decoy": 2075, "chrUn_JTFH01001985v1_decoy": 2075, "chrUn_JTFH01001986v1_decoy": 2072, "chrUn_JTFH01001987v1_decoy": 2068, "chrUn_JTFH01001988v1_decoy": 2067, "chrUn_JTFH01001989v1_decoy": 2055, "chrUn_JTFH01001990v1_decoy": 2051, "chrUn_JTFH01001991v1_decoy": 2050, "chrUn_JTFH01001992v1_decoy": 2033, "chrUn_JTFH01001993v1_decoy": 2024, "chrUn_JTFH01001994v1_decoy": 2016, "chrUn_JTFH01001995v1_decoy": 2011, "chrUn_JTFH01001996v1_decoy": 2009, "chrUn_JTFH01001997v1_decoy": 2003, "chrUn_JTFH01001998v1_decoy": 2001}
+# Mus musculus
+mm7 = {
+    "chr1": 194923535,
+    "chr2": 182548267,
+    "chrX": 164906252,
+    "chr3": 159849039,
+    "chr4": 155175443,
+    "chr5": 153054177,
+    "chr6": 149646834,
+    "chr7": 141766352,
+    "chr10": 130066766,
+    "chr8": 127874053,
+    "chr9": 123828236,
+    "chr11": 122091587,
+    "chr14": 119226840,
+    "chr12": 117814103,
+    "chr13": 116696528,
+    "chr15": 103647385,
+    "chr16": 98481019,
+    "chr17": 93276925,
+    "chr18": 90918714,
+    "chr19": 61223509,
+    "chrY": 15523453
+}
+mm8 = {
+    "chr1": 197069962,
+    "chr2": 181976762,
+    "chr3": 159872112,
+    "chr4": 155029701,
+    "chr5": 152003063,
+    "chr6": 149525685,
+    "chr7": 145134094,
+    "chr8": 132085098,
+    "chr9": 124000669,
+    "chrX": 165556469,
+    "chrY": 16029404,
+    "chr10": 129959148,
+    "chr11": 121798632,
+    "chr12": 120463159,
+    "chr13": 120614378,
+    "chr14": 123978870,
+    "chr15": 103492577,
+    "chr16": 98252459,
+    "chr17": 95177420,
+    "chr18": 90736837,
+    "chr19": 61321190,
+}
+mm9 = {
+    "chr1": 197195432,
+    "chr2": 181748087,
+    "chr3": 159599783,
+    "chr4": 155630120,
+    "chr5": 152537259,
+    "chr6": 149517037,
+    "chr7": 152524553,
+    "chr8": 131738871,
+    "chr9": 124076172,
+    "chr10": 129993255,
+    "chr11": 121843856,
+    "chr12": 121257530,
+    "chr13": 120284312,
+    "chr14": 125194864,
+    "chr15": 103494974,
+    "chr16": 98319150,
+    "chr17": 95272651,
+    "chr18": 90772031,
+    "chr19": 61342430,
+    "chrX": 166650296,
+    "chrY": 15902555
+}
+mm10 = {
+    "chr1": 195471971,
+    "chr2": 182113224,
+    "chrX": 171031299,
+    "chr3": 160039680,
+    "chr4": 156508116,
+    "chr5": 151834684,
+    "chr6": 149736546,
+    "chr7": 145441459,
+    "chr10": 130694993,
+    "chr8": 129401213,
+    "chr14": 124902244,
+    "chr9": 124595110,
+    "chr11": 122082543,
+    "chr13": 120421639,
+    "chr12": 120129022,
+    "chr15": 104043685,
+    "chr16": 98207768,
+    "chr17": 94987271,
+    "chrY": 91744698,
+    "chr18": 90702639,
+    "chr19": 61431566
+}
+mm39 = {
+    "chr1": 195154279,
+    "chr2": 181755017,
+    "chrX": 169476592,
+    "chr3": 159745316,
+    "chr4": 156860686,
+    "chr5": 151758149,
+    "chr6": 149588044,
+    "chr7": 144995196,
+    "chr10": 130530862,
+    "chr8": 130127694,
+    "chr14": 125139656,
+    "chr9": 124359700,
+    "chr11": 121973369,
+    "chr13": 120883175,
+    "chr12": 120092757,
+    "chr15": 104073951,
+    "chr16": 98008968,
+    "chr17": 95294699,
+    "chrY": 91455967,
+    "chr18": 90720763,
+    "chr19": 61420004,
+}
+# Drosophila melanogaster
+dm5 = {
+    "X": 22422827,
+    "2L": 23011544,
+    "2R": 21146708,
+    "3L": 24543557,
+    "3R": 27905053,
+    "4": 1351857,
+    "XHet": 204112,
+    "2LHet": 368872,
+    "2RHet": 3288761,
+    "3LHet": 2555491,
+    "3RHet": 2517507,
+    "YHet": 347038,
+    "MT": 19517
+}
+dm6 = {
+    "X": 23542271,
+    "2L": 23513712,
+    "2R": 25286936,
+    "3L": 28110227,
+    "3R": 32079331,
+    "4": 1348131,
+    "Y": 3667352
+}
+# Danio Rerio
+danRer10 = {
+    "Chromosome 1": 58871917,
+    "Chromosome 2": 59543403,
+    "Chromosome 3": 62385949,
+    "Chromosome 4": 76625712,
+    "Chromosome 5": 71715914,
+    "Chromosome 6": 60272633,
+    "Chromosome 7": 74082188,
+    "Chromosome 8": 54191831,
+    "Chromosome 9": 56892771,
+    "Chromosome 10": 45574255,
+    "Chromosome 11": 45107271,
+    "Chromosome 12": 49229541,
+    "Chromosome 13": 51780250,
+    "Chromosome 14": 51944548,
+    "Chromosome 15": 47771147,
+    "Chromosome 16": 55381981,
+    "Chromosome 17": 53345113,
+    "Chromosome 18": 51008593,
+    "Chromosome 19": 48790377,
+    "Chromosome 20": 55370968,
+    "Chromosome 21": 45895719,
+    "Chromosome 22": 39226288,
+    "Chromosome 23": 46272358,
+    "Chromosome 24": 42251103,
+    "Chromosome 25": 36898761
+}
+danRer11 = {
+    "Chromosome 1": 59578282,
+    "Chromosome 2": 59640629,
+    "Chromosome 3": 62628489,
+    "Chromosome 4": 78093715,
+    "Chromosome 5": 72500376,
+    "Chromosome 6": 60270059,
+    "Chromosome 7": 74282399,
+    "Chromosome 8": 54304671,
+    "Chromosome 9": 56459846,
+    "Chromosome 10": 45420867,
+    "Chromosome 11": 45484837,
+    "Chromosome 12": 49182954,
+    "Chromosome 13": 52186027,
+    "Chromosome 14": 52660232,
+    "Chromosome 15": 48040578,
+    "Chromosome 16": 55266484,
+    "Chromosome 17": 53461100,
+    "Chromosome 18": 51023478,
+    "Chromosome 19": 48449771,
+    "Chromosome 20": 55201332,
+    "Chromosome 21": 45934066,
+    "Chromosome 22": 39133080,
+    "Chromosome 23": 46223584,
+    "Chromosome 24": 42172926,
+    "Chromosome 25": 37502051
+}
+# Caenorhabditis elegans
+WBcel215 = {
+    "Chromosome I": 15072423,
+    "Chromosome II": 15279345,
+    "Chromosome III": 13783700,
+    "Chromosome IV": 17493793,
+    "Chromosome V": 20924149,
+    "Chromosome X": 17718866
+}
+WBcel235 = {
+    "I": 15072434,
+    "II": 15279421,
+    "III": 13783801,
+    "IV": 17493829,
+    "V": 20924180,
+    "X": 17718942,
+    "MT": 13794
+}
+# Rattus norvegicus
+mRatBN7_2 = {
+    "1": 260522016,
+    "2": 249053267,
+    "3": 169034231,
+    "4": 182687754,
+    "5": 166875058,
+    "6": 140994061,
+    "7": 135012528,
+    "8": 123900184,
+    "9": 114175309,
+    "10": 107211142,
+    "11": 86241447,
+    "12": 46669029,
+    "13": 106807694,
+    "14": 104886043,
+    "15": 101769107,
+    "16": 84729064,
+    "17": 86533673,
+    "18": 83828827,
+    "19": 57337602,
+    "20": 54435887,
+    "X": 152453651,
+    "Y": 18315841
+}
+Rnor_6_0 = {
+    "1": 282763074,
+    "2": 266435125,
+    "3": 177699992,
+    "4": 184226339,
+    "5": 173707219,
+    "6": 147991367,
+    "7": 145729302,
+    "8": 133307652,
+    "9": 122095297,
+    "10": 112626471,
+    "11": 90463843,
+    "12": 52716770,
+    "13": 114033958,
+    "14": 115493446,
+    "15": 111246239,
+    "16": 90668790,
+    "17": 90843779,
+    "18": 88201929,
+    "19": 62275575,
+    "20": 56205956,
+    "X": 159970021,
+    "Y": 3310458
+}
+# Saccharomyces cerevisiae
+R64 = {
+    "I": 230218,
+    "II": 813184,
+    "III": 316620,
+    "IV": 1531933,
+    "V": 576874,
+    "VI": 270161,
+    "VII": 1090940,
+    "VIII": 562643,
+    "IX": 439888,
+    "X": 745751,
+    "XI": 666816,
+    "XII": 1078177,
+    "XIII": 924431,
+    "XIV": 784333,
+    "XV": 1091291,
+    "XVI": 948066,
+    "MT": 85779
+}
+# E. coli
+ASM584v2 = {
+    "GCF_000005845.2": 4641652
+}
+ASM886v2 = {
+    "chromosome": 2778819,
+    "pOSAK1": 1435,
+    "pO157": 44135
+}
+# Pan troglodytes
+pantro3_0 = {
+    "1": 228573443,
+    "2A": 111504155,
+    "2B": 133216015,
+    "3": 202621043,
+    "4": 194502333,
+    "5": 181907262,
+    "6": 175400573,
+    "7": 166211670,
+    "8": 147911612,
+    "9": 116767853,
+    "10": 135926727,
+    "11": 135753878,
+    "12": 137163284,
+    "13": 100452976,
+    "14": 91965084,
+    "15": 83230942,
+    "16": 81586097,
+    "17": 83181570,
+    "18": 78221452,
+    "19": 61309027,
+    "20": 66533130,
+    "21": 33445071,
+    "22": 37823149,
+    "X": 155549662,
+    "Y": 26350515
+}
+pantro_2_1_4 = {
+    "1": 228333871,
+    "2A": 113622374,
+    "2B": 247518478,
+    "3": 202329955,
+    "4": 193495092,
+    "5": 182651097,
+    "6": 172623881,
+    "7": 161824586,
+    "8": 143986469,
+    "9": 137840987,
+    "10": 133524379,
+    "11": 133121534,
+    "12": 134246214,
+    "13": 115123233,
+    "14": 106544938,
+    "15": 99548318,
+    "16": 89983829,
+    "17": 82630442,
+    "18": 76611499,
+    "19": 63644993,
+    "20": 61729293,
+    "21": 32799110,
+    "22": 49737984,
+    "X": 156848144,
+    "Y": 23952694
+}
+# Macaca mulatta
+Mmul10 = {
+    "1": 223616942,
+    "2": 196197964,
+    "3": 185288947,
+    "4": 169963040,
+    "5": 187317192,
+    "6": 179085566,
+    "7": 169868564,
+    "8": 145679320,
+    "9": 134124166,
+    "10": 99517758,
+    "11": 133066086,
+    "12": 130043856,
+    "13": 108737130,
+    "14": 128056306,
+    "15": 113283604,
+    "16": 79627064,
+    "17": 95433459,
+    "18": 74474043,
+    "19": 58315233,
+    "20": 77137495,
+    "X": 153388924,
+    "Y": 11753682
+}
+rheMac8 = {
+    "chr1": 225584828,
+    "chr2": 204787373,
+    "chr5": 190429646,
+    "chr3": 185818997,
+    "chr6": 180051392,
+    "chr4": 172585720,
+    "chr7": 169600520,
+    "chrX": 149150640,
+    "chr8": 144306982,
+    "chr11": 133663169,
+    "chr9": 129882849,
+    "chr14": 127894412,
+    "chr12": 125506784,
+    "chr15": 111343173,
+    "chr13": 108979918,
+    "chr17": 95684472,
+    "chr10": 92844088,
+    "chr16": 77216781,
+    "chr20": 74971481,
+    "chr18": 70235451,
+    "chr19": 53671032,
+    "chrY": 11753682,
+}
+rheMac3 = {
+    "1": 229590362,
+    "2": 192599291,
+    "3": 198365852,
+    "4": 169853907,
+    "5": 184069350,
+    "6": 180491593,
+    "7": 170124641,
+    "8": 150158102,
+    "9": 130959383,
+    "10": 95678458,
+    "11": 134985053,
+    "12": 106825570,
+    "13": 137160470,
+    "14": 135538710,
+    "15": 112192347,
+    "16": 80904711,
+    "17": 94676912,
+    "18": 74429130,
+    "19": 64156825,
+    "20": 88476065,
+    "X": 155416530
+}
+# Arabidopsis thaliana
+TAIR = {
+    "GCF_000001735.4_1": 30427671,
+    "GCF_000001735.4_2": 19698289,
+    "GCF_000001735.4_3": 23459830,
+    "GCF_000001735.4_4": 18585056,
+    "GCF_000001735.4_5": 26975502,
+    "GCF_000001735.4_6": 367808,
+    "GCF_000001735.4_7": 154478
+}
+# Sus scrofa
+Sscrofa10_2 = {
+    "chr1": 315321322,
+    "chr2": 162569375,
+    "chr3": 144787322,
+    "chr4": 143465943,
+    "chr5": 111506441,
+    "chr6": 157765593,
+    "chr7": 134764511,
+    "chr8": 148491826,
+    "chr9": 153670197,
+    "chr10": 79102373,
+    "chr11": 87690581,
+    "chr12": 63588571,
+    "chr13": 218635234,
+    "chr14": 153851969,
+    "chr15": 157681621,
+    "chr16": 86898991,
+    "chr17": 69701581,
+    "chr18": 61220071,
+    "chrX": 144288218,
+    "chrY": 1637716
+}
+Sscrofa11_1 = {
+    "chr1": 274330532,
+    "chr2": 151935994,
+    "chr3": 132848913,
+    "chr4": 130910915,
+    "chr5": 104526007,
+    "chr6": 170843587,
+    "chr7": 121844099,
+    "chr8": 138966237,
+    "chr9": 139512083,
+    "chr10": 69359453,
+    "chr11": 79169978,
+    "chr12": 61602749,
+    "chr13": 208334590,
+    "chr14": 141755446,
+    "chr15": 140412725,
+    "chr16": 79944280,
+    "chr17": 63494081,
+    "chr18": 55982971,
+    "chrX": 125939595
+}
+## Lists and dictionaries for comparison()
+#major_releases = {"hg16": hg16, "hg17": hg17, "hg18": hg18, "GRCh37": GRCh37, "GRCh38": GRCh38, "T2T": T2T}
+major_releases = {"hg16": {"ref_gen": hg16, "build": "hg16", "species": "Homo sapiens"},
+                  "hg17": {"ref_gen": hg17, "build": "hg17", "species": "Homo sapiens"},
+                  "hg18": {"ref_gen": hg18, "build": "hg18", "species": "Homo sapiens"},
+                  "GRCh37": {"ref_gen": GRCh37, "build": "GRCh37", "species": "Homo sapiens"},
+                  "GRCh38": {"ref_gen": GRCh38, "build": "GRCh38", "species": "Homo sapiens"},
+                  "T2T": {"ref_gen": T2T, "build": "T2T", "species": "Homo sapiens"},
+                  "mm7": {"ref_gen": mm7, "build": "mm7", "species": "Mus Musculus"},
+                  "mm8": {"ref_gen": mm8, "build": "mm8", "species": "Mus musculus"},
+                  "mm9": {"ref_gen": mm9, "build": "mm9", "species": "Mus musculus"},
+                  "mm10": {"ref_gen": mm10, "build": "mm10", "species": "Mus musculus"},
+                  "mm39": {"ref_gen": mm39, "build": "mm39", "species": "Mus musculus"},
+                  "dm5": {"ref_gen": dm5, "build": "dm5", "species": "Drosophila Melanogaster"},
+                  #"dm6": {"ref_gen": dm6, "build": "dm6", "species": "Drosophila Melanogaster"},
+                  "danRer10": {"ref_gen": danRer10, "build": "danRer10", "species": "Danio Rerio"},
+                  "danRer11": {"ref_gen": danRer11, "build": "danRer11", "species": "Danio Rerio"},
+                  "WBcel215": {"ref_gen": WBcel215, "build": "WBcel215", "species": "Caenorhabditis elegans"},
+                  "WBcel235": {"ref_gen": WBcel235, "build": "WBcel235", "species": "Caenorhabditis elegans"},
+                  "mRatBN7_2": {"ref_gen": mRatBN7_2, "build": "mRatBN7_2", "species": "Rattus norvegicus"},
+                  "Rnor_6_0": {"ref_gen": Rnor_6_0, "build": "Rnor_6_0", "species": "Rattus norvegicus"},
+                  "R64": {"ref_gen": R64, "build": "R64", "species": "Saccharomyces cerevisiae"},
+                  "ASM886v2": {"ref_gen": ASM886v2, "build": "ASM886v2", "species": "Escherichia coli"},
+                  "ASM584v2": {"ref_gen": ASM584v2, "build": "ASM584v2", "species": "Escherichia Coli"},
+                  "pantro3_0": {"ref_gen": pantro3_0, "build": "pantro3_0", "species": "Pan troglodytes"},
+                  "pantro_2_1_4": {"ref_gen": pantro_2_1_4, "build": "pantro_2_1_4",
+                                   "species": "Pan troglodytes"},
+                  "Mmul10": {"ref_gen": Mmul10, "build": "Mmul10", "species": "Macaca mulatta"},
+                  "rheMac8": {"ref_gen": rheMac8, "build": "rheMac8", "species": "Macaca mulatta"},
+                  "rheMac3": {"ref_gen": rheMac3, "build": "rheMac3", "species": "Macaca mulatta"},
+                  "TAIR": {"ref_gen": TAIR, "build": "TAIR", "species": "Arabidopsis thaliana"},
+                  "Sscrofa10_2": {"ref_gen": Sscrofa10_2, "build": "Sscrofa10_2", "species": "Sus scrofa"},
+                  "Sscrofa11_1": {"ref_gen": Sscrofa11_1, "build": "Sscrofa11_1", "species": "Sus scrofa"}
+                  }
+## Add custom references if present
+CUSTOM_DB = Path("custom_references.json")
+if CUSTOM_DB.exists():
+    with open(CUSTOM_DB) as f:
+        custom_refs = json.load(f)
+    major_releases.update(custom_refs)
+flavors_GRCh37 = {"b37":  {"ref_gen": b37, "build": "b37", "species": "Homo sapiens"},
+                  "hs37d5": {"ref_gen": hs37d5, "build": "hs37d5", "species": "Homo sapiens"},
+                  "hg19":  {"ref_gen": hg19, "build": "hg19", "species": "Homo sapiens"}
+                  }  # GRCh37 flavors that can be inferred
+"""
+IMPORTANT NOTE
+The order of the keys in flavors_GRCh37 is not modifiable.
+"""
+avail_dicts = ["hg16","hg17","hg18","GRCh37","GRCh38","T2T","mm7","mm8","mm9","mm10","mm39","dm5","dm6","danRer10","danRer11","WBcel215","WBcel235","mRatBN7_2","Rnor_6_0","R64","ASM886v2","ASM584v2","pantro3_0","pantro_2_1_4","Mmul10","rheMac8","rheMac3","TAIR","Sscrofa10_2","Sscrofa11_1"]
+min_values = {
+    'hg16': 46976097,
+     'hg17': 46944323,
+     'hg18': 46944323,
+     'GRCh37': 48129895,
+     'GRCh38': 46709983,
+     'T2T': 45090682,
+     'mm7': 15523453,
+     'mm8': 16029404,
+     'mm9': 15902555,
+     'mm10': 61431566,
+     'mm39': 61420004,
+     'dm5': 19517,
+     'dm6': 1348131,
+     'danRer10': 36898761,
+     'danRer11': 37502051,
+     'WBcel215': 13783700,
+     'WBcel235': 13794,
+     'mRatBN7_2': 18315841,
+     'Rnor_6_0': 3310458,
+     'R64': 85779,
+     'ASM886v2': 1435,
+     'ASM584v2': 4641652,
+     'pantro3_0': 26350515,
+     'pantro_2_1_4': 23952694,
+     'Mmul10': 11753682,
+     'rheMac8': 11753682,
+     'rheMac3': 64156825,
+     'TAIR': 154478,
+     'Sscrofa10_2': 1637716,
+     'Sscrofa11_1': 55982971
+}
+mit_contigs = {"NC_001807.4":16571, "NC_012920": 16569} # chrM , rCRS
+def get_duplicate_lengths():
+    nested_list = []
+    for key, value in major_releases.items():
+        ref_gen_dict = value["ref_gen"]
+        nested_list.append(list(ref_gen_dict.values()))  # Convert dict values to a list before appending
+    values_list = []
+    for i in nested_list:
+        for j in i:
+            values_list.append(j)
+    from collections import Counter
+    # Count occurrences
+    counts = Counter(values_list)
+    # Filter duplicates
+    duplicates = {item: count for item, count in counts.items() if count > 1}
+    print(duplicates)
+def get_min_values():
+    min_values = {}
+    for name in avail_dicts:
+        d = globals()[name]  # Get dictionary by name
+        min_values[name] = d[min(d, key=d.get)]  # Store min value
+    print(min_values)  # Output the dictionary