// #include <vector>
// #include <string>
// #include <unordered_map>
// #include <set>
// #include <iostream>
// #include <testthat.h>
// #include <Rcpp.h>
// #include "../classes/StartEndPair.h"
// #include "../classes/junctions.h"
// #include "../classes/types.h"
// #include "test_utilities.h"
// static std::unordered_map<std::string, transcriptvector>
// gene_to_transcript = {
// {"SIRV5", {"SIRV508", "SIRV509", "SIRV502", "SIRV503", "SIRV501", "SIRV506", "SIRV507", "SIRV504", "SIRV505", "SIRV512", "SIRV510"}},
// {"SIRV4", {"SIRV403", "SIRV410", "SIRV406", "SIRV405", "SIRV404", "SIRV409", "SIRV408"}},
// {"SIRV7", {"SIRV708", "SIRV701", "SIRV702", "SIRV703", "SIRV704", "SIRV706"}},
// {"SIRV6", {"SIRV618", "SIRV617", "SIRV601", "SIRV616", "SIRV603", "SIRV602", "SIRV605", "SIRV604", "SIRV607", "SIRV606", "SIRV609", "SIRV608", "SIRV614", "SIRV615", "SIRV612", "SIRV613", "SIRV610", "SIRV611"}},
// {"SIRV1", {"SIRV108", "SIRV109", "SIRV106", "SIRV107", "SIRV105", "SIRV102", "SIRV103", "SIRV101"}},
// {"SIRV3", {"SIRV310", "SIRV311", "SIRV308", "SIRV309", "SIRV304", "SIRV305", "SIRV306", "SIRV307", "SIRV301", "SIRV302", "SIRV303"}},
// {"SIRV2", {"SIRV205", "SIRV204", "SIRV206", "SIRV201", "SIRV203", "SIRV202"}}
// };
// // gene_to_transcript = {
// // "SIRV5": ["SIRV508", "SIRV509", "SIRV502", "SIRV503", "SIRV501", "SIRV506", "SIRV507", "SIRV504", "SIRV505", "SIRV512", "SIRV510"],
// // "SIRV4": ["SIRV403", "SIRV410", "SIRV406", "SIRV405", "SIRV404", "SIRV409", "SIRV408"],
// // "SIRV7": ["SIRV708", "SIRV701", "SIRV702", "SIRV703", "SIRV704", "SIRV706"],
// // "SIRV6": ["SIRV618", "SIRV617", "SIRV601", "SIRV616", "SIRV603", "SIRV602", "SIRV605", "SIRV604", "SIRV607", "SIRV606", "SIRV609", "SIRV608", "SIRV614", "SIRV615", "SIRV612", "SIRV613", "SIRV610", "SIRV611"],
// // "SIRV1": ["SIRV108", "SIRV109", "SIRV106", "SIRV107", "SIRV105", "SIRV102", "SIRV103", "SIRV101"],
// // "SIRV3": ["SIRV310", "SIRV311", "SIRV308", "SIRV309", "SIRV304", "SIRV305", "SIRV306", "SIRV307", "SIRV301", "SIRV302", "SIRV303"],
// // "SIRV2": ["SIRV205", "SIRV204", "SIRV206", "SIRV201", "SIRV203", "SIRV202"]
// // }
// static std::unordered_map<std::string, std::vector<exon>>
// transcript_to_exon = {
// {"SIRV410", {{1455, 1885}, {2251, 2771}}},
// {"SIRV706", {{56031, 56097}, {70883, 70987}, {78841, 78963}, {114680, 114988}, {147608, 147957}}},
// {"SIRV618", {{2358, 2547}}},
// {"SIRV511", {{1008, 1143}, {1987, 2398}}},
// {"SIRV510", {{1028, 1149}, {1987, 2033}, {2119, 2156}, {2270, 2315}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8016}, {8277, 8381}, {8454, 8585}, {10858, 10991}, {11133, 11867}}},
// {"SIRV512", {{2177, 2406}}},
// {"SIRV601", {{1000, 1186}, {1468, 1534}, {1640, 1735}, {2470, 2620}, {2740, 2828}, {3106, 3164}, {10724, 10818}, {11031, 11108}, {11205, 11826}}},
// {"SIRV616", {{2285, 2620}, {2740, 2814}, {3106, 3164}, {10724, 10788}}},
// {"SIRV603", {{8999, 10968}}},
// {"SIRV509", {{8315, 8381}, {8454, 8585}, {10858, 10991}, {11311, 11866}}},
// {"SIRV605", {{1130, 1186}, {1468, 1534}, {1640, 1735}, {1845, 2026}, {2470, 2620}, {2740, 2828}, {3106, 3164}, {10724, 10818}, {11031, 11331}}},
// {"SIRV604", {{1087, 1186}, {1468, 1534}, {1640, 1735}, {1845, 2026}, {2470, 2620}, {2740, 2828}, {3106, 3164}, {10724, 10818}, {11034, 11108}, {11205, 11837}}},
// {"SIRV607", {{1130, 1186}, {1468, 1735}, {1845, 2026}, {2470, 2540}}},
// {"SIRV606", {{2285, 2620}, {2740, 2828}, {3106, 3164}, {10724, 10788}}},
// {"SIRV609", {{1137, 1186}, {1468, 1534}, {1640, 1735}, {1845, 2120}}},
// {"SIRV608", {{3023, 3164}, {10724, 10818}, {11031, 11108}, {11205, 11270}}},
// {"SIRV702", {{1000, 2675}, {2993, 3111}, {4095, 4179}, {4725, 4810}, {43028, 43077}, {114680, 114916}}},
// {"SIRV703", {{1000, 2675}, {2993, 3111}, {3809, 3896}, {114680, 114988}, {147608, 147918}}},
// {"SIRV704", {{55849, 56097}, {78841, 78963}, {114680, 114738}}},
// {"SIRV614", {{2516, 2620}, {2740, 2828}, {3106, 3164}, {7805, 7923}, {10724, 10815}}},
// {"SIRV311", {{4601, 4762}}},
// {"SIRV310", {{8759, 8966}, {9189, 9324}, {9667, 9914}}},
// {"SIRV615", {{10237, 10818}, {11031, 11108}, {11205, 11330}}},
// {"SIRV705", {{1005, 2675}, {2993, 3111}, {43028, 43077}, {114680, 114988}, {147608, 147925}}},
// {"SIRV701", {{1003, 2675}, {2993, 3111}, {43028, 43077}, {114680, 114988}, {147608, 147923}}},
// {"SIRV613", {{3105, 3164}, {7104, 7448}, {7805, 7923}, {10724, 10818}, {11031, 11108}, {11205, 11824}}},
// {"SIRV610", {{2472, 2620}, {2740, 2828}, {3106, 3164}, {10724, 11108}, {11205, 11690}}},
// {"SIRV611", {{1303, 1381}, {1468, 1534}, {1640, 1950}}},
// {"SIRV403", {{8322, 8372}, {8629, 8990}, {13672, 13828}, {15019, 15122}}},
// {"SIRV508", {{8315, 8382}, {8453, 8585}, {10859, 10991}, {11311, 11866}}},
// {"SIRV501", {{1056, 1149}, {1987, 2033}, {2119, 2315}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6658, 6722}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8016}, {8277, 8381}, {8454, 8585}, {10858, 10991}}},
// {"SIRV406", {{3637, 4103}, {5007, 5158}}},
// {"SIRV405", {{8629, 8990}, {13672, 13937}}},
// {"SIRV404", {{8322, 8372}, {8629, 8990}, {13672, 13822}, {14592, 14623}}},
// {"SIRV502", {{1019, 1149}, {1987, 2033}, {2119, 2156}, {2270, 2488}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6658, 6722}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8016}, {8277, 8381}, {8454, 8585}, {10858, 10989}}},
// {"SIRV503", {{8201, 8585}, {10858, 10991}, {11133, 11142}}},
// {"SIRV409", {{1000, 1346}, {1678, 1885}, {2389, 3403}}},
// {"SIRV408", {{8323, 8372}, {8629, 8747}, {8846, 8990}, {13672, 13828}, {15019, 15122}}},
// {"SIRV506", {{1008, 1149}, {1987, 2398}}},
// {"SIRV507", {{1027, 1149}, {1925, 2033}, {2119, 2156}, {2270, 2315}, {3298, 3404}, {3483, 3598}}},
// {"SIRV504", {{11133, 13606}}},
// {"SIRV505", {{1000, 1149}, {1987, 2033}, {2119, 2156}, {2270, 2315}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8381}, {8454, 8585}, {10858, 10991}}},
// {"SIRV205", {{1108, 1631}}},
// {"SIRV204", {{3643, 3825}, {3966, 4479}, {4687, 4732}}},
// {"SIRV617", {{1544, 1820}}},
// {"SIRV206", {{4033, 4457}}},
// {"SIRV308", {{1000, 1167}, {1532, 1764}, {1902, 1982}}},
// {"SIRV309", {{8797, 8975}, {9189, 9298}, {9434, 9943}}},
// {"SIRV203", {{3665, 3825}, {3966, 4094}, {4338, 4479}, {4687, 4800}, {5751, 5895}}},
// {"SIRV202", {{1035, 1661}, {1741, 1853}, {1973, 2064}, {2674, 2802}, {2881, 3010}, {3105, 3325}, {3665, 3825}, {3966, 4094}, {4338, 4479}, {4687, 4800}, {5788, 5911}}},
// {"SIRV304", {{1963, 2005}, {4003, 4080}, {4568, 4779}, {6057, 6333}, {7270, 7366}, {7872, 7988}, {8124, 8207}, {8755, 8937}}},
// {"SIRV305", {{4003, 4080}, {4568, 4779}, {6570, 6718}}},
// {"SIRV306", {{1944, 2005}, {4003, 4080}, {6057, 8292}}},
// {"SIRV307", {{1963, 2005}, {4003, 4080}, {4574, 4774}, {6057, 6333}, {8755, 8939}}},
// {"SIRV612", {{1087, 1186}, {1468, 1534}, {1640, 1735}, {1845, 2026}, {2470, 2620}, {2740, 2828}, {3106, 3164}, {10724, 10818}, {11031, 11108}, {11205, 11825}}},
// {"SIRV301", {{1944, 2005}, {4568, 4779}, {6057, 7988}, {8127, 8207}, {8755, 8939}}},
// {"SIRV302", {{1963, 2005}, {6057, 7822}}},
// {"SIRV303", {{1963, 2005}, {4568, 4779}, {6057, 7822}}},
// {"SIRV708", {{56037, 56097}, {70883, 70987}, {78841, 78908}, {78928, 78963}, {114686, 114960}, {147608, 147957}}},
// {"SIRV108", {{10582, 10791}, {10897, 11187}, {11403, 11606}}},
// {"SIRV109", {{10711, 10791}, {10882, 11057}, {11434, 11643}}},
// {"SIRV106", {{1000, 1484}, {7552, 7808}, {10553, 10786}}},
// {"SIRV107", {{10647, 10791}, {10882, 11242}, {11403, 11643}}},
// {"SIRV105", {{6449, 6473}, {6560, 6813}, {7552, 7814}, {10282, 10366}, {10593, 10640}}},
// {"SIRV102", {{1006, 1484}, {6337, 6813}, {7552, 7814}, {10282, 10366}}},
// {"SIRV103", {{1000, 1484}, {6337, 6473}, {6560, 6813}, {7552, 7814}, {10282, 10366}, {10647, 10791}}},
// {"SIRV101", {{1000, 1484}, {6337, 6473}, {6560, 6813}, {7552, 7814}, {10282, 10366}, {10444, 10786}}},
// {"SIRV602", {{1124, 1186}, {1468, 1534}, {1640, 1735}, {2780, 2828}, {3106, 3164}, {10724, 10818}, {11031, 11108}, {11205, 11279}}},
// {"SIRV201", {{1000, 1661}, {1741, 1853}, {1973, 2064}, {2674, 2802}, {2881, 3010}, {3105, 3374}, {3665, 3825}, {3966, 4094}, {4338, 4479}, {4687, 4800}, {5788, 5907}}}
// };
// // transcript_to_exon = {
// // "SIRV410": [[1455, 1885], [2251, 2771]],
// // "SIRV706": [[56031, 56097], [70883, 70987], [78841, 78963], [114680, 114988], [147608, 147957]],
// // "SIRV618": [[2358, 2547]],
// // "SIRV511": [[1008, 1143], [1987, 2398]],
// // "SIRV510": [[1028, 1149], [1987, 2033], [2119, 2156], [2270, 2315], [3298, 3404], [3483, 3643], [5380, 5450], [5543, 5626], [6111, 6169], [6327, 6452], [6826, 6957], [7144, 7307], [7681, 7762], [7870, 8016], [8277, 8381], [8454, 8585], [10858, 10991], [11133, 11867]],
// // "SIRV512": [[2177, 2406]],
// // "SIRV601": [[1000, 1186], [1468, 1534], [1640, 1735], [2470, 2620], [2740, 2828], [3106, 3164], [10724, 10818], [11031, 11108], [11205, 11826]],
// // "SIRV616": [[2285, 2620], [2740, 2814], [3106, 3164], [10724, 10788]],
// // "SIRV603": [[8999, 10968]],
// // "SIRV509": [[8315, 8381], [8454, 8585], [10858, 10991], [11311, 11866]],
// // "SIRV605": [[1130, 1186], [1468, 1534], [1640, 1735], [1845, 2026], [2470, 2620], [2740, 2828], [3106, 3164], [10724, 10818], [11031, 11331]],
// // "SIRV604": [[1087, 1186], [1468, 1534], [1640, 1735], [1845, 2026], [2470, 2620], [2740, 2828], [3106, 3164], [10724, 10818], [11034, 11108], [11205, 11837]],
// // "SIRV607": [[1130, 1186], [1468, 1735], [1845, 2026], [2470, 2540]],
// // "SIRV606": [[2285, 2620], [2740, 2828], [3106, 3164], [10724, 10788]],
// // "SIRV609": [[1137, 1186], [1468, 1534], [1640, 1735], [1845, 2120]],
// // "SIRV608": [[3023, 3164], [10724, 10818], [11031, 11108], [11205, 11270]],
// // "SIRV702": [[1000, 2675], [2993, 3111], [4095, 4179], [4725, 4810], [43028, 43077], [114680, 114916]],
// // "SIRV703": [[1000, 2675], [2993, 3111], [3809, 3896], [114680, 114988], [147608, 147918]],
// // "SIRV704": [[55849, 56097], [78841, 78963], [114680, 114738]],
// // "SIRV614": [[2516, 2620], [2740, 2828], [3106, 3164], [7805, 7923], [10724, 10815]],
// // "SIRV311": [[4601, 4762]],
// // "SIRV310": [[8759, 8966], [9189, 9324], [9667, 9914]],
// // "SIRV615": [[10237, 10818], [11031, 11108], [11205, 11330]],
// // "SIRV705": [[1005, 2675], [2993, 3111], [43028, 43077], [114680, 114988], [147608, 147925]],
// // "SIRV701": [[1003, 2675], [2993, 3111], [43028, 43077], [114680, 114988], [147608, 147923]],
// // "SIRV613": [[3105, 3164], [7104, 7448], [7805, 7923], [10724, 10818], [11031, 11108], [11205, 11824]],
// // "SIRV610": [[2472, 2620], [2740, 2828], [3106, 3164], [10724, 11108], [11205, 11690]],
// // "SIRV611": [[1303, 1381], [1468, 1534], [1640, 1950]],
// // "SIRV403": [[8322, 8372], [8629, 8990], [13672, 13828], [15019, 15122]],
// // "SIRV508": [[8315, 8382], [8453, 8585], [10859, 10991], [11311, 11866]],
// // "SIRV501": [[1056, 1149], [1987, 2033], [2119, 2315], [3298, 3404], [3483, 3643], [5380, 5450], [5543, 5626], [6111, 6169], [6327, 6452], [6658, 6722], [6826, 6957], [7144, 7307], [7681, 7762], [7870, 8016], [8277, 8381], [8454, 8585], [10858, 10991]],
// // "SIRV406": [[3637, 4103], [5007, 5158]],
// // "SIRV405": [[8629, 8990], [13672, 13937]],
// // "SIRV404": [[8322, 8372], [8629, 8990], [13672, 13822], [14592, 14623]],
// // "SIRV502": [[1019, 1149], [1987, 2033], [2119, 2156], [2270, 2488], [3298, 3404], [3483, 3643], [5380, 5450], [5543, 5626], [6111, 6169], [6327, 6452], [6658, 6722], [6826, 6957], [7144, 7307], [7681, 7762], [7870, 8016], [8277, 8381], [8454, 8585], [10858, 10989]],
// // "SIRV503": [[8201, 8585], [10858, 10991], [11133, 11142]],
// // "SIRV409": [[1000, 1346], [1678, 1885], [2389, 3403]],
// // "SIRV408": [[8323, 8372], [8629, 8747], [8846, 8990], [13672, 13828], [15019, 15122]],
// // "SIRV506": [[1008, 1149], [1987, 2398]],
// // "SIRV507": [[1027, 1149], [1925, 2033], [2119, 2156], [2270, 2315], [3298, 3404], [3483, 3598]],
// // "SIRV504": [[11133, 13606]],
// // "SIRV505": [[1000, 1149], [1987, 2033], [2119, 2156], [2270, 2315], [3298, 3404], [3483, 3643], [5380, 5450], [5543, 5626], [6111, 6169], [6327, 6452], [6826, 6957], [7144, 7307], [7681, 7762], [7870, 8381], [8454, 8585], [10858, 10991]],
// // "SIRV205": [[1108, 1631]],
// // "SIRV204": [[3643, 3825], [3966, 4479], [4687, 4732]],
// // "SIRV617": [[1544, 1820]],
// // "SIRV206": [[4033, 4457]],
// // "SIRV308": [[1000, 1167], [1532, 1764], [1902, 1982]],
// // "SIRV309": [[8797, 8975], [9189, 9298], [9434, 9943]],
// // "SIRV203": [[3665, 3825], [3966, 4094], [4338, 4479], [4687, 4800], [5751, 5895]],
// // "SIRV202": [[1035, 1661], [1741, 1853], [1973, 2064], [2674, 2802], [2881, 3010], [3105, 3325], [3665, 3825], [3966, 4094], [4338, 4479], [4687, 4800], [5788, 5911]],
// // "SIRV304": [[1963, 2005], [4003, 4080], [4568, 4779], [6057, 6333], [7270, 7366], [7872, 7988], [8124, 8207], [8755, 8937]],
// // "SIRV305": [[4003, 4080], [4568, 4779], [6570, 6718]],
// // "SIRV306": [[1944, 2005], [4003, 4080], [6057, 8292]],
// // "SIRV307": [[1963, 2005], [4003, 4080], [4574, 4774], [6057, 6333], [8755, 8939]],
// // "SIRV612": [[1087, 1186], [1468, 1534], [1640, 1735], [1845, 2026], [2470, 2620], [2740, 2828], [3106, 3164], [10724, 10818], [11031, 11108], [11205, 11825]],
// // "SIRV301": [[1944, 2005], [4568, 4779], [6057, 7988], [8127, 8207], [8755, 8939]],
// // "SIRV302": [[1963, 2005], [6057, 7822]],
// // "SIRV303": [[1963, 2005], [4568, 4779], [6057, 7822]],
// // "SIRV708": [[56037, 56097], [70883, 70987], [78841, 78908], [78928, 78963], [114686, 114960], [147608, 147957]],
// // "SIRV108": [[10582, 10791], [10897, 11187], [11403, 11606]],
// // "SIRV109": [[10711, 10791], [10882, 11057], [11434, 11643]],
// // "SIRV106": [[1000, 1484], [7552, 7808], [10553, 10786]],
// // "SIRV107": [[10647, 10791], [10882, 11242], [11403, 11643]],
// // "SIRV105": [[6449, 6473], [6560, 6813], [7552, 7814], [10282, 10366], [10593, 10640]],
// // "SIRV102": [[1006, 1484], [6337, 6813], [7552, 7814], [10282, 10366]],
// // "SIRV103": [[1000, 1484], [6337, 6473], [6560, 6813], [7552, 7814], [10282, 10366], [10647, 10791]],
// // "SIRV101": [[1000, 1484], [6337, 6473], [6560, 6813], [7552, 7814], [10282, 10366], [10444, 10786]],
// // "SIRV602": [[1124, 1186], [1468, 1534], [1640, 1735], [2780, 2828], [3106, 3164], [10724, 10818], [11031, 11108], [11205, 11279]],
// // "SIRV201": [[1000, 1661], [1741, 1853], [1973, 2064], [2674, 2802], [2881, 3010], [3105, 3374], [3665, 3825], [3966, 4094], [4338, 4479], [4687, 4800], [5788, 5907]]
// // }
// static std::unordered_map<std::string, std::vector<std::string>>
// chr_to_gene = {{"SIRV1", {"SIRV1"}}, {"SIRV2", {"SIRV2"}}, {"SIRV3", {"SIRV3"}}, {"SIRV4", {"SIRV4"}}, {"SIRV5", {"SIRV5"}}, {"SIRV6", {"SIRV6"}},{"SIRV7", {"SIRV7"}}};
// static std::unordered_map<std::string, std::vector<exon>>
// gene_dict = {
// {"SIRV1", {{1000, 1484}, {6337, 6813}, {7552, 7814}, {10282, 10366}, {10444, 10791}, {10882, 11242}, {11403, 11643}}},
// {"SIRV2", {{1000, 1661}, {1741, 1853}, {1973, 2064}, {2674, 2802}, {2881, 3010}, {3105, 3374}, {3643, 3825}, {3966, 4479}, {4687, 4800}, {5751, 5911}}},
// {"SIRV3", {{1000, 1167}, {1532, 1764}, {1902, 2005}, {4003, 4080}, {4568, 4779}, {6057, 8292}, {8755, 8975}, {9189, 9324}, {9434, 9943}}},
// {"SIRV4", {{1000, 1346}, {1455, 1885}, {2251, 3403}, {3637, 4103}, {5007, 5158}, {8322, 8372}, {8629, 8990}, {13672, 13937}, {14592, 14623}, {15019, 15122}}},
// {"SIRV5", {{1000, 1149}, {1925, 2488}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6658, 6722}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8585}, {10858, 10991}, {11133, 13606}}},
// {"SIRV6", {{1000, 1186}, {1303, 1381}, {1468, 2120}, {2285, 2620}, {2740, 2828}, {3023, 3164}, {7104, 7448}, {7805, 7923}, {8999, 11837}}},
// {"SIRV7", {{1000, 2675}, {2993, 3111}, {3809, 3896}, {4095, 4179}, {4725, 4810}, {43028, 43077}, {55849, 56097}, {70883, 70987}, {78841, 78963}, {114680, 114988}, {147608, 147957}}}
// };
// static std::unordered_map<std::string, Junctions>
// transcript_to_junctions = {
// {"SIRV410", {1455, {1885, 2251}, 2771}},
// {"SIRV203", {3665, {3825, 3966, 4094, 4338, 4479, 4687, 4800, 5751}, 5895}},
// {"SIRV408", {8323, {8372, 8629, 8747, 8846, 8990, 13672, 13828, 15019}, 15122}},
// {"SIRV511", {1008, {1143, 1987}, 2398}},
// {"SIRV510", {1028, {1149, 1987, 2033, 2119, 2156, 2270, 2315, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8016, 8277, 8381, 8454, 8585, 10858, 10991, 11133}, 11867}},
// {"SIRV512", {2177, {}, 2406}},
// {"SIRV601", {1000, {1186, 1468, 1534, 1640, 1735, 2470, 2620, 2740, 2828, 3106, 3164, 10724, 10818, 11031, 11108, 11205}, 11826}},
// {"SIRV304", {1963, {2005, 4003, 4080, 4568, 4779, 6057, 6333, 7270, 7366, 7872, 7988, 8124, 8207, 8755}, 8937}},
// {"SIRV603", {8999, {}, 10968}},
// {"SIRV602", {1124, {1186, 1468, 1534, 1640, 1735, 2780, 2828, 3106, 3164, 10724, 10818, 11031, 11108, 11205}, 11279}},
// {"SIRV605", {1130, {1186, 1468, 1534, 1640, 1735, 1845, 2026, 2470, 2620, 2740, 2828, 3106, 3164, 10724, 10818, 11031}, 11331}},
// {"SIRV604", {1087, {1186, 1468, 1534, 1640, 1735, 1845, 2026, 2470, 2620, 2740, 2828, 3106, 3164, 10724, 10818, 11034, 11108, 11205}, 11837}},
// {"SIRV607", {1130, {1186, 1468, 1735, 1845, 2026, 2470}, 2540}},
// {"SIRV606", {2285, {2620, 2740, 2828, 3106, 3164, 10724}, 10788}},
// {"SIRV609", {1137, {1186, 1468, 1534, 1640, 1735, 1845}, 2120}},
// {"SIRV608", {3023, {3164, 10724, 10818, 11031, 11108, 11205}, 11270}},
// {"SIRV702", {1000, {2675, 2993, 3111, 4095, 4179, 4725, 4810, 43028, 43077, 114680}, 114916}},
// {"SIRV703", {1000, {2675, 2993, 3111, 3809, 3896, 114680, 114988, 147608}, 147918}},
// {"SIRV704", {55849, {56097, 78841, 78963, 114680}, 114738}},
// {"SIRV705", {1005, {2675, 2993, 3111, 43028, 43077, 114680, 114988, 147608}, 147925}},
// {"SIRV311", {4601, {}, 4762}},
// {"SIRV310", {8759, {8966, 9189, 9324, 9667}, 9914}},
// {"SIRV307", {1963, {2005, 4003, 4080, 4574, 4774, 6057, 6333, 8755}, 8939}},
// {"SIRV612", {1087, {1186, 1468, 1534, 1640, 1735, 1845, 2026, 2470, 2620, 2740, 2828, 3106, 3164, 10724, 10818, 11031, 11108, 11205}, 11825}},
// {"SIRV701", {1003, {2675, 2993, 3111, 43028, 43077, 114680, 114988, 147608}, 147923}},
// {"SIRV301", {1944, {2005, 4568, 4779, 6057, 7988, 8127, 8207, 8755}, 8939}},
// {"SIRV706", {56031, {56097, 70883, 70987, 78841, 78963, 114680, 114988, 147608}, 147957}},
// {"SIRV303", {1963, {2005, 4568, 4779, 6057}, 7822}},
// {"SIRV305", {4003, {4080, 4568, 4779, 6570}, 6718}},
// {"SIRV403", {8322, {8372, 8629, 8990, 13672, 13828, 15019}, 15122}},
// {"SIRV508", {1008, {1149, 1987, 2033, 2119, 2156, 2270, 2315, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6658, 6722, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8381, 8454, 8585, 10858}, 10991}},
// {"SIRV509", {8315, {8381, 8454, 8585, 10858, 10991, 11311}, 11866}},
// {"SIRV406", {3637, {4103, 5007}, 5158}},
// {"SIRV405", {8629, {8990, 13672}, 13937}},
// {"SIRV404", {8322, {8372, 8629, 8990, 13672, 13822, 14592}, 14623}},
// {"SIRV502", {1019, {1149, 1987, 2033, 2119, 2156, 2270, 2488, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6658, 6722, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8016, 8277, 8381, 8454, 8585, 10858}, 10989}},
// {"SIRV503", {8201, {8585, 10858, 10991, 11133}, 11142}},
// {"SIRV409", {1000, {1346, 1678, 1885, 2389}, 3403}},
// {"SIRV501", {1056, {1149, 1987, 2033, 2119, 2315, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6658, 6722, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8016, 8277, 8381, 8454, 8585, 10858}, 10991}},
// {"SIRV506", {1008, {1149, 1987}, 2398}},
// {"SIRV507", {1027, {1149, 1925, 2033, 2119, 2156, 2270, 2315, 3298, 3404, 3483}, 3598}},
// {"SIRV504", {11133, {}, 13606}},
// {"SIRV505", {1000, {1149, 1987, 2033, 2119, 2156, 2270, 2315, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8381, 8454, 8585, 10858}, 10991}},
// {"SIRV205", {1108, {}, 1631}},
// {"SIRV204", {3643, {3825, 3966, 4479, 4687}, 4732}},
// {"SIRV206", {4033, {}, 4457}},
// {"SIRV308", {1000, {1167, 1532, 1764, 1902}, 1982}},
// {"SIRV309", {8797, {8975, 9189, 9298, 9434}, 9943}},
// {"SIRV618", {2358, {}, 2547}},
// {"SIRV202", {1035, {1661, 1741, 1853, 1973, 2064, 2674, 2802, 2881, 3010, 3105, 3325, 3665, 3825, 3966, 4094, 4338, 4479, 4687, 4800, 5788}, 5911}},
// {"SIRV616", {2285, {2620, 2740, 2814, 3106, 3164, 10724}, 10788}},
// {"SIRV617", {1544, {}, 1820}},
// {"SIRV614", {2516, {2620, 2740, 2828, 3106, 3164, 7805, 7923, 10724}, 10815}},
// {"SIRV615", {10237, {10818, 11031, 11108, 11205}, 11330}},
// {"SIRV306", {1944, {2005, 4003, 4080, 6057}, 8292}},
// {"SIRV613", {3105, {3164, 7104, 7448, 7805, 7923, 10724, 10818, 11031, 11108, 11205}, 11824}},
// {"SIRV610", {2472, {2620, 2740, 2828, 3106, 3164, 10724, 11108, 11205}, 11690}},
// {"SIRV611", {1303, {1381, 1468, 1534, 1640}, 1950}},
// {"SIRV708", {56037, {56097, 70883, 70987, 78841, 78908, 78928, 78963, 114686, 114960, 147608}, 147957}},
// {"SIRV108", {10582, {10791, 10897, 11187, 11403}, 11606}},
// {"SIRV302", {1963, {2005, 6057}, 7822}},
// {"SIRV109", {10711, {10791, 10882, 11057, 11434}, 11643}},
// {"SIRV106", {1000, {1484, 7552, 7808, 10553}, 10786}},
// {"SIRV107", {10647, {10791, 10882, 11242, 11403}, 11643}},
// {"SIRV105", {6449, {6473, 6560, 6813, 7552, 7814, 10282, 10366, 10593}, 10640}},
// {"SIRV102", {1006, {1484, 6337, 6813, 7552, 7814, 10282}, 10366}},
// {"SIRV103", {1000, {1484, 6337, 6473, 6560, 6813, 7552, 7814, 10282, 10366, 10647}, 10791}},
// {"SIRV101", {1000, {1484, 6337, 6473, 6560, 6813, 7552, 7814, 10282, 10366, 10444}, 10786}},
// {"SIRV201", {1000, {1661, 1741, 1853, 1973, 2064, 2674, 2802, 2881, 3010, 3105, 3374, 3665, 3825, 3966, 4094, 4338, 4479, 4687, 4800, 5788}, 5907}}
// };
// context("Junctions Functions") {
// // is_exon_similar
// test_that("exons compare correctly") {
// std::vector<exon> exon1 {
// {1008, 1149}, {1987, 2033}, {2119, 2156}, {2270, 2315}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6658, 6722}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8381}, {8454, 8585}, {10858, 10991}
// };
// std::vector<exon> exon2 {
// {8315, 8381}, {8454, 8585}, {10858, 10991}, {11311, 11866}
// };
// expect_true(!is_exon_similar(exon1, exon2, 10));
// std::vector<exon> exon3 {
// {1008, 1149}, {1987, 2398}
// };
// std::vector<exon> exon4 {
// {1008, 1143}, {1987, 2398}
// };
// expect_true(is_exon_similar(exon3, exon4, 10));
// }
// // remove_similar_tr
// test_that("similar transcripts are correctly removed") {
// auto unique_tr = remove_similar_tr(gene_to_transcript, transcript_to_exon, 10);
// std::unordered_map<std::string, transcriptvector> res_gene {
// {"SIRV5", {"SIRV508", "SIRV502", "SIRV503", "SIRV501", "SIRV506", "SIRV507", "SIRV504", "SIRV505", "SIRV512", "SIRV510"}},
// {"SIRV4", {"SIRV403", "SIRV410", "SIRV406", "SIRV405", "SIRV404", "SIRV409", "SIRV408"}},
// {"SIRV7", {"SIRV708", "SIRV701", "SIRV702", "SIRV703", "SIRV704", "SIRV706"}},
// {"SIRV6", {"SIRV618", "SIRV617", "SIRV601", "SIRV616", "SIRV603", "SIRV602", "SIRV605", "SIRV604", "SIRV607", "SIRV606", "SIRV609", "SIRV608", "SIRV614", "SIRV615", "SIRV612", "SIRV613", "SIRV610", "SIRV611"}},
// {"SIRV1", {"SIRV108", "SIRV109", "SIRV106", "SIRV107", "SIRV105", "SIRV102", "SIRV103", "SIRV101"}},
// {"SIRV3", {"SIRV310", "SIRV311", "SIRV308", "SIRV309", "SIRV304", "SIRV305", "SIRV306", "SIRV307", "SIRV301", "SIRV302", "SIRV303"}},
// {"SIRV2", {"SIRV205", "SIRV204", "SIRV206", "SIRV201", "SIRV203", "SIRV202"}}
// };
// expect_true(compare_map(res_gene, unique_tr));
// }
// // get_gene_flat
// test_that("genes can be flattened correctly") {
// std::unordered_map<std::string, transcriptvector> gsmall {
// {"SIRV5", gene_to_transcript["SIRV5"]}
// };
// auto flat = get_gene_flat(gsmall, transcript_to_exon);
// std::unordered_map<std::string, std::vector<exon>> real {
// {"SIRV5", {{1000, 1149}, {1925, 2488}, {3298, 3404}, {3483, 3643}, {5380, 5450}, {5543, 5626}, {6111, 6169}, {6327, 6452}, {6658, 6722}, {6826, 6957}, {7144, 7307}, {7681, 7762}, {7870, 8585}, {10858, 10991}, {11133, 13606}}}
// };
// expect_true(compare_map(real, flat));
// }
// // get_gene_blocks
// test_that("genes blocks can be correctly calculated") {
// std::unordered_map<std::string, std::vector<GeneBlocks>>
// chr = get_gene_blocks(gene_dict, chr_to_gene, gene_to_transcript);
// std::unordered_map<std::string, std::vector<int>> chr_to_blocks = {
// {"SIRV1", {1000, 11643, 8, 1}},
// {"SIRV2", {1000, 5911, 6, 1}},
// {"SIRV3", {1000, 9943, 11, 1}},
// {"SIRV4", {1000, 15122, 7, 1}},
// {"SIRV5", {1000, 13606, 11, 1}},
// {"SIRV6", {1000, 11837, 18, 1}},
// {"SIRV7", {1000, 147957, 6, 1}}
// };
// expect_true(chr.size() == chr_to_blocks.size());
// for (const auto &[ch, blocks] : chr) {
// expect_true(chr_to_blocks[ch][0] == blocks[0].start);
// expect_true(chr_to_blocks[ch][1] == blocks[0].end);
// expect_true(chr_to_blocks[ch][2] == blocks[0].transcript_list.size());
// expect_true(chr_to_blocks[ch][3] == blocks[0].gene_to_transcript.size());
// }
// }
// // get_TSS_TES_site
// test_that("TSS_TES Sites can be acquired") {
// // // python :
// // // from sc_longread import blocks_to_junctions, get_TSS_TES_site
// // // from parse_gene_anno import parse_gff_tree
// // // gff3 = "/Volumes/voogd.o/FLAMES/inst/extdata/SIRV_anno.gtf"
// // // chr, tran, gene, exon = parse_gff_tree(gff3)
// // // transcript_to_junctions = {tr : blocks_to_junctions(exon[tr]) for tr in exon}
// // // remove_similar_tr(tran, gene, exon)
// // // gene_dict = get_gene_flat(gene, exon)
// // // chr_to_blocks = get_gene_blocks(gene_dict, chr, gene)
// // // ch = chr_to_blocks.keys()[0]
// // // bl = chr_to_blocks[ch][0]
// // // TSS_TES_site = get_TSS_TES_site(transcript_to_junctions, bl.transcript_list)
// const std::vector<std::string> tr_list {
// "SIRV508", "SIRV509", "SIRV502", "SIRV503", "SIRV501", "SIRV506", "SIRV507", "SIRV504", "SIRV505", "SIRV512", "SIRV510", "SIRV511"
// };
// DoubleJunctions sites = get_TSS_TES_site(transcript_to_junctions, tr_list);
// DoubleJunctions real_sites {
// {1000, 1008, 1019, 1027, 1056, 2177, 8201, 8315, 11133},
// {2398, 2406, 3598, 10991, 11142, 11866, 13606}
// };
// expect_true(compare_unordered(sites.left, real_sites.left));
// expect_true(compare_unordered(sites.right, real_sites.right));
// const std::vector<std::string> tr_list2 {
// "SIRV310", "SIRV311", "SIRV308", "SIRV309", "SIRV304", "SIRV305", "SIRV306", "SIRV307", "SIRV301", "SIRV302", "SIRV303"
// };
// DoubleJunctions sites2 = get_TSS_TES_site(transcript_to_junctions, tr_list2);
// DoubleJunctions real_sites2 {
// {1000, 1944, 1963, 4003, 4601, 8759, 8797},
// {1982, 4762, 6718, 7822, 8292, 8937, 9914, 9943}
// };
// expect_true(compare_unordered(sites2.left, real_sites2.left));
// expect_true(compare_unordered(sites2.right, real_sites2.right));
// }
// // take_closest
// test_that("take_closest takes the closest") {
// std::vector<int> sample {1,2,3,4,5,8,10,20,30,60,100};
// expect_true(take_closest(sample, 6) == 5);
// expect_true(take_closest(sample, 80) == 60);
// expect_true(take_closest(sample, 14) == 10);
// }
// // get_splice_site
// test_that("splice sites can be aquired") {
// std::vector<std::string> tr_list {
// "SIRV508", "SIRV509", "SIRV502", "SIRV503", "SIRV501", "SIRV506", "SIRV507", "SIRV504", "SIRV505", "SIRV512", "SIRV510"
// };
// std::set<int> out_site = get_splice_site(transcript_to_junctions, tr_list);
// std::set<int> real_site {
// 1149, 1925, 1987, 2033, 2119, 2156, 2270, 2315, 2488, 3298, 3404, 3483, 3643, 5380, 5450, 5543, 5626, 6111, 6169, 6327, 6452, 6658, 6722, 6826, 6957, 7144, 7307, 7681, 7762, 7870, 8016, 8277, 8381, 8454, 8585, 10858, 10991, 11133, 11311
// };
// expect_true(compare_stream(real_site, out_site));
// }
// // find_best_splice_chain
// // blocks_to_junctions
// // map_transcripts_to_junctions
// // exon_overlap
// // checkExonSubset
// // get_exon_sim_pct
// }
