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Updating ci ref #88

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Merged
aineniamh merged 3 commits into from
Jan 26, 2026
Merged

Updating ci ref #88

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181ee9a
upper comparison for alignment
aineniamh Jan 21, 2026
0e73af8
updating c1 ref, gene coordinates and mask file for resequencing of t…
aineniamh Jan 26, 2026
05c0e69
adding in the old boundaries and old mask file for cladei for record
aineniamh Jan 26, 2026
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2,817 changes: 2,817 additions & 0 deletions squirrel/data/PX667572.fasta
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351 changes: 171 additions & 180 deletions squirrel/data/gene_boundaries.cladei.csv
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Original file line number Diff line number Diff line change
@@ -1,181 +1,172 @@
Reference,Name,Minimum,Maximum,Length,Direction
NC_003310,OPG001 CDS,195248,195988,741,forward
NC_003310,OPG002 CDS,194073,195119,1047,forward
NC_003310,OPG003 CDS,192219,193982,1764,forward
NC_003310,OPG015 CDS,190749,192062,1314,forward
NC_003310,OPG016 CDS,190103,190633,531,forward
NC_003310,OPG005 CDS,188894,189355,462,forward
NC_003310,OPG210 CDS,181046,186685,5640,forward
NC_003310,OPG209 CDS,180215,180787,573,forward
NC_003310,OPG208 CDS,178963,180036,1074,forward
NC_003310,OPG205 CDS,175330,177711,2382,forward
NC_003310,OPG204 CDS,174203,175261,1059,forward
NC_003310,OPG201 CDS,172403,173383,981,forward
NC_003310,OPG200 CDS,171868,172317,450,forward
NC_003310,OPG199 CDS,170707,171741,1035,forward
NC_003310,OPG198 CDS,169744,170592,849,forward
NC_003310,OPG195 CDS,167957,168622,666,forward
NC_003310,OPG193 CDS,167061,167864,804,forward
NC_003310,OPG192 CDS,166458,167006,549,forward
NC_003310,OPG191 CDS,165891,166421,531,forward
NC_003310,OPG190 CDS,164845,165798,954,forward
NC_003310,OPG189 CDS,163058,164743,1686,forward
NC_003310,OPG188 CDS,161299,162810,1512,forward
NC_003310,OPG187 CDS,160325,161224,900,forward
NC_003310,OPG185 CDS,158617,159558,942,forward
NC_003310,OPG181 CDS,156366,157370,1005,forward
NC_003310,OPG180 CDS,154648,156312,1665,forward
NC_003310,OPG178 CDS,153468,154082,615,forward
NC_003310,OPG176 CDS,151666,152388,723,forward
NC_003310,OPG175 CDS,151299,151676,378,forward
NC_003310,OPG174 CDS,150212,151252,1041,reverse
NC_003310,OPG173 CDS,149894,150118,225,forward
NC_003310,OPG172 CDS,149281,149874,594,forward
NC_003310,OPG171 CDS,148842,149243,402,forward
NC_003310,OPG170 CDS,147981,148646,666,reverse
NC_003310,OPG167 CDS,146421,147254,834,reverse
NC_003310,OPG166 CDS,146245,146424,180,forward
NC_003310,OPG165 CDS,145363,146169,807,forward
NC_003310,OPG164 CDS,144611,145249,639,forward
NC_003310,OPG163 CDS,144036,144566,531,forward
NC_003310,OPG162 CDS,143486,143992,507,forward
NC_003310,OPG161 CDS,142936,143481,546,forward
NC_003310,OPG160 CDS,142006,142908,903,reverse
NC_003310,OPG159 CDS,141611,142039,429,forward
NC_003310,OPG158 CDS,141484,141612,129,reverse
NC_003310,OPG157 CDS,141218,141451,234,reverse
NC_003310,OPG156 CDS,140338,141255,918,reverse
NC_003310,OPG155 CDS,139897,140337,441,reverse
NC_003310,OPG154 CDS,139564,139896,333,reverse
NC_003310,OPG153 CDS,137951,139513,1563,reverse
NC_003310,OPG151 CDS,131207,134701,3495,forward
NC_003310,OPG150 CDS,130062,131210,1149,forward
NC_003310,OPG149 CDS,129479,130042,564,forward
NC_003310,OPG148 CDS,128269,129549,1281,forward
NC_003310,OPG147 CDS,127923,128270,348,reverse
NC_003310,OPG146 CDS,127689,127922,234,reverse
NC_003310,OPG145 CDS,126230,127708,1479,forward
NC_003310,OPG144 CDS,125601,126215,615,reverse
NC_003310,OPG143 CDS,124465,125598,1134,reverse
NC_003310,OPG142 CDS,124197,124481,285,reverse
NC_003310,OPG141 CDS,124046,124207,162,reverse
NC_003310,OPG140 CDS,123757,124029,273,reverse
NC_003310,OPG139 CDS,123439,123651,213,reverse
NC_003310,OPG138 CDS,122843,123415,573,reverse
NC_003310,OPG137 CDS,121885,122841,957,forward
NC_003310,OPG136 CDS,119195,121870,2676,reverse
NC_003310,OPG135 CDS,118892,119194,303,reverse
NC_003310,OPG134 CDS,118033,118911,879,forward
NC_003310,OPG133 CDS,115847,117979,2133,reverse
NC_003310,OPG132 CDS,114705,115823,1119,reverse
NC_003310,OPG131 CDS,114223,114708,486,forward
NC_003310,OPG130 CDS,113340,114185,846,reverse
NC_003310,OPG129 CDS,111353,113287,1935,reverse
NC_003310,OPG128 CDS,111105,111338,234,reverse
NC_003310,OPG127 CDS,110434,111108,675,reverse
NC_003310,OPG126 CDS,109961,110413,453,reverse
NC_003310,OPG125 CDS,108281,109936,1656,reverse
NC_003310,OPG124 CDS,107387,108250,864,reverse
NC_003310,OPG123 CDS,105457,107352,1896,reverse
NC_003310,OPG122 CDS,104710,105456,747,forward
NC_003310,OPG121 CDS,104072,104713,642,forward
NC_003310,OPG120 CDS,103116,104030,915,reverse
NC_003310,OPG119 CDS,102668,103153,486,forward
NC_003310,OPG118 CDS,100728,102641,1914,forward
NC_003310,OPG117 CDS,98331,100688,2358,forward
NC_003310,OPG116 CDS,97643,98299,657,forward
NC_003310,OPG115 CDS,96942,97643,702,forward
NC_003310,OPG114 CDS,96509,96949,441,reverse
NC_003310,OPG113 CDS,94013,96550,2538,forward
NC_003310,OPG112 CDS,93529,93969,441,forward
NC_003310,OPG111 CDS,92547,93491,945,forward
NC_003310,OPG110 CDS,91905,92546,642,forward
NC_003310,OPG109 CDS,89333,91720,2388,reverse
NC_003310,OPG108 CDS,88358,89332,975,reverse
NC_003310,OPG107 CDS,87785,88354,570,forward
NC_003310,OPG106 CDS,87256,87771,516,reverse
NC_003310,OPG105 CDS,83399,87259,3861,forward
NC_003310,OPG104 CDS,82891,83292,402,reverse
NC_003310,OPG103 CDS,82274,82831,558,forward
NC_003310,OPG102 CDS,81358,82359,1002,forward
NC_003310,OPG101 CDS,80759,81292,534,forward
NC_003310,OPG100 CDS,80281,80739,459,forward
NC_003310,OPG099 CDS,79938,80324,387,forward
NC_003310,OPG098 CDS,79173,79928,756,forward
NC_003310,OPG097 CDS,78114,79148,1035,reverse
NC_003310,OPG096 CDS,77860,78138,279,forward
NC_003310,OPG095 CDS,77076,77828,753,forward
NC_003310,OPG094 CDS,76053,77075,1023,forward
NC_003310,OPG093 CDS,75251,76033,783,forward
NC_003310,OPG092 CDS,74105,75220,1116,reverse
NC_003310,OPG091 CDS,73643,74140,498,forward
NC_003310,OPG090 CDS,73452,73643,192,forward
NC_003310,OPG089 CDS,72140,73444,1305,forward
NC_003310,OPG088 CDS,71763,72137,375,reverse
NC_003310,OPG087 CDS,71131,71793,663,forward
NC_003310,OPG086 CDS,70802,71137,336,reverse
NC_003310,OPG085 CDS,69030,70805,1776,reverse
NC_003310,OPG084 CDS,66996,69026,2031,forward
NC_003310,OPG083 CDS,65719,66990,1272,reverse
NC_003310,OPG082 CDS,64578,65726,1149,reverse
NC_003310,OPG081 CDS,64320,64559,240,reverse
NC_003310,OPG080 CDS,61976,64291,2316,reverse
NC_003310,OPG079 CDS,61085,61894,810,reverse
NC_003310,OPG078 CDS,60863,61084,222,reverse
NC_003310,OPG077 CDS,59918,60856,939,reverse
NC_003310,OPG076 CDS,59796,59903,108,reverse
NC_003310,OPG075 CDS,59445,59771,327,reverse
NC_003310,OPG074 CDS,57401,59398,1998,reverse
NC_003310,OPG073 CDS,57025,57414,390,reverse
NC_003310,OPG072 CDS,56743,57030,288,forward
NC_003310,OPG071 CDS,53691,56711,3021,reverse
NC_003310,OPG070 CDS,52862,53683,822,forward
NC_003310,OPG069 CDS,52262,52762,501,forward
NC_003310,OPG068 CDS,50477,52180,1704,forward
NC_003310,OPG066 CDS,48670,49449,780,reverse
NC_003310,OPG065 CDS,48048,48509,462,reverse
NC_003310,OPG064 CDS,45711,47924,2214,reverse
NC_003310,OPG063 CDS,44275,45714,1440,reverse
NC_003310,OPG062 CDS,43973,44278,306,forward
NC_003310,OPG061 CDS,43216,43911,696,reverse
NC_003310,OPG060 CDS,42733,43209,477,reverse
NC_003310,OPG059 CDS,42514,42660,147,reverse
NC_003310,OPG058 CDS,42240,42461,222,reverse
NC_003310,OPG057 CDS,41104,42222,1119,reverse
NC_003310,OPG056 CDS,39154,41061,1908,reverse
NC_003310,OPG055 CDS,38046,39110,1065,reverse
NC_003310,OPG054 CDS,36704,38023,1320,reverse
NC_003310,OPG053 CDS,36079,36717,639,reverse
NC_003310,OPG052 CDS,35828,36022,195,reverse
NC_003310,OPG051 CDS,35452,35676,225,reverse
NC_003310,OPG050 CDS,35215,35436,222,reverse
NC_003310,OPG049 CDS,34227,35180,954,reverse
NC_003310,OPG048 CDS,33236,34195,960,reverse
NC_003310,OPG047 CDS,31762,33225,1464,reverse
NC_003310,OPG046 CDS,31290,31745,456,reverse
NC_003310,OPG045 CDS,30619,31278,660,reverse
NC_003310,OPG044 CDS,30126,30575,450,forward
NC_003310,OPG043 CDS,29160,29990,831,reverse
NC_003310,OPG042 CDS,27859,29133,1275,reverse
NC_003310,OPG040 CDS,26384,27511,1128,reverse
NC_003310,OPG039 CDS,25299,26153,855,reverse
NC_003310,OPG038 CDS,24508,25170,663,reverse
NC_003310,OPG037 CDS,23110,24438,1329,reverse
NC_003310,OPG036 CDS,22536,23069,534,reverse
NC_003310,OPG035 CDS,22056,22409,354,reverse
NC_003310,OPG034 CDS,21366,22010,645,reverse
NC_003310,OPG032 CDS,19060,19710,651,reverse
NC_003310,OPG031 CDS,17931,18878,948,reverse
NC_003310,OPG030 CDS,17266,17886,621,reverse
NC_003310,OPG029 CDS,16661,17122,462,reverse
NC_003310,OPG027 CDS,15980,16432,453,reverse
NC_003310,OPG025 CDS,13433,15325,1893,reverse
NC_003310,OPG024 CDS,13079,13273,195,reverse
NC_003310,OPG023 CDS,10963,12945,1983,reverse
NC_003310,OPG022 CDS,10523,10903,381,reverse
NC_003310,OPG021 CDS,9567,10295,729,forward
NC_003310,OPG019 CDS,7556,7984,429,forward
NC_003310,OPG015 CDS,4797,6110,1314,reverse
NC_003310,OPG003 CDS,2877,4640,1764,reverse
NC_003310,OPG002 CDS,1740,2786,1047,reverse
NC_003310,OPG001 CDS,871,1611,741,reverse
PX667572,OPG001 CDS,195322,196062,741,forward
PX667572,OPG002 CDS,194147,195193,1047,forward
PX667572,OPG015 CDS,190824,192137,1314,forward
PX667572,OPG016 CDS,190178,190708,531,forward
PX667572,OPG005 CDS,188969,189430,462,forward
PX667572,OPG210 CDS,181120,186759,5640,forward
PX667572,OPG209 CDS,180289,180861,573,forward
PX667572,OPG208 CDS,179037,180110,1074,forward
PX667572,OPG205 CDS,175404,177785,2382,forward
PX667572,OPG204 CDS,174280,175335,1056,forward
PX667572,OPG200 CDS,171942,172391,450,forward
PX667572,OPG199 CDS,170781,171815,1035,forward
PX667572,OPG198 CDS,169818,170666,849,forward
PX667572,OPG195 CDS,168006,168671,666,forward
PX667572,OPG193 CDS,167108,167911,804,forward
PX667572,OPG192 CDS,166505,167053,549,forward
PX667572,OPG190 CDS,164892,165845,954,forward
PX667572,OPG189 CDS,163105,164790,1686,forward
PX667572,OPG188 CDS,161346,162857,1512,forward
PX667572,OPG185 CDS,158664,159605,942,forward
PX667572,OPG181 CDS,156413,157417,1005,forward
PX667572,OPG178 CDS,153515,154129,615,forward
PX667572,OPG176 CDS,151713,152435,723,forward
PX667572,OPG175 CDS,151346,151723,378,forward
PX667572,OPG174 CDS,150259,151299,1041,reverse
PX667572,OPG173 CDS,149941,150165,225,forward
PX667572,OPG172 CDS,149331,149921,591,forward
PX667572,OPG171 CDS,148889,149290,402,forward
PX667572,OPG170 CDS,148028,148693,666,reverse
PX667572,OPG167 CDS,146468,147301,834,reverse
PX667572,OPG166 CDS,146292,146471,180,forward
PX667572,OPG165 CDS,145410,146216,807,forward
PX667572,OPG163 CDS,144083,144613,531,forward
PX667572,OPG162 CDS,143533,144039,507,forward
PX667572,OPG161 CDS,142983,143528,546,forward
PX667572,OPG160 CDS,142053,142955,903,reverse
PX667572,OPG159 CDS,141658,142086,429,forward
PX667572,OPG158 CDS,141531,141659,129,reverse
PX667572,OPG157 CDS,141265,141498,234,reverse
PX667572,OPG156 CDS,140385,141302,918,reverse
PX667572,OPG155 CDS,139944,140384,441,reverse
PX667572,OPG154 CDS,139611,139943,333,reverse
PX667572,OPG153 CDS,137998,139560,1563,reverse
PX667572,OPG151 CDS,131254,134748,3495,forward
PX667572,OPG150 CDS,130109,131257,1149,forward
PX667572,OPG149 CDS,129526,130089,564,forward
PX667572,OPG148 CDS,128316,129596,1281,forward
PX667572,OPG147 CDS,127970,128317,348,reverse
PX667572,OPG146 CDS,127736,127969,234,reverse
PX667572,OPG145 CDS,126277,127755,1479,forward
PX667572,OPG144 CDS,125648,126262,615,reverse
PX667572,OPG143 CDS,124512,125645,1134,reverse
PX667572,OPG142 CDS,124244,124528,285,reverse
PX667572,OPG141 CDS,124093,124254,162,reverse
PX667572,OPG140 CDS,123804,124076,273,reverse
PX667572,OPG139 CDS,123486,123698,213,reverse
PX667572,OPG138 CDS,122890,123462,573,reverse
PX667572,OPG137 CDS,121932,122888,957,forward
PX667572,OPG136 CDS,119242,121917,2676,reverse
PX667572,OPG135 CDS,118939,119241,303,reverse
PX667572,OPG134 CDS,118080,118958,879,forward
PX667572,OPG133 CDS,115894,118026,2133,reverse
PX667572,OPG132 CDS,114752,115870,1119,reverse
PX667572,OPG131 CDS,114270,114755,486,forward
PX667572,OPG130 CDS,113387,114232,846,reverse
PX667572,OPG129 CDS,111400,113334,1935,reverse
PX667572,OPG128 CDS,111152,111385,234,reverse
PX667572,OPG127 CDS,110481,111155,675,reverse
PX667572,OPG126 CDS,110008,110460,453,reverse
PX667572,OPG125 CDS,108328,109983,1656,reverse
PX667572,OPG124 CDS,107434,108297,864,reverse
PX667572,OPG123 CDS,105504,107399,1896,reverse
PX667572,OPG122 CDS,104757,105503,747,forward
PX667572,OPG121 CDS,104119,104760,642,forward
PX667572,OPG120 CDS,103163,104077,915,reverse
PX667572,OPG119 CDS,102715,103200,486,forward
PX667572,OPG118 CDS,100775,102688,1914,forward
PX667572,OPG117 CDS,98378,100735,2358,forward
PX667572,OPG116 CDS,97690,98346,657,forward
PX667572,OPG115 CDS,96989,97690,702,forward
PX667572,OPG114 CDS,96556,96996,441,reverse
PX667572,OPG113 CDS,94060,96597,2538,forward
PX667572,OPG112 CDS,93576,94016,441,forward
PX667572,OPG111 CDS,92594,93538,945,forward
PX667572,OPG110 CDS,91952,92593,642,forward
PX667572,OPG109 CDS,89380,91767,2388,reverse
PX667572,OPG108 CDS,88405,89379,975,reverse
PX667572,OPG107 CDS,87832,88401,570,forward
PX667572,OPG106 CDS,87303,87818,516,reverse
PX667572,OPG105 CDS,83446,87306,3861,forward
PX667572,OPG104 CDS,82938,83339,402,reverse
PX667572,OPG103 CDS,82321,82878,558,forward
PX667572,OPG102 CDS,81405,82406,1002,forward
PX667572,OPG101 CDS,80806,81339,534,forward
PX667572,OPG100 CDS,80328,80786,459,forward
PX667572,OPG099 CDS,79985,80371,387,forward
PX667572,OPG098 CDS,79220,79975,756,forward
PX667572,OPG097 CDS,78161,79195,1035,reverse
PX667572,OPG096 CDS,77907,78185,279,forward
PX667572,OPG095 CDS,77123,77875,753,forward
PX667572,OPG094 CDS,76100,77122,1023,forward
PX667572,OPG093 CDS,75298,76080,783,forward
PX667572,OPG092 CDS,74152,75267,1116,reverse
PX667572,OPG091 CDS,73690,74187,498,forward
PX667572,OPG090 CDS,73499,73690,192,forward
PX667572,OPG089 CDS,72187,73491,1305,forward
PX667572,OPG088 CDS,71810,72184,375,reverse
PX667572,OPG087 CDS,71178,71840,663,forward
PX667572,OPG086 CDS,70849,71184,336,reverse
PX667572,OPG085 CDS,69077,70852,1776,reverse
PX667572,OPG084 CDS,67043,69073,2031,forward
PX667572,OPG083 CDS,65766,67037,1272,reverse
PX667572,OPG082 CDS,64625,65773,1149,reverse
PX667572,OPG081 CDS,64367,64606,240,reverse
PX667572,OPG080 CDS,62023,64338,2316,reverse
PX667572,OPG079 CDS,61132,61941,810,reverse
PX667572,OPG078 CDS,60910,61131,222,reverse
PX667572,OPG077 CDS,59965,60903,939,reverse
PX667572,OPG076 CDS,59843,59950,108,reverse
PX667572,OPG075 CDS,59492,59818,327,reverse
PX667572,OPG074 CDS,57448,59445,1998,reverse
PX667572,OPG073 CDS,57072,57461,390,reverse
PX667572,OPG072 CDS,56790,57077,288,forward
PX667572,OPG071 CDS,53738,56758,3021,reverse
PX667572,OPG070 CDS,52909,53730,822,forward
PX667572,OPG069 CDS,52309,52809,501,forward
PX667572,OPG068 CDS,50524,52227,1704,forward
PX667572,OPG066 CDS,48717,49496,780,reverse
PX667572,OPG065 CDS,48095,48556,462,reverse
PX667572,OPG064 CDS,45758,47971,2214,reverse
PX667572,OPG063 CDS,44322,45761,1440,reverse
PX667572,OPG062 CDS,44020,44325,306,forward
PX667572,OPG061 CDS,43263,43958,696,reverse
PX667572,OPG060 CDS,42780,43256,477,reverse
PX667572,OPG059 CDS,42558,42707,150,reverse
PX667572,OPG058 CDS,42287,42508,222,reverse
PX667572,OPG057 CDS,41151,42269,1119,reverse
PX667572,OPG056 CDS,39202,41109,1908,reverse
PX667572,OPG055 CDS,38094,39158,1065,reverse
PX667572,OPG054 CDS,36752,38071,1320,reverse
PX667572,OPG053 CDS,36127,36765,639,reverse
PX667572,OPG052 CDS,35876,36070,195,reverse
PX667572,OPG051 CDS,35500,35724,225,reverse
PX667572,OPG049 CDS,34275,35228,954,reverse
PX667572,OPG048 CDS,33285,34244,960,reverse
PX667572,OPG047 CDS,31811,33274,1464,reverse
PX667572,OPG046 CDS,31339,31794,456,reverse
PX667572,OPG045 CDS,30668,31327,660,reverse
PX667572,OPG044 CDS,30175,30624,450,forward
PX667572,OPG043 CDS,29209,30039,831,reverse
PX667572,OPG042 CDS,27907,29181,1275,reverse
PX667572,OPG040 CDS,26432,27559,1128,reverse
PX667572,OPG039 CDS,25347,26201,855,reverse
PX667572,OPG038 CDS,24556,25218,663,reverse
PX667572,OPG037 CDS,23158,24486,1329,reverse
PX667572,OPG036 CDS,22584,23117,534,reverse
PX667572,OPG035 CDS,22104,22457,354,reverse
PX667572,OPG034 CDS,21414,22058,645,reverse
PX667572,OPG031 CDS,17979,18926,948,reverse
PX667572,OPG030 CDS,17314,17934,621,reverse
PX667572,OPG029 CDS,16709,17170,462,reverse
PX667572,OPG027 CDS,16028,16480,453,reverse
PX667572,OPG025 CDS,13481,15373,1893,reverse
PX667572,OPG024 CDS,13127,13321,195,reverse
PX667572,OPG023 CDS,11011,12993,1983,reverse
PX667572,OPG022 CDS,10571,10951,381,reverse
PX667572,OPG021 CDS,9615,10343,729,forward
PX667572,OPG019 CDS,7604,8032,429,forward
PX667572,OPG015 CDS,4845,6158,1314,reverse
PX667572,OPG002 CDS,1789,2835,1047,reverse
PX667572,OPG001 CDS,920,1660,741,reverse
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