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Fix context_counts #227

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Fix context_counts #227

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460d874
Fix last chromosome duplication in save_context_distribution
PilarGallego May 14, 2025
ced2d0a
Fix last chromosome duplication in save_context_distribution
PilarGallego May 14, 2025
70f1694
Fix context_counts rn7, mm39 and add rn6_DBS
PilarGallego May 16, 2025
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1,024 changes: 512 additions & 512 deletions ...MatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_1536.csv
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16 changes: 8 additions & 8 deletions ...erMatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_24.csv
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
,X,Y,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19
N:C,47148417,33235763,46868196,40485598,41712254,38487785,34544018,34769874,34023589,30127201,27669599,30113882,26668891,31633165,31522135,30697385,25424222,22894585,22293840,22471976,22471976
N:T,72889305,52058996,68706678,57132432,62761160,54814602,48762917,50309393,47018709,43141294,38257215,43953608,35834097,45074315,44750823,45274387,36590336,34144245,31274052,32556784,32556784
U:T,13920519,1185514,20795489,24181636,15999583,16851143,18439362,18745514,17809608,15739540,14177253,15470327,14226250,14048759,10928724,13520069,10796574,10792545,11659418,9552160,9552160
U:C,8917154,682559,15224456,18109491,11226763,13186880,14311005,13244446,14078218,12920737,10983909,11330866,11625278,10330344,7891240,10018497,8119150,7857959,9291225,7069908,7069908
T:C,8297569,486744,16720265,16252030,10129276,12716174,13939252,12425573,12286817,9662094,12859045,10942724,13510238,6753742,9280770,8969414,8643743,7799817,7515488,6689732,6689732
T:T,12757564,834232,23256959,21724748,14118721,16237103,17668675,16463083,15108875,13005303,16705621,14761431,16417186,8900718,12626936,12282659,10987970,10722264,9565243,9100738,9100738
B:C,116509,988,168623,211575,254095,182116,160657,187834,620264,539973,240671,259904,248790,81919,109006,177822,162139,280642,103416,73495,73495
B:T,159284,1171,213367,256507,336324,233985,180263,237324,728615,541252,291541,323018,291639,99793,146541,233920,199817,358902,112815,90965,90965
N:C,47148417,33235763,46868196,40485598,41712254,38487785,34544018,34769874,34023589,30127201,27669599,30113882,26668891,31633165,31522135,30697385,25424222,22894585,22293840,22471976,12762431
N:T,72889305,52058996,68706678,57132432,62761160,54814602,48762917,50309393,47018709,43141294,38257215,43953608,35834097,45074315,44750823,45274387,36590336,34144245,31274052,32556784,17689544
U:T,13920519,1185514,20795489,24181636,15999583,16851143,18439362,18745514,17809608,15739540,14177253,15470327,14226250,14048759,10928724,13520069,10796574,10792545,11659418,9552160,7207944
U:C,8917154,682559,15224456,18109491,11226763,13186880,14311005,13244446,14078218,12920737,10983909,11330866,11625278,10330344,7891240,10018497,8119150,7857959,9291225,7069908,5624890
T:C,8297569,486744,16720265,16252030,10129276,12716174,13939252,12425573,12286817,9662094,12859045,10942724,13510238,6753742,9280770,8969414,8643743,7799817,7515488,6689732,6431862
T:T,12757564,834232,23256959,21724748,14118721,16237103,17668675,16463083,15108875,13005303,16705621,14761431,16417186,8900718,12626936,12282659,10987970,10722264,9565243,9100738,8389277
B:C,116509,988,168623,211575,254095,182116,160657,187834,620264,539973,240671,259904,248790,81919,109006,177822,162139,280642,103416,73495,57938
B:T,159284,1171,213367,256507,336324,233985,180263,237324,728615,541252,291541,323018,291639,99793,146541,233920,199817,358902,112815,90965,56118
256 changes: 128 additions & 128 deletions ...rMatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_384.csv
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4 changes: 2 additions & 2 deletions ...lerMatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_6.csv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
,X,Y,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19
C,64479649,34406054,78981540,75058694,63322388,64572955,62954932,60627727,61008888,53250005,51753224,52647376,52053197,48799170,48803151,49863118,42349254,38833003,39203969,36305111,36305111
T,99726672,54079913,112972493,103295323,93215788,88136833,85051217,85755314,80665807,72427389,69431630,74508384,66769172,68123585,68453024,71311035,58574697,56017956,52611528,51300647,51300647
C,64479649,34406054,78981540,75058694,63322388,64572955,62954932,60627727,61008888,53250005,51753224,52647376,52053197,48799170,48803151,49863118,42349254,38833003,39203969,36305111,24877121
T,99726672,54079913,112972493,103295323,93215788,88136833,85051217,85755314,80665807,72427389,69431630,74508384,66769172,68123585,68453024,71311035,58574697,56017956,52611528,51300647,33342883
4,094 changes: 2,047 additions & 2,047 deletions ...MatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_6144.csv
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64 changes: 32 additions & 32 deletions ...erMatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_96.csv
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Original file line number Diff line number Diff line change
@@ -1,33 +1,33 @@
,X,Y,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19
GCC,2934940,1476265,3875219,3920576,2995920,3404292,3327200,3025568,3289429,2775756,2749230,2627388,2946918,2479764,2431764,2450558,2182864,1901246,2089434,1803005,1803005
CCA,5810063,3041556,6932593,6640422,5511615,5737388,5575521,5324598,5542784,4707934,4583692,4594454,4658882,4299228,4281498,4378346,3736203,3377568,3480221,3175316,3175316
TTG,6576445,3634165,7251981,6611218,5997615,5645402,5410461,5497616,5221521,4622475,4434502,4757293,4244594,4355305,4414107,4592921,3739395,3567645,3361889,3295933,3295933
ATT,8200533,4457773,8508973,7500197,7267845,6377799,6079884,6393437,5623362,5199827,4858644,5566270,4450734,5018734,5028858,5394107,4304492,4279957,3734770,3809050,3809050
ATG,6346372,3391807,7296805,6651220,5977377,5632910,5516859,5542242,5240128,4723653,4474787,4803608,4250602,4410112,4435112,4614698,3790638,3630380,3383092,3313873,3313873
ACA,7237491,4060190,8853884,8178875,7187989,6932587,6859947,6735348,6414554,5821758,5584857,5879149,5407806,5362477,5417998,5580240,4602709,4386198,4230358,4052537,4052537
GTT,5117530,2843352,5852548,5351818,4844784,4555489,4398031,4439813,4154999,3739569,3611228,3882647,3469051,3522492,3581090,3696851,3019336,2891444,2726398,2675749,2675749
TTT,12277144,6930475,12996373,11670966,11010357,9913716,9429078,9813726,8730268,8030974,7668110,8563933,7224323,7718637,7792312,8205796,6572033,6487507,5831322,5867795,5867795
TCC,5221121,2828994,6205190,5851944,4963516,5084682,4914338,4764109,4878281,4175173,4050510,4106444,4067344,3826808,3823908,3929020,3327868,3027889,3077854,2836275,2836275
CTC,5244356,2839951,6705553,6402143,5308589,5538621,5398427,5161012,5270032,4557133,4484479,4460720,4551904,4161126,4138269,4216662,3612513,3286258,3362035,3079392,3079392
ACT,5397072,2845200,6285417,5810772,5158504,4937692,4767426,4792707,4550772,4037706,3935549,4123988,3801272,3818126,3833073,3964958,3273769,3104679,2944929,2872809,2872809
GTG,4574318,2474008,6118388,5859782,4853396,4988353,5016489,4715908,4737446,4224594,4091571,4099313,4111397,3786447,3807471,3845487,3279243,3021820,3089530,2835467,2835467
CCC,3939873,1997648,4952518,4887384,3850647,4280597,4224009,3838547,4174559,3517481,3420877,3362702,3639817,3136774,3081599,3119944,2779583,2406008,2638737,2283374,2283374
GCT,4164219,1920128,5441094,5267385,4308152,4499972,4395251,4174439,4237797,3711597,3664170,3615960,3736839,3396544,3382928,3420574,2937512,2667665,2732117,2517234,2517234
CTG,6057799,3201868,7819402,7598150,6187256,6542553,6376773,6036173,6250588,5357340,5292671,5192772,5422289,4905288,4857892,4951272,4246326,3830311,3991116,3608767,3608767
ACC,3694811,2017677,4455102,4250983,3546161,3675351,3583929,3413817,3524785,3025101,2941010,2971858,2993125,2763718,2765194,2810181,2397820,2175003,2238194,2042739,2042739
CCT,5535317,3024093,6827652,6566447,5380822,5692002,5514250,5267257,5476213,4655082,4578736,4528211,4693834,4263506,4224904,4321323,3701843,3336558,3456038,3129601,3129601
TCA,6358355,3459942,7398338,6821401,6076626,5818851,5632458,5644696,5408239,4792544,4610618,4857849,4438372,4497205,4522025,4687693,3869319,3662197,3478735,3371659,3371659
GCA,4149027,2140160,5301761,5079671,4239416,4320393,4252656,4087299,4084106,3605826,3514365,3521534,3523822,3298242,3293061,3358099,2847371,2624190,2636314,2454527,2454527
CTT,7081856,3787463,8234402,7573774,6729013,6450752,6178632,6259654,5954649,5292366,5140211,5402013,4970725,4969246,5037144,5177752,4268128,4042812,3838456,3756374,3756374
GTC,3145505,1756721,3971449,3793610,3176121,3259285,3177357,3048675,3097413,2697112,2621121,2655672,2629526,2471740,2475585,2516085,2142822,1953613,1990402,1836152,1836152
GTA,4019830,2137735,4479527,4065717,3695986,3457455,3350868,3388517,3148145,2842873,2722060,2957033,2600332,2692836,2707052,2825937,2311403,2226746,2066274,2027290,2027290
TTA,6791430,3567716,7428260,6616558,6296858,5578030,5368960,5578018,4850361,4567026,4333011,4908550,4018523,4404664,4416990,4674841,3766453,3743390,3276224,3345598,3345598
ATC,4775852,2680109,5239466,4749225,4327472,4091736,3933140,3982325,3824002,3365144,3200274,3443420,3046864,3151013,3175306,3312437,2718617,2576607,2433106,2368301,2368301
TCG,535583,313055,731611,730157,600365,635354,637882,573845,586434,539140,509918,537503,534031,466298,483175,463895,418670,373358,400940,354732,354732
GCG,385730,173613,621364,666254,493008,592524,601555,496184,539924,497517,469398,474534,532419,409660,416580,393689,380505,316466,382220,306800,306800
CCG,505496,257287,775265,816634,613161,734931,735696,611639,673498,613014,578324,583025,654671,507556,514464,490089,470507,390013,469224,377100,377100
TTC,7032043,3886707,7915679,7198013,6547166,6160609,5877125,6017269,5661128,5042260,4842571,5185087,4627394,4750502,4815994,5000949,4086108,3903179,3661512,3599643,3599643
TCT,8082646,4561449,9497008,8739481,7718840,7511352,7201365,7226628,6979610,6154779,5977397,6243101,5815941,5744067,5776041,5965518,4944203,4656211,4489521,4320821,4320821
CTA,4795238,2521588,5291816,4810019,4341463,4109089,3924460,4004193,3769123,3352325,3238494,3455757,3102967,3186583,3183641,3326687,2730361,2605731,2430997,2395933,2395933
ACG,527805,288749,827508,830297,677633,714954,731443,651042,647892,619583,584564,619670,608103,529194,554933,528981,478506,427743,459122,406573,406573
ATA,7690375,3968475,7861859,6842910,6654476,5835007,5614671,5876728,5132639,4812716,4417887,5174294,4047944,4618855,4586199,4958547,3986829,3970545,3434398,3485327,3485327
GCC,2934940,1476265,3875219,3920576,2995920,3404292,3327200,3025568,3289429,2775756,2749230,2627388,2946918,2479764,2431764,2450558,2182864,1901246,2089434,1803005,1329092
CCA,5810063,3041556,6932593,6640422,5511615,5737388,5575521,5324598,5542784,4707934,4583692,4594454,4658882,4299228,4281498,4378346,3736203,3377568,3480221,3175316,2192192
TTG,6576445,3634165,7251981,6611218,5997615,5645402,5410461,5497616,5221521,4622475,4434502,4757293,4244594,4355305,4414107,4592921,3739395,3567645,3361889,3295933,2132339
ATT,8200533,4457773,8508973,7500197,7267845,6377799,6079884,6393437,5623362,5199827,4858644,5566270,4450734,5018734,5028858,5394107,4304492,4279957,3734770,3809050,2339389
ATG,6346372,3391807,7296805,6651220,5977377,5632910,5516859,5542242,5240128,4723653,4474787,4803608,4250602,4410112,4435112,4614698,3790638,3630380,3383092,3313873,2125058
ACA,7237491,4060190,8853884,8178875,7187989,6932587,6859947,6735348,6414554,5821758,5584857,5879149,5407806,5362477,5417998,5580240,4602709,4386198,4230358,4052537,2651854
GTT,5117530,2843352,5852548,5351818,4844784,4555489,4398031,4439813,4154999,3739569,3611228,3882647,3469051,3522492,3581090,3696851,3019336,2891444,2726398,2675749,1744196
TTT,12277144,6930475,12996373,11670966,11010357,9913716,9429078,9813726,8730268,8030974,7668110,8563933,7224323,7718637,7792312,8205796,6572033,6487507,5831322,5867795,3716079
TCC,5221121,2828994,6205190,5851944,4963516,5084682,4914338,4764109,4878281,4175173,4050510,4106444,4067344,3826808,3823908,3929020,3327868,3027889,3077854,2836275,1941865
CTC,5244356,2839951,6705553,6402143,5308589,5538621,5398427,5161012,5270032,4557133,4484479,4460720,4551904,4161126,4138269,4216662,3612513,3286258,3362035,3079392,2141270
ACT,5397072,2845200,6285417,5810772,5158504,4937692,4767426,4792707,4550772,4037706,3935549,4123988,3801272,3818126,3833073,3964958,3273769,3104679,2944929,2872809,1889758
GTG,4574318,2474008,6118388,5859782,4853396,4988353,5016489,4715908,4737446,4224594,4091571,4099313,4111397,3786447,3807471,3845487,3279243,3021820,3089530,2835467,1945703
CCC,3939873,1997648,4952518,4887384,3850647,4280597,4224009,3838547,4174559,3517481,3420877,3362702,3639817,3136774,3081599,3119944,2779583,2406008,2638737,2283374,1664563
GCT,4164219,1920128,5441094,5267385,4308152,4499972,4395251,4174439,4237797,3711597,3664170,3615960,3736839,3396544,3382928,3420574,2937512,2667665,2732117,2517234,1752552
CTG,6057799,3201868,7819402,7598150,6187256,6542553,6376773,6036173,6250588,5357340,5292671,5192772,5422289,4905288,4857892,4951272,4246326,3830311,3991116,3608767,2518634
ACC,3694811,2017677,4455102,4250983,3546161,3675351,3583929,3413817,3524785,3025101,2941010,2971858,2993125,2763718,2765194,2810181,2397820,2175003,2238194,2042739,1414767
CCT,5535317,3024093,6827652,6566447,5380822,5692002,5514250,5267257,5476213,4655082,4578736,4528211,4693834,4263506,4224904,4321323,3701843,3336558,3456038,3129601,2190498
TCA,6358355,3459942,7398338,6821401,6076626,5818851,5632458,5644696,5408239,4792544,4610618,4857849,4438372,4497205,4522025,4687693,3869319,3662197,3478735,3371659,2203741
GCA,4149027,2140160,5301761,5079671,4239416,4320393,4252656,4087299,4084106,3605826,3514365,3521534,3523822,3298242,3293061,3358099,2847371,2624190,2636314,2454527,1673947
CTT,7081856,3787463,8234402,7573774,6729013,6450752,6178632,6259654,5954649,5292366,5140211,5402013,4970725,4969246,5037144,5177752,4268128,4042812,3838456,3756374,2475648
GTC,3145505,1756721,3971449,3793610,3176121,3259285,3177357,3048675,3097413,2697112,2621121,2655672,2629526,2471740,2475585,2516085,2142822,1953613,1990402,1836152,1259548
GTA,4019830,2137735,4479527,4065717,3695986,3457455,3350868,3388517,3148145,2842873,2722060,2957033,2600332,2692836,2707052,2825937,2311403,2226746,2066274,2027290,1309979
TTA,6791430,3567716,7428260,6616558,6296858,5578030,5368960,5578018,4850361,4567026,4333011,4908550,4018523,4404664,4416990,4674841,3766453,3743390,3276224,3345598,2095242
ATC,4775852,2680109,5239466,4749225,4327472,4091736,3933140,3982325,3824002,3365144,3200274,3443420,3046864,3151013,3175306,3312437,2718617,2576607,2433106,2368301,1531023
TCG,535583,313055,731611,730157,600365,635354,637882,573845,586434,539140,509918,537503,534031,466298,483175,463895,418670,373358,400940,354732,262251
GCG,385730,173613,621364,666254,493008,592524,601555,496184,539924,497517,469398,474534,532419,409660,416580,393689,380505,316466,382220,306800,248323
CCG,505496,257287,775265,816634,613161,734931,735696,611639,673498,613014,578324,583025,654671,507556,514464,490089,470507,390013,469224,377100,303033
TTC,7032043,3886707,7915679,7198013,6547166,6160609,5877125,6017269,5661128,5042260,4842571,5185087,4627394,4750502,4815994,5000949,4086108,3903179,3661512,3599643,2331652
TCT,8082646,4561449,9497008,8739481,7718840,7511352,7201365,7226628,6979610,6154779,5977397,6243101,5815941,5744067,5776041,5965518,4944203,4656211,4489521,4320821,2855634
CTA,4795238,2521588,5291816,4810019,4341463,4109089,3924460,4004193,3769123,3352325,3238494,3455757,3102967,3186583,3183641,3326687,2730361,2605731,2430997,2395933,1552891
ACG,527805,288749,827508,830297,677633,714954,731443,651042,647892,619583,584564,619670,608103,529194,554933,528981,478506,427743,459122,406573,303047
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20 changes: 10 additions & 10 deletions ...rMatrixGenerator/references/chromosomes/context_distributions/context_counts_mm39_DBS.csv
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