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Expected output results when run on sample test data.
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snadim02 authored Feb 22, 2024
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43 changes: 43 additions & 0 deletions test/output/test_comphet_cohort_recurrence.txt
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file_names ensembl_gene_id gene_name P_val P_cond P_comphet poisson_lambda false_diagnosis_rate variant_info
test_patient5.tsv ENSG00000101220 C20orf27 2.148021806414702e-05 0.11168316306743772 0.0001923317487988463 0.00019235024692149588 0.0 chr20:G_3754424_A|CS|3.90395|P|test_patient5.tsv&chr20:G_3761023_C|IS|0.63|M|test_patient5.tsv
test_patient9.tsv ENSG00000080293 SCTR 2.6077297643100892e-05 0.021586685901861552 0.0012080269181501402 0.001208757170836845 0.0 chr2:G_119452036_A|CS|4.43205|P|test_patient9.tsv&chr2:G_119452036_A|CS|4.43205|M|test_patient9.tsv
test_patient4.tsv ENSG00000114656 CFAP92 7.393698802523214e-05 0.08658753589849612 0.0008538987425615874 0.0008542635217639556 0.0 chr3:C_128970364_G|IS|0.39|P|test_patient4.tsv&chr3:C_128970364_G|IS|0.39|M|test_patient4.tsv
test_patient8.tsv ENSG00000186806 VSIG10L 7.754000596163234e-05 0.048217443592192974 0.001608131833314097 0.001609426265241646 0.0 chr19:C_51341368_T|CS|3.94935|P|test_patient8.tsv&chr19:G_51338205_T|CS|3.82217|M|test_patient8.tsv
test_patient2.tsv ENSG00000010318 PHF7 0.00017873256409123487 0.5158461850227705 0.0003464842220037845 0.0003465442615306923 0.0 chr3:G_52422746_T|IS|0.2|P|test_patient2.tsv&chr3:T_52422267_A|CS|6.58568|M|test_patient2.tsv
test_patient8.tsv ENSG00000105219 CCNP 0.0002892059757170139 0.960945933319282 0.0003009596749299348 0.00030100497238165394 0.0 chr19:G_40222369_T|CS|1.55743|P|test_patient8.tsv&chr19:G_40223236_A|CS|3.52521|M|test_patient8.tsv
test_patient7.tsv ENSG00000103196 CRISPLD2 0.00033885834491722134 0.17979846729316812 0.0018846564713185243 0.0018864346708740724 0.0 chr16:G_84868866_A|CS|4.54509|P|test_patient7.tsv&chr16:C_84840821_T|IS|0.29|M|test_patient7.tsv
test_patient7.tsv ENSG00000145916 RMND5B 0.0003508884912207386 0.4550658789596972 0.000771071854525518 0.0007713692833304566 0.0 chr5:G_178138183_GGGCAGCACT|CI|2.645243|P|test_patient7.tsv&chr5:G_178146273_A|CS|2.96878|M|test_patient7.tsv
test_patient2.tsv ENSG00000218823 PAPOLB 0.0003692225120410811 0.5290512395424902 0.0006978955617992222 0.0006981392042714553 0.0 chr7:TGA_4860012_T|CI|4.095266|P|test_patient2.tsv&chr7:T_4861637_G|CS|2.29967|M|test_patient2.tsv
test_patient6.tsv ENSG00000159216 RUNX1 0.0003874263586071864 0.1696082940508568 0.002284241821871147 0.0022868546819159678 0.0 chr21:T_34834592_A|CS|3.95425|P|test_patient6.tsv&chr21:C_34880568_T|CS|4.44113|M|test_patient6.tsv
test_patient6.tsv ENSG00000135624 CCT7 0.00048381489440958486 0.47906344710519444 0.0010099182004661422 0.0010104285114624979 0.0 chr2:T_73249822_A|CS|3.71215|P|test_patient6.tsv&chr2:G_73252845_A|CS|3.31355|M|test_patient6.tsv
test_patient5.tsv ENSG00000215262 KCNU1 0.0006736184161919917 0.17597918613748567 0.00382783004613807 0.0038351749368891806 0.0 chr8:G_36787239_A|IS|0.3|P|test_patient5.tsv&chr8:G_36909360_T|CS|3.57366|M|test_patient5.tsv
test_patient9.tsv ENSG00000173193 PARP14 0.0006778168933768957 0.1991280256199051 0.0034039251444731855 0.0034097316780827337 0.0 chr3:G_122685319_A|IS|0.76|P|test_patient9.tsv&chr3:G_122713923_A|CS|3.39003|M|test_patient9.tsv
test_patient7.tsv ENSG00000114770 ABCC5 0.0008355608591900176 0.0903488168862666 0.009248166030130123 0.009291195820830676 0.0 chr3:A_183947367_T|CS|4.05246|P|test_patient7.tsv&chr3:G_183949816_C|CS|4.37386|M|test_patient7.tsv
test_patient9.tsv ENSG00000196591 HDAC2 0.0010749787719244038 0.8813883279187219 0.0012196426227504276 0.0012203869921186615 0.0 chr6:G_113956702_T|IS|0.16|P|test_patient9.tsv&chr6:G_113956702_T|IS|0.16|M|test_patient9.tsv
test_patient6.tsv ENSG00000164934 DCAF13 0.0012400247136536318 0.9028275735017219 0.0013734900772293113 0.0013744341793009898 0.0 chr8:G_103440560_C|IS|0.53|P|test_patient6.tsv&chr8:C_103415196_G|CS|1.54288|M|test_patient6.tsv
test_patient2.tsv ENSG00000188779 SKOR1 0.0018077912135076376 0.8131742975834898 0.0022231288161466134 0.002225603635588472 0.0 chr15:T_67826673_G|CS|2.05706|P|test_patient2.tsv&chr15:C_67828134_T|CS|2.45427|M|test_patient2.tsv
test_patient2.tsv ENSG00000132849 PATJ 0.002082539509081194 0.15600260121077092 0.013349389644263243 0.013439293752656746 0.0 chr1:C_62148357_T|CS|2.2905|P|test_patient2.tsv&chr1:T_62049551_C|IS|0.39|M|test_patient2.tsv
test_patient3.tsv ENSG00000008226 DLEC1 0.0029111329272343933 0.3254782805047925 0.008944169554783943 0.008984408756486378 0.0 chr3:G_38117210_A|IS|0.25|P|test_patient3.tsv&chr3:G_38116772_T|IS|0.81|M|test_patient3.tsv
test_patient4.tsv ENSG00000156395 SORCS3 0.0036769580983089336 0.38723714336655074 0.009495365207847328 0.009540733609499075 0.0 chr10:T_104977372_C|CS|3.11537|P|test_patient4.tsv&chr10:C_105139436_G|CS|3.10482|M|test_patient4.tsv
test_patient9.tsv ENSG00000131697 NPHP4 0.004316870930759805 0.328954205670853 0.01312301486450429 0.013209882437335925 0.0 chr1:G_5882861_A|IS|0.53|P|test_patient9.tsv&chr1:T_5875004_C|CS|1.76576|M|test_patient9.tsv
test_patient7.tsv ENSG00000068976 PYGM 0.004356407315695673 0.9463659674163782 0.0046033009065075126 0.004613928724029089 0.0 chr11:T_64752486_C|CS|1.88515|P|test_patient7.tsv&chr11:G_64759751_A|CS|5.66247|M|test_patient7.tsv
test_patient8.tsv ENSG00000055118 KCNH2 0.004674946956037011 0.5927731893790524 0.007886569500442753 0.00791783297253498 0.0 chr7:G_150958202_A|CS|2.53237|P|test_patient8.tsv&chr7:G_150958449_A|CS|3.27642|M|test_patient8.tsv
test_patient9.tsv ENSG00000138002 IFT172 0.005081900268301298 0.3823378389083952 0.01329164877536193 0.013380773361747637 0.0 chr2:A_27447624_G|CS|4.2879|P|test_patient9.tsv&chr2:G_27476652_C|CS|3.12065|M|test_patient9.tsv
test_patient1.tsv ENSG00000091428 RAPGEF4 0.0051108273997115755 0.6752798562588769 0.007568458250814869 0.007597244367287079 0.0 chr2:G_173014459_T|IS|0.28|P|test_patient1.tsv&chr2:G_173019594_C|IS|0.18|M|test_patient1.tsv
test_patient4.tsv ENSG00000197748 CFAP43 0.00536376184226492 0.7845712591639886 0.006836551530042478 0.006860027807488871 0.0 chr10:T_104143495_G|CS|1.99241|P|test_patient4.tsv&chr10:A_104147961_G|CS|3.87771|M|test_patient4.tsv
test_patient8.tsv ENSG00000121210 TMEM131L 0.006287812421651071 0.8485791169845791 0.007409812822161799 0.007437401856065239 0.0 chr4:A_153593821_T|CS|2.26947|P|test_patient8.tsv&chr4:A_153479364_G|IS|0.16|M|test_patient8.tsv
test_patient7.tsv ENSG00000187720 THSD4 0.0072071766087168435 0.7015622436312373 0.010273039454650523 0.010326171321546436 0.0 chr15:G_71771107_A|CS|3.5644|P|test_patient7.tsv&chr15:G_71531803_T|IS|0.17|M|test_patient7.tsv
test_patient5.tsv ENSG00000184347 SLIT3 0.009314903287505708 0.4073172360516191 0.022868915093799846 0.023134465104041144 0.0 chr5:T_169077795_C|IS|0.2|P|test_patient5.tsv&chr5:A_168806478_C|CS|2.61546|M|test_patient5.tsv
test_patient5.tsv ENSG00000112159 MDN1 0.011009974667099773 0.1505575139656002 0.07312803178734317 0.07593983707286883 1.0 chr6:T_89654004_C|IS|0.49|P|test_patient5.tsv&chr6:C_89758288_T|CS|3.7985|M|test_patient5.tsv
test_patient1.tsv ENSG00000103197 TSC2 0.011309728968291386 0.3737345208652806 0.030261397695098613 0.03072872596144594 0.0 chr16:G_2062557_A|CS|3.33142|P|test_patient1.tsv&chr16:C_2056759_G|CS|3.4387|M|test_patient1.tsv
test_patient5.tsv ENSG00000166833 NAV2 0.012477089676526937 0.400135242513416 0.03118218129988537 0.03167869436479569 0.0 chr11:T_19718559_G|IS|0.2|P|test_patient5.tsv&chr11:C_19934094_T|CS|3.41417|M|test_patient5.tsv
test_patient1.tsv,test_patient9.tsv ENSG00000164199 ADGRV1 0.013552668541129229 0.16161873948379835 0.08385579905161822 0.08758150208182405 1.0 chr5:C_90629537_A|CS|2.02571|P|test_patient1.tsv&chr5:A_90778464_G|CS|3.70419|M|test_patient1.tsv,chr5:G_90763365_T|CS|3.01374|P|test_patient9.tsv&chr5:C_90855803_A|CS|3.95323|M|test_patient9.tsv
test_patient5.tsv ENSG00000131149 GSE1 0.017789435898676934 0.926884726113861 0.01919271663183242 0.019379287881425098 0.0 chr16:C_85654404_G|CS|1.72958|P|test_patient5.tsv&chr16:A_85616904_G|IS|0.24|M|test_patient5.tsv
test_patient9.tsv ENSG00000164061 BSN 0.02189216610667306 0.5997223022790761 0.03650383856574624 0.03718677511670675 0.0 chr3:G_49656797_A|CS|3.88631|P|test_patient9.tsv&chr3:C_49661891_T|CS|2.49044|M|test_patient9.tsv
test_patient3.tsv ENSG00000149256 TENM4 0.02695407659716365 0.6879857864620426 0.03917824630618405 0.03996636724263877 0.0 chr11:C_79116852_T|IS|0.38|P|test_patient3.tsv&chr11:G_79064959_T|CS|2.62637|M|test_patient3.tsv
test_patient6.tsv ENSG00000163359 COL6A3 0.02865347639163457 0.8514638607999415 0.03365201708586307 0.034231278877165476 0.0 chr2:A_237324784_G|CS|1.87558|P|test_patient6.tsv&chr2:C_237327211_A|IS|0.26|M|test_patient6.tsv
test_patient2.tsv ENSG00000054654 SYNE2 0.028854977229636012 0.3899308411757089 0.07400024358840984 0.0768813073904305 1.0 chr14:G_64224488_A|CS|2.91873|P|test_patient2.tsv&chr14:C_64209453_G|CS|3.1526|M|test_patient2.tsv
test_patient7.tsv ENSG00000130702 LAMA5 0.03897947849007256 0.5829504926342018 0.06686584707036514 0.06920630183697957 1.0 chr20:A_62311050_C|CS|3.41239|P|test_patient7.tsv&chr20:G_62312300_A|CS|2.50571|M|test_patient7.tsv
test_patient4.tsv ENSG00000142798 HSPG2 0.07929217469578631 0.6766589144682678 0.1171818962262482 0.12463609758989856 1.0 chr1:C_21833508_T|CS|3.21122|P|test_patient4.tsv&chr1:C_21880484_T|CS|2.52561|M|test_patient4.tsv
test_patient1.tsv,test_patient4.tsv,test_patient5.tsv,test_patient7.tsv ENSG00000155657 TTN 0.14721405202170884 0.16050998305858694 0.9171644605306262 2.490898089035142 5.0 chr2:A_178573986_G|CS|3.52354|P|test_patient1.tsv&chr2:C_178782896_T|CS|3.22483|M|test_patient1.tsv,chr2:C_178728283_A|CS|2.79666|P|test_patient4.tsv&chr2:T_178597640_C|CS|1.70749|M|test_patient4.tsv,chr2:G_178586727_A|CS|3.72524|P|test_patient5.tsv&chr2:G_178630241_A|CS|3.13464|M|test_patient5.tsv,chr2:G_178532670_A|CS|16.7948|P|test_patient7.tsv&chr2:C_178718186_T|CS|2.65789|M|test_patient7.tsv
test_patient2.tsv ENSG00000154358 OBSCN 0.23368614253709996 0.9604412719396987 0.2433112251258731 0.2788032397063109 1.0 chr1:G_228280211_T|CS|3.41403|P|test_patient2.tsv&chr1:C_228309111_G|CS|1.6097|M|test_patient2.tsv
10 changes: 10 additions & 0 deletions test/output/test_comphet_individual_level.txt
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file_name ensembl_gene_id gene_name P_val P_cond y_stat poisson_lambda variant_info
test_patient1.tsv ENSG00000103197 TSC2 0.8805262468318172 0.9037104556163108 0.5800264118709461 3.663037625547644 chr16:G_2062557_A|CS|3.33142|P|test_patient1.tsv&chr16:C_2056759_G|CS|3.4387|M|test_patient1.tsv
test_patient2.tsv ENSG00000010318 PHF7 0.16085670053023618 0.16175438590073787 0.033764592462501825 5.194014687316723 chr3:G_52422746_T|IS|0.2|P|test_patient2.tsv&chr3:T_52422267_A|CS|6.58568|M|test_patient2.tsv
test_patient3.tsv ENSG00000008226 DLEC1 0.8562956915370973 0.8623243118350665 0.3908831825752294 4.963113253481458 chr3:G_38117210_A|IS|0.25|P|test_patient3.tsv&chr3:G_38116772_T|IS|0.81|M|test_patient3.tsv
test_patient4.tsv ENSG00000114656 CFAP92 0.2646588887467117 0.2671156302705057 0.06556427892050695 4.6888457487416195 chr3:C_128970364_G|IS|0.39|P|test_patient4.tsv&chr3:C_128970364_G|IS|0.39|M|test_patient4.tsv
test_patient5.tsv ENSG00000101220 C20orf27 0.021496499411909818 0.021732007478409074 0.004802628289345945 4.524796286270406 chr20:G_3754424_A|CS|3.90395|P|test_patient5.tsv&chr20:G_3761023_C|IS|0.63|M|test_patient5.tsv
test_patient6.tsv ENSG00000159216 RUNX1 0.24523827437376353 0.2474227340920225 0.05948609868786205 4.729729818341644 chr21:T_34834592_A|CS|3.95425|P|test_patient6.tsv&chr21:C_34880568_T|CS|4.44113|M|test_patient6.tsv
test_patient7.tsv ENSG00000145916 RMND5B 0.2638358237441326 0.26720706926225035 0.07004807174401698 4.372741632103667 chr5:G_178138183_GGGCAGCACT|CI|2.645243|P|test_patient7.tsv&chr5:G_178146273_A|CS|2.96878|M|test_patient7.tsv
test_patient8.tsv ENSG00000186806 VSIG10L 0.08110054269891298 0.08178160020462166 0.017664103261028106 4.788160815292933 chr19:C_51341368_T|CS|3.94935|P|test_patient8.tsv&chr19:G_51338205_T|CS|3.82217|M|test_patient8.tsv
test_patient9.tsv ENSG00000080293 SCTR 0.010189456342487475 0.01029704494587668 0.002245353255283013 4.561297508934969 chr2:G_119452036_A|CS|4.43205|P|test_patient9.tsv&chr2:G_119452036_A|CS|4.43205|M|test_patient9.tsv
49 changes: 49 additions & 0 deletions test/output/test_comphet_mutational_targets.txt
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# Compound heterozygous mutational targets computed for processed variant files in test/input/
# variant types are in the format paternal_variant_type,maternal_variant_type
variant_type ensembl_gene_id per_patient_mutational_targets
IS,CS ENSG00000131697 0.3260042015110388
CS,CS ENSG00000142798 0.6592794640361354
CS,IS ENSG00000132849 0.152720854388882
CS,CS ENSG00000154358 0.954520885815634
CS,CS ENSG00000138002 0.3794763008048035
CS,CS ENSG00000135624 0.47886894650201167
CS,CS ENSG00000080293 0.021284615867876524
IS,IS ENSG00000091428 0.6742448592678627
CS,CS ENSG00000155657 0.18437758707551505
CS,CS ENSG00000155657 0.9409320231226761
CS,CS ENSG00000155657 0.2346752253595933
CS,CS ENSG00000155657 0.4300563552308008
CS,IS ENSG00000163359 0.8490873358262157
IS,IS ENSG00000008226 0.3234678521264028
CS,CS ENSG00000164061 0.5937237755612464
IS,CS ENSG00000010318 0.5157826182381667
IS,CS ENSG00000173193 0.19830912689664312
IS,IS ENSG00000114656 0.08637555828441287
CS,CS ENSG00000114770 0.08804346711580001
CS,IS ENSG00000121210 0.8480575778847543
CS,CS ENSG00000164199 0.7609341566695156
CS,CS ENSG00000164199 0.3792004097206957
IS,CS ENSG00000184347 0.4024764882783488
CI,CS ENSG00000145916 0.454913048644159
IS,CS ENSG00000112159 0.1318848358182284
IS,IS ENSG00000196591 0.8813204679326655
CI,CS ENSG00000218823 0.5289256198347109
CS,CS ENSG00000055118 0.5914872257725904
IS,CS ENSG00000215262 0.1750497641754769
IS,CS ENSG00000164934 0.9027643280397302
CS,CS ENSG00000197748 0.7839107511680166
CS,CS ENSG00000156395 0.3852068743568498
IS,CS ENSG00000166833 0.3934525283906666
CS,CS ENSG00000068976 0.9462453823413233
IS,CS ENSG00000149256 0.6826743975891878
CS,CS ENSG00000054654 0.3734526220921216
CS,CS ENSG00000188779 0.8129857043998733
CS,IS ENSG00000187720 0.7002481468833333
CS,CS ENSG00000103197 0.36709691817894835
CS,IS ENSG00000103196 0.17934202598203886
CS,IS ENSG00000131149 0.9261983632213022
CS,CS ENSG00000105219 0.9609401849054968
CS,CS ENSG00000186806 0.047815981254394596
CS,IS ENSG00000101220 0.11163568005357706
CS,CS ENSG00000130702 0.571369914575868
CS,CS ENSG00000159216 0.16905291400653366
19 changes: 19 additions & 0 deletions test/output/test_comphet_variant_counts.txt
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# Sum (across cohort) of all products of (# paternally-inherited variants)x(# maternally-inherited variants) for each variant type pair
# Variant input files processed from: test/input/
paternal_variant_type maternal_variant_type total_product_of_variant_counts
CS CS 155313
CS CI 6949
CS IS 55883
CS II 3968
CI CS 8876
CI CI 414
CI IS 3309
CI II 220
IS CS 60783
IS CI 2727
IS IS 21945
IS II 1484
II CS 2405
II CI 112
II IS 886
II II 64
58 changes: 58 additions & 0 deletions test/output/test_comphet_variant_distribution.txt
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# Variant count distribution computed from input variant files in test/input/
# variant_annotations: CI
# CADD_threshold: 1.5
# SpliceAI_threshold: 0.15
inheritance variant_type variant_count number_samples
P CS 103 1
P CS 116 1
P CS 129 1
P CS 130 1
P CS 133 1
P CS 136 2
P CS 140 1
P CS 142 1
P CI 3 1
P CI 5 2
P CI 7 1
P CI 8 1
P CI 9 1
P CI 10 3
P IS 41 1
P IS 43 1
P IS 45 1
P IS 46 1
P IS 50 1
P IS 52 2
P IS 61 1
P IS 68 1
P II 1 4
P II 2 3
P II 3 1
P II 5 1
M CS 121 2
M CS 124 1
M CS 125 1
M CS 129 1
M CS 130 1
M CS 146 2
M CS 158 1
M CI 2 1
M CI 4 1
M CI 5 3
M CI 6 1
M CI 8 2
M CI 10 1
M IS 36 1
M IS 42 2
M IS 47 1
M IS 48 1
M IS 49 1
M IS 53 1
M IS 56 1
M IS 60 1
M II 1 1
M II 2 2
M II 3 2
M II 4 2
M II 5 1
M II 6 1
139 changes: 139 additions & 0 deletions test/output/test_comphet_variant_product_distribution.txt
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# Number of input variant files with specific (paternal_variant_count)x(maternal_variant_count) values
# Variant input files processed from: test/input/
paternal_variant_type maternal_variant_type product_of_variant_counts number_samples
CS CS 12463 1
CS CS 16120 1
CS CS 16456 1
CS CS 16770 1
CS CS 17000 1
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CI II 40 1
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II II 4 3
II II 6 1
II II 8 1
II II 9 1
II II 25 1
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