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They now buffer by 10bp in order to ensure variants in question are covered.
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28 changes: 14 additions & 14 deletions
28
repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,18 @@ | ||
| { | ||
| "TP": 19, | ||
| "TN": 10, | ||
| "FP": 17, | ||
| "TP": 17, | ||
| "TN": 6, | ||
| "FP": 23, | ||
| "FN": 58, | ||
| "base P": 78, | ||
| "base N": 14, | ||
| "comp P": 81, | ||
| "comp N": 11, | ||
| "PPV": 0.2345679012345679, | ||
| "TPR": 0.24358974358974358, | ||
| "TNR": 0.7142857142857143, | ||
| "NPV": 0.9090909090909091, | ||
| "ACC": 0.31521739130434784, | ||
| "BA": 0.47893772893772896, | ||
| "F1": 0.2389937106918239, | ||
| "base P": 76, | ||
| "base N": 16, | ||
| "comp P": 85, | ||
| "comp N": 7, | ||
| "PPV": 0.2, | ||
| "TPR": 0.2236842105263158, | ||
| "TNR": 0.375, | ||
| "NPV": 0.8571428571428571, | ||
| "ACC": 0.25, | ||
| "BA": 0.2993421052631579, | ||
| "F1": 0.2111801242236025, | ||
| "UND": 0 | ||
| } |
184 changes: 92 additions & 92 deletions
184
repo_utils/answer_key/refine/refine_output_three/refine.regions.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,93 +1,93 @@ | ||
| chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state | ||
| chr20 278929 279069 2 3 1 0 False 2 3 1 0 FN | ||
| chr20 641912 642420 2 3 2 0 False 2 3 2 0 FN | ||
| chr20 2240960 2241290 0 1 5 1 True 1 1 4 1 FN,FP | ||
| chr20 4032357 4033228 2 1 2 1 True 0 0 2 1 FN,FP | ||
| chr20 5040476 5040477 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 5041941 5042268 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 7720952 7720968 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 8661944 8662119 0 1 2 1 True 2 2 0 0 TP | ||
| chr20 10802727 10802844 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 13848272 13848544 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 14862054 14862644 4 4 5 1 True 3 3 1 0 FN | ||
| chr20 16257854 16259205 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 16395201 16395373 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 17081293 17081365 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 18209139 18210134 3 3 2 1 True 3 3 0 1 FP | ||
| chr20 20296014 20296330 1 1 2 1 True 4 4 0 0 TP | ||
| chr20 20320339 20320519 0 1 2 1 True 3 3 0 0 TP | ||
| chr20 20337285 20337624 1 1 6 2 True 1 1 0 0 TP | ||
| chr20 20354912 20355435 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 20356530 20357810 2 3 8 1 True 8 8 2 0 FN | ||
| chr20 21120298 21120461 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 21721451 21721646 0 2 1 0 False 0 2 1 0 FN | ||
| chr20 22082266 22083905 3 3 3 1 True 3 3 4 1 FN,FP | ||
| chr20 23155578 23155857 3 3 1 2 True 3 3 1 1 FN,FP | ||
| chr20 23560939 23561098 1 1 2 2 True 2 2 0 0 TP | ||
| chr20 24408073 24408820 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 24682066 24682125 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 25781790 25781791 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 32723044 32723045 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 34235898 34235981 0 0 1 1 True 1 1 0 0 TP | ||
| chr20 35539212 35539582 4 4 1 0 False 4 4 1 0 FN | ||
| chr20 35580686 35580756 1 1 2 1 True 1 1 2 1 FN,FP | ||
| chr20 37361785 37361886 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 38123799 38124003 0 1 1 4 True 1 1 2 3 FN,FP | ||
| chr20 38463997 38464344 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 41196370 41196495 2 3 1 0 False 2 3 1 0 FN | ||
| chr20 41257714 41258003 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 44764150 44764203 0 1 1 0 False 0 1 1 0 FN | ||
| chr20 45600655 45600695 0 2 2 0 False 0 2 2 0 FN | ||
| chr20 48449794 48450385 4 4 1 0 False 4 4 1 0 FN | ||
| chr20 49834182 49834469 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 50775646 50775832 0 0 1 1 True 0 0 0 0 TN | ||
| chr20 51953819 51953820 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 53204099 53204252 0 1 2 0 False 0 1 2 0 FN | ||
| chr20 55624808 55625652 6 6 6 0 False 6 6 6 0 FN | ||
| chr20 55627638 55628305 7 7 4 0 False 7 7 4 0 FN | ||
| chr20 55944272 55945175 2 2 1 1 True 1 1 2 0 FN | ||
| chr20 56280541 56281913 4 4 4 1 True 5 5 2 1 FN,FP | ||
| chr20 57090868 57091166 1 1 2 0 False 1 1 2 0 FN | ||
| chr20 57110450 57110593 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 57190256 57190428 0 0 3 1 True 0 0 0 0 TN | ||
| chr20 57350856 57350920 1 1 0 0 False 1 1 0 0 TP | ||
| chr20 57949001 57949346 1 1 4 1 True 0 0 4 1 FN,FP | ||
| chr20 59384366 59384743 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 60314443 60314711 2 1 1 0 False 2 1 1 0 FN | ||
| chr20 60703005 60703087 2 2 1 1 True 3 3 0 0 TP | ||
| chr20 61100921 61102405 1 1 3 1 True 4 4 0 0 TP | ||
| chr20 61201822 61202242 1 2 4 1 True 1 1 0 0 TP | ||
| chr20 61282925 61283479 3 3 2 0 False 3 3 2 0 FN | ||
| chr20 61289662 61290273 1 1 2 1 True 0 0 0 0 TN | ||
| chr20 61329345 61329441 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 61562109 61562252 0 0 1 1 True 1 1 0 0 TP | ||
| chr20 61744401 61744592 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 61783958 61784698 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 62057602 62058768 1 1 2 1 True 1 1 0 0 TP | ||
| chr20 62270413 62270827 1 1 3 1 True 3 3 0 0 TP | ||
| chr20 62321396 62321730 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 62349641 62349826 1 1 4 1 True 0 0 2 1 FN,FP | ||
| chr20 62360410 62360602 0 0 6 2 True 1 1 1 1 FN,FP | ||
| chr20 62830650 62830697 2 2 1 1 True 1 1 0 0 TP | ||
| chr20 62875241 62875404 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 63028066 63029030 4 4 1 1 True 2 2 0 0 TP | ||
| chr20 63049093 63049159 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 63154687 63154921 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 63167473 63167564 2 2 0 0 False 2 2 0 0 TP | ||
| chr20 63221509 63221721 1 1 1 1 True 0 0 0 0 TN | ||
| chr20 63372214 63372400 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 63491957 63492390 1 1 2 1 True 2 2 1 0 FN | ||
| chr20 63535751 63536002 1 1 2 0 False 1 1 2 0 FN | ||
| chr20 63559415 63559719 1 1 4 1 True 3 3 0 0 TP | ||
| chr20 63641847 63642015 0 0 1 0 False 0 0 1 0 FN | ||
| chr20 63693449 63693732 1 1 5 1 True 10 10 0 0 TP | ||
| chr20 63770936 63771014 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 63948594 63948653 2 2 0 0 False 2 2 0 0 TP | ||
| chr20 63964805 63966113 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 64065882 64065883 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 64090733 64091007 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 64097039 64097040 0 0 0 0 False 0 0 0 0 TN | ||
| chr20 64125360 64127875 3 3 3 0 False 3 3 3 0 FN | ||
| chr20 64131913 64133856 4 5 8 1 True 5 5 6 5 FN,FP | ||
| chr20 64134990 64136330 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 64173438 64176330 4 4 7 3 True 10 10 5 2 FN,FP | ||
| chr20 278919 279079 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 641902 642430 3 3 2 0 False 3 3 2 0 FN | ||
| chr20 2240950 2241300 1 1 5 1 True 1 1 4 1 FN,FP | ||
| chr20 4032347 4033238 2 2 2 1 True 1 1 2 1 FN,FP | ||
| chr20 5040466 5040487 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 5041931 5042278 1 1 1 1 True 2 2 0 0 TP | ||
| chr20 7720942 7720978 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 8661934 8662129 1 1 3 1 True 2 2 0 0 TP | ||
| chr20 10802717 10802854 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 13848262 13848554 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 14862044 14862654 5 5 5 1 True 4 4 1 0 FN | ||
| chr20 16257844 16259215 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 16395191 16395383 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 17081283 17081375 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 18209129 18210144 3 3 2 1 True 5 5 0 1 FP | ||
| chr20 20296004 20296340 2 2 2 1 True 5 5 0 0 TP | ||
| chr20 20320329 20320529 1 1 2 1 True 3 3 0 0 TP | ||
| chr20 20337275 20337634 1 1 6 2 True 1 1 0 0 TP | ||
| chr20 20354902 20355445 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 20356520 20357820 4 4 8 1 True 8 8 2 0 FN | ||
| chr20 21120288 21120471 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 21721441 21721656 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 22082256 22083915 4 4 3 1 True 3 3 4 1 FN,FP | ||
| chr20 23155568 23155867 3 3 2 2 True 3 3 1 1 FN,FP | ||
| chr20 23560929 23561108 1 1 2 2 True 2 2 0 0 TP | ||
| chr20 24408063 24408830 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 24682056 24682135 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 25781780 25781801 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 32723034 32723055 0 0 1 0 False 0 0 1 0 FN | ||
| chr20 34235888 34235991 0 0 2 1 True 2 2 0 0 TP | ||
| chr20 35539202 35539592 4 4 1 0 False 4 4 1 0 FN | ||
| chr20 35580676 35580766 1 1 2 1 True 1 1 2 1 FN,FP | ||
| chr20 37361775 37361896 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 38123789 38124013 2 2 1 4 True 1 1 2 3 FN,FP | ||
| chr20 38463987 38464354 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 41196360 41196505 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 41257704 41258013 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 44764140 44764213 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 45600645 45600705 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 48449784 48450395 4 4 2 0 False 4 4 2 0 FN | ||
| chr20 49834172 49834479 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 50775636 50775842 1 1 2 1 True 0 0 0 0 TN | ||
| chr20 51953809 51953830 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 53204089 53204262 2 2 2 1 True 0 0 0 0 TN | ||
| chr20 55624798 55625662 6 6 6 0 False 6 6 6 0 FN | ||
| chr20 55627628 55628315 7 7 4 0 False 7 7 4 0 FN | ||
| chr20 55944262 55945185 2 2 2 1 True 1 1 2 0 FN | ||
| chr20 56280531 56281923 4 4 5 1 True 4 4 2 1 FN,FP | ||
| chr20 57090858 57091176 1 1 2 0 False 1 1 2 0 FN | ||
| chr20 57110440 57110603 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 57190246 57190438 0 0 3 1 True 1 1 0 0 TP | ||
| chr20 57350846 57350930 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 57948991 57949356 1 1 4 1 True 0 0 5 1 FN,FP | ||
| chr20 59384356 59384753 3 3 2 0 False 3 3 2 0 FN | ||
| chr20 60314433 60314721 2 2 2 0 False 2 2 2 0 FN | ||
| chr20 60702995 60703097 2 2 2 1 True 3 3 0 0 TP | ||
| chr20 61100911 61102415 1 1 4 1 True 4 4 0 0 TP | ||
| chr20 61201812 61202252 2 2 4 1 True 0 0 0 0 TN | ||
| chr20 61282915 61283489 4 4 2 0 False 4 4 2 0 FN | ||
| chr20 61289652 61290283 1 1 2 1 True 0 0 0 0 TN | ||
| chr20 61329335 61329451 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 61562099 61562262 0 0 2 1 True 1 1 0 0 TP | ||
| chr20 61744391 61744602 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 61783948 61784708 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 62057592 62058778 1 1 3 1 True 1 1 0 0 TP | ||
| chr20 62270403 62270837 1 1 3 1 True 3 3 0 0 TP | ||
| chr20 62321386 62321740 2 2 3 0 False 2 2 3 0 FN | ||
| chr20 62349631 62349836 1 1 5 1 True 0 0 2 1 FN,FP | ||
| chr20 62360400 62360612 0 0 8 2 True 2 2 2 1 FN,FP | ||
| chr20 62830640 62830707 2 2 1 1 True 1 1 0 0 TP | ||
| chr20 62875231 62875414 2 2 3 0 False 2 2 3 0 FN | ||
| chr20 63028056 63029040 4 4 1 1 True 2 2 0 0 TP | ||
| chr20 63049083 63049169 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 63154677 63154931 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 63167463 63167574 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 63221499 63221731 1 1 2 1 True 0 0 0 0 TN | ||
| chr20 63372204 63372410 2 2 1 0 False 2 2 1 0 FN | ||
| chr20 63491947 63492400 1 1 3 1 True 4 4 0 0 TP | ||
| chr20 63535741 63536012 1 1 2 0 False 1 1 2 0 FN | ||
| chr20 63559405 63559729 1 1 4 1 True 3 3 0 0 TP | ||
| chr20 63641837 63642025 1 1 2 1 True 0 0 0 0 TN | ||
| chr20 63693439 63693742 1 1 6 1 True 10 10 1 0 FN | ||
| chr20 63770926 63771024 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 63948584 63948663 2 2 1 1 True 0 0 0 1 FP | ||
| chr20 63964795 63966123 1 1 1 0 False 1 1 1 0 FN | ||
| chr20 64065872 64065893 0 0 0 1 False 0 0 0 1 FP | ||
| chr20 64090723 64091017 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 64097029 64097050 0 0 0 2 False 0 0 0 2 FP | ||
| chr20 64125350 64127885 3 3 3 0 False 3 3 3 0 FN | ||
| chr20 64131903 64133866 5 5 8 1 True 5 5 6 5 FN,FP | ||
| chr20 64134980 64136340 3 3 1 0 False 3 3 1 0 FN | ||
| chr20 64173428 64176340 4 4 7 3 True 8 8 3 6 FN,FP |
18 changes: 9 additions & 9 deletions
18
repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,11 @@ | ||
| { | ||
| "TP-base": 422, | ||
| "TP-comp": 416, | ||
| "FP": 38, | ||
| "FN": 129, | ||
| "precision": 0.9162995594713657, | ||
| "recall": 0.7658802177858439, | ||
| "f1": 0.8343646923508332, | ||
| "base cnt": 551, | ||
| "comp cnt": 454 | ||
| "TP-base": 411, | ||
| "TP-comp": 411, | ||
| "FP": 39, | ||
| "FN": 107, | ||
| "precision": 0.9133333333333333, | ||
| "recall": 0.7934362934362934, | ||
| "f1": 0.8491735537190082, | ||
| "base cnt": 518, | ||
| "comp cnt": 450 | ||
| } |
55 changes: 55 additions & 0 deletions
55
repo_utils/test_files/external/fake_mafft/lookup/fm_044d295f667d84ae550fa2608e24e03f.msa
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| >syndip_1_chr20:57948891-57949456 | ||
| tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg | ||
| gattaatggatggatgaatggatgatggatggatgaatgagatggatggatt-------- | ||
| --------gatggatggatggatggatggatggatggaagaatggatgatggatggatga | ||
| --------------------gatggatggatggatggatggaagaatggatgatggatgg | ||
| atga--------gatggatggatggatggggggttggatggatggatgg----------- | ||
| -------------------------------------------atggatggatggatagt | ||
| ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg | ||
| atggatgaatgagatggatggatt------------gatggatggatggatggatggaag | ||
| aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg | ||
| gatggatggatggatggcagatggat | ||
| >syndip_2_chr20:57948891-57949456 | ||
| tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg | ||
| gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg | ||
| gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga | ||
| gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg | ||
| atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg | ||
| gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt | ||
| ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg | ||
| atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag | ||
| aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg | ||
| gatggatggatggatggcagatggat | ||
| >p:HG002_1_chr20:57948891-57949456 | ||
| tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg | ||
| gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg | ||
| gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga | ||
| gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg | ||
| atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg | ||
| gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt | ||
| ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg | ||
| atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag | ||
| aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg | ||
| gatggatggatggatggcagatggat | ||
| >p:HG002_2_chr20:57948891-57949456 | ||
| tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg | ||
| gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg | ||
| gatggatggatggatggatggatggatggatggatggaaga------------------- | ||
| -----------------atggatggatggatggatggatggaagaatggatgatggatgg | ||
| atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg | ||
| gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt | ||
| ggatagatg--tgatggatggatggatggatggatggatggatggaagaatggatgatgg | ||
| atggatgaatgagatgggtggattgatggatggatggatggatggatggatggatgga-- | ||
| ------------------------------------------------------------ | ||
| ----------tggatggcagatggat | ||
| >ref_chr20:57948891-57949456 | ||
| tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg | ||
| gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg | ||
| gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga | ||
| gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg | ||
| atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg | ||
| gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt | ||
| ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg | ||
| atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag | ||
| aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg | ||
| gatggatggatggatggcagatggat |
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