From b5b78b1821039e723ae83e5b9fe88cde9eb5b61d Mon Sep 17 00:00:00 2001 From: Adam English Date: Thu, 1 Aug 2024 20:22:30 -0400 Subject: [PATCH] func test update refine inputs had star alleles --- .../refine_output_one/refine.regions.txt | 34 +++++++++---------- .../refine.variant_summary.json | 14 ++++---- .../refine.region_summary.json | 16 ++++----- .../refine_output_three/refine.regions.txt | 24 ++++--------- .../refine.variant_summary.json | 8 ++--- .../refine_output_two/refine.regions.txt | 20 +++++------ 6 files changed, 53 insertions(+), 63 deletions(-) diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt index 41bfa0b8..f617c30b 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt @@ -6,7 +6,7 @@ chr20 709729 709975 2 2 0 0 False 2 2 0 0 TP chr20 1149807 1150220 2 2 0 0 False 2 2 0 0 TP chr20 1257933 1260528 2 2 0 0 False 2 2 0 0 TP chr20 1301599 1302667 2 2 0 0 False 2 2 0 0 TP -chr20 2240925 2241726 1 1 5 1 True 5 5 0 0 TP +chr20 2240925 2241726 1 1 4 1 True 5 5 0 0 TP chr20 2442966 2443943 2 2 0 0 False 2 2 0 0 TP chr20 2842574 2842997 2 2 0 0 False 2 2 0 0 TP chr20 4032219 4033601 2 2 2 1 True 4 4 0 0 TP @@ -19,7 +19,7 @@ chr20 5554104 5554185 0 0 0 0 False 0 0 0 0 TN chr20 5962327 5962410 0 0 0 0 False 0 0 0 0 TN chr20 7435215 7435749 2 2 0 0 False 2 2 0 0 TP chr20 7719330 7719414 1 1 0 0 False 1 1 0 0 TP -chr20 7720911 7721003 1 1 1 0 True 1 1 0 0 TP +chr20 7720911 7721003 1 1 0 0 False 1 1 0 0 TP chr20 7721059 7721319 0 0 0 0 False 0 0 0 0 TN chr20 8661911 8662657 1 1 3 1 True 9 9 0 0 TP chr20 9015548 9016039 1 1 0 0 False 1 1 0 0 TP @@ -33,7 +33,7 @@ chr20 16226954 16228487 3 3 0 0 False 3 3 0 0 TP chr20 16257741 16259345 2 2 2 0 True 4 4 1 0 FN chr20 16395149 16395421 3 3 1 0 True 3 3 0 0 TP chr20 16894360 16894435 1 1 0 0 False 1 1 0 0 TP -chr20 17081216 17081410 2 2 1 0 True 2 2 0 0 TP +chr20 17081216 17081410 2 2 0 0 False 2 2 0 0 TP chr20 17197123 17197241 2 2 0 0 False 2 2 0 0 TP chr20 17303131 17303609 1 1 0 0 False 1 1 0 0 TP chr20 18209097 18210727 3 3 2 1 True 5 5 0 0 TP @@ -43,9 +43,9 @@ chr20 19663366 19663526 2 2 0 0 False 2 2 0 0 TP chr20 20295955 20296565 2 2 2 1 True 3 3 0 0 TP chr20 20320285 20320579 1 1 2 1 True 1 1 0 0 TP chr20 20337200 20337707 1 1 6 2 True 3 3 0 0 TP -chr20 20354570 20358323 7 7 9 1 True 16 16 0 0 TP +chr20 20354570 20358323 7 7 8 1 True 16 16 0 0 TP chr20 20458640 20458937 2 2 0 0 False 2 2 0 0 TP -chr20 21120212 21120539 2 2 1 0 True 1 1 0 0 TP +chr20 21120212 21120539 2 2 0 0 False 2 2 0 0 TP chr20 21721174 21721735 2 2 1 0 True 3 3 0 0 TP chr20 22081961 22084122 4 4 3 1 True 9 9 0 0 TP chr20 22471831 22472129 2 2 0 0 False 2 2 0 0 TP @@ -54,7 +54,7 @@ chr20 23155504 23155975 3 3 2 2 True 5 5 0 0 TP chr20 23267965 23268087 2 2 0 0 False 2 2 0 0 TP chr20 23560883 23561191 1 1 2 2 True 3 3 0 0 TP chr20 23942431 23942955 1 1 0 0 False 1 1 0 0 TP -chr20 24407983 24408997 3 3 1 0 True 2 2 0 0 TP +chr20 24407983 24408997 3 3 0 0 False 3 3 0 0 TP chr20 24681988 24682277 2 2 1 0 True 2 2 0 0 TP chr20 24836081 24836384 2 2 0 0 False 2 2 0 0 TP chr20 24956961 24957198 2 2 0 0 False 2 2 0 0 TP @@ -71,10 +71,10 @@ chr20 32723469 32724637 0 0 0 0 False 0 0 0 0 TN chr20 32724927 32724999 0 0 0 0 False 0 0 0 0 TN chr20 34205619 34205960 1 1 0 0 False 1 1 0 0 TP chr20 34235750 34236213 0 0 2 1 True 2 2 0 0 TP -chr20 35539120 35539724 4 4 1 0 True 4 4 0 0 TP +chr20 35539120 35539724 4 4 0 0 False 4 4 0 0 TP chr20 35580013 35580886 1 1 2 1 True 7 7 0 0 TP chr20 36642142 36642222 1 1 0 0 False 1 1 0 0 TP -chr20 37361752 37362058 2 2 1 0 True 2 2 0 0 TP +chr20 37361752 37362058 2 2 0 0 False 2 2 0 0 TP chr20 38123590 38124705 2 2 1 4 True 7 7 0 0 TP chr20 38194533 38194666 2 2 0 0 False 2 2 0 0 TP chr20 38313618 38315069 3 3 0 0 False 3 3 0 0 TP @@ -113,13 +113,13 @@ chr20 53913028 53913352 2 2 0 0 False 2 2 0 0 TP chr20 54690771 54690873 2 2 0 0 False 2 2 0 0 TP chr20 55532159 55533378 1 1 0 0 False 1 1 0 0 TP chr20 55624482 55625807 6 6 6 0 True 11 11 0 0 TP -chr20 55627344 55628450 7 7 4 0 True 8 8 0 0 TP +chr20 55627344 55628450 7 7 3 0 True 8 8 0 0 TP chr20 55943919 55945807 2 2 2 1 True 5 5 0 0 TP chr20 56280422 56282114 4 4 5 1 True 10 10 0 0 TP chr20 56284258 56284407 2 2 0 0 False 2 2 0 0 TP chr20 56710555 56711193 2 2 0 0 False 2 2 0 0 TP chr20 57090672 57091411 1 1 2 0 True 4 4 0 0 TP -chr20 57110212 57110785 2 2 1 0 True 2 2 0 0 TP +chr20 57110212 57110785 2 2 0 0 False 2 2 0 0 TP chr20 57189946 57190540 0 0 3 1 True 1 1 0 0 TP chr20 57350808 57350987 1 1 1 0 True 3 3 0 0 TP chr20 57417271 57418234 2 2 0 0 False 2 2 0 0 TP @@ -143,7 +143,7 @@ chr20 61176725 61176974 2 2 0 0 False 2 2 0 0 TP chr20 61201683 61202474 2 2 4 1 True 7 7 0 0 TP chr20 61229587 61229717 2 2 0 0 False 2 2 0 0 TP chr20 61282506 61283669 4 4 2 0 True 6 6 0 0 TP -chr20 61289625 61290555 1 1 2 1 True 2 2 0 0 TP +chr20 61289625 61290555 1 1 1 1 True 2 2 0 0 TP chr20 61329258 61329577 0 0 0 2 False 0 0 0 2 FP chr20 61331528 61331753 2 2 0 0 False 2 2 0 0 TP chr20 61337205 61337590 2 2 0 0 False 2 2 0 0 TP @@ -152,8 +152,8 @@ chr20 61475406 61475726 2 2 0 0 False 2 2 0 0 TP chr20 61561920 61562503 0 0 2 1 True 2 2 0 0 TP chr20 61653427 61654067 1 1 0 0 False 1 1 0 0 TP chr20 61723833 61724244 1 1 0 0 False 1 1 0 0 TP -chr20 61744188 61744654 2 2 1 0 True 2 2 0 0 TP -chr20 61783403 61784839 3 3 1 0 True 4 4 0 0 TP +chr20 61744188 61744654 2 2 0 0 False 2 2 0 0 TP +chr20 61783403 61784839 3 3 0 0 False 3 3 0 0 TP chr20 61919676 61921374 2 2 0 0 False 2 2 0 0 TP chr20 62057573 62059139 1 1 3 1 True 7 7 0 0 TP chr20 62212844 62213874 4 4 0 0 False 4 4 0 0 TP @@ -161,7 +161,7 @@ chr20 62270279 62271094 1 1 3 1 True 4 4 0 0 TP chr20 62317837 62318459 2 2 0 0 False 2 2 0 0 TP chr20 62321031 62321873 2 2 3 0 True 5 5 0 0 TP chr20 62349612 62349932 1 1 5 1 True 6 6 0 0 TP -chr20 62360190 62360712 0 0 8 2 True 5 5 0 0 TP +chr20 62360190 62360712 0 0 7 2 True 5 5 0 0 TP chr20 62417424 62418062 3 3 0 0 False 3 3 0 0 TP chr20 62422444 62422791 2 2 0 0 False 2 2 0 0 TP chr20 62504279 62504614 2 2 0 0 False 2 2 0 0 TP @@ -190,7 +190,7 @@ chr20 63294079 63294266 2 2 0 0 False 2 2 0 0 TP chr20 63303655 63304858 2 2 0 0 False 2 2 0 0 TP chr20 63334892 63335504 2 2 0 0 False 2 2 0 0 TP chr20 63361274 63361471 2 2 0 0 False 2 2 0 0 TP -chr20 63372065 63372691 2 2 1 0 True 2 2 0 0 TP +chr20 63372065 63372691 2 2 0 0 False 2 2 0 0 TP chr20 63392592 63392812 1 1 0 0 False 1 1 0 0 TP chr20 63401702 63402319 1 1 0 0 False 1 1 0 0 TP chr20 63450491 63450613 2 2 0 0 False 2 2 0 0 TP @@ -199,7 +199,7 @@ chr20 63491589 63493064 1 1 3 1 True 4 4 0 0 TP chr20 63535674 63536245 1 1 2 0 True 1 1 0 0 TP chr20 63546436 63546842 1 1 0 0 False 1 1 0 0 TP chr20 63553294 63553757 1 1 0 0 False 1 1 0 0 TP -chr20 63559288 63559963 1 1 4 1 True 4 4 0 0 TP +chr20 63559288 63559963 1 1 2 1 True 4 4 0 0 TP chr20 63641779 63642135 1 1 2 1 True 2 2 0 0 TP chr20 63669579 63670496 2 2 0 0 False 2 2 0 0 TP chr20 63693325 63693884 1 1 6 1 True 10 10 0 0 TP @@ -217,7 +217,7 @@ chr20 64042716 64043061 1 1 0 0 False 1 1 0 0 TP chr20 64065853 64066011 0 0 0 1 False 0 0 0 1 FP chr20 64090704 64091389 0 0 0 2 False 0 0 0 2 FP chr20 64096658 64097164 0 0 0 2 False 0 0 0 2 FP -chr20 64125109 64127974 3 3 3 0 True 12 12 0 0 TP +chr20 64125109 64127974 3 3 2 0 True 12 12 0 0 TP chr20 64131804 64133955 5 5 8 1 True 24 24 0 0 TP chr20 64134883 64136386 3 3 1 0 True 4 4 0 0 TP chr20 64157894 64158976 2 2 0 0 False 2 2 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json index edc91450..b9464c8e 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json @@ -1,11 +1,11 @@ { - "TP-base": 593, - "TP-comp": 593, + "TP-base": 594, + "TP-comp": 594, "FP": 15, "FN": 2, - "precision": 0.975328947368421, - "recall": 0.9966386554621849, - "f1": 0.9858686616791356, - "base cnt": 595, - "comp cnt": 608 + "precision": 0.9753694581280788, + "recall": 0.9966442953020134, + "f1": 0.9858921161825727, + "base cnt": 596, + "comp cnt": 609 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json index af76b54f..20e8fdaa 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json @@ -2,17 +2,17 @@ "TP": 22, "TN": 0, "FP": 24, - "FN": 58, - "base P": 83, + "FN": 48, + "base P": 73, "base N": 9, - "comp P": 91, + "comp P": 81, "comp N": 1, - "PPV": 0.24175824175824176, - "TPR": 0.26506024096385544, + "PPV": 0.2716049382716049, + "TPR": 0.3013698630136986, "TNR": 0.0, "NPV": 0.0, - "ACC": 0.2391304347826087, - "BA": 0.13253012048192772, - "F1": 0.25287356321839083, + "ACC": 0.2682926829268293, + "BA": 0.1506849315068493, + "F1": 0.2857142857142857, "UND": 0 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt index 4866a470..18097dbd 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt @@ -1,37 +1,31 @@ chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state chr20 278819 279179 3 3 1 0 False 3 3 1 0 FN chr20 641802 642530 3 3 2 0 False 3 3 2 0 FN -chr20 2240850 2241400 1 1 5 1 True 1 1 4 1 FN,FP +chr20 2240850 2241400 1 1 4 1 True 1 1 4 1 FN,FP chr20 4032247 4033338 2 2 2 1 True 2 2 2 2 FN,FP chr20 5040366 5040587 0 0 0 2 False 0 0 0 2 FP chr20 5041831 5042378 1 1 1 1 True 2 2 0 0 TP -chr20 7720842 7721078 1 1 1 0 False 1 1 1 0 FN chr20 8661834 8662229 1 1 3 1 True 4 4 0 0 TP chr20 10802617 10802954 1 1 1 0 False 1 1 1 0 FN chr20 13848162 13848654 3 3 1 0 False 3 3 1 0 FN chr20 14861944 14862754 5 5 5 1 True 6 6 1 0 FN chr20 16257744 16259315 2 2 2 0 False 2 2 2 0 FN chr20 16395091 16395483 3 3 1 0 False 3 3 1 0 FN -chr20 17081183 17081475 2 2 1 0 False 2 2 1 0 FN chr20 18209029 18210244 3 3 2 1 True 6 6 0 2 FP chr20 20295904 20296440 2 2 2 1 True 5 5 0 0 TP chr20 20320229 20320629 1 1 2 1 True 4 4 0 0 TP chr20 20337175 20337734 1 1 6 2 True 3 3 0 0 TP chr20 20354802 20355545 3 3 1 0 False 3 3 1 0 FN -chr20 20356420 20357920 4 4 8 1 True 9 9 2 0 FN -chr20 21120188 21120571 2 2 1 0 False 2 2 1 0 FN +chr20 20356420 20357920 4 4 7 1 True 9 9 2 0 FN chr20 21721341 21721756 2 2 1 0 False 2 2 1 0 FN chr20 22082156 22084015 4 4 3 1 True 3 3 4 1 FN,FP chr20 23155468 23155967 3 3 2 2 True 4 4 1 1 FN,FP chr20 23560829 23561208 1 1 2 2 True 2 2 0 0 TP -chr20 24407963 24408930 3 3 1 0 False 3 3 1 0 FN chr20 24681956 24682235 2 2 1 0 False 2 2 1 0 FN chr20 25781680 25781901 0 0 0 1 False 0 0 0 1 FP chr20 32722934 32723155 0 0 1 0 False 0 0 1 0 FN chr20 34235788 34236091 0 0 2 1 True 2 2 0 0 TP -chr20 35539102 35539692 4 4 1 0 False 4 4 1 0 FN chr20 35580576 35580866 1 1 2 1 True 3 3 2 1 FN,FP -chr20 37361675 37361996 2 2 1 0 False 2 2 1 0 FN chr20 38123689 38124113 2 2 1 4 True 3 3 3 4 FN,FP chr20 38463887 38464454 2 2 2 0 False 2 2 2 0 FN chr20 41196260 41196605 3 3 1 0 False 3 3 1 0 FN @@ -44,11 +38,10 @@ chr20 50775536 50775942 1 1 2 1 True 1 1 0 1 FP chr20 51953709 51953930 0 0 0 1 False 0 0 0 1 FP chr20 53203989 53204362 2 2 2 1 True 2 2 0 0 TP chr20 55624698 55625762 6 6 6 0 False 6 6 6 0 FN -chr20 55627528 55628415 7 7 4 0 False 7 7 4 0 FN +chr20 55627528 55628415 7 7 3 0 False 7 7 3 0 FN chr20 55944162 55945285 2 2 2 1 True 2 2 2 0 FN chr20 56280431 56282023 4 4 5 1 True 4 4 2 1 FN,FP chr20 57090758 57091276 1 1 2 0 False 1 1 2 0 FN -chr20 57110340 57110703 2 2 1 0 False 2 2 1 0 FN chr20 57190146 57190538 0 0 3 1 True 1 1 0 0 TP chr20 57350746 57351030 1 1 1 0 False 1 1 1 0 FN chr20 57948891 57949456 1 1 4 1 True 1 1 4 1 FN,FP @@ -58,16 +51,14 @@ chr20 60702895 60703197 2 2 2 1 True 3 3 0 0 TP chr20 61100811 61102515 1 1 4 1 True 4 4 0 0 TP chr20 61201712 61202352 2 2 4 1 True 3 3 0 0 TP chr20 61282815 61283589 4 4 2 0 False 4 4 2 0 FN -chr20 61289552 61290383 1 1 2 1 True 2 2 0 0 TP +chr20 61289552 61290383 1 1 1 1 True 2 2 0 0 TP chr20 61329235 61329551 0 0 0 2 False 0 0 0 2 FP chr20 61561999 61562362 0 0 2 1 True 1 1 0 0 TP -chr20 61744291 61744702 2 2 1 0 False 2 2 1 0 FN -chr20 61783848 61784808 3 3 1 0 False 3 3 1 0 FN chr20 62057492 62058878 1 1 3 1 True 2 2 0 0 TP chr20 62270303 62270937 1 1 3 1 True 4 4 0 0 TP chr20 62321286 62321840 2 2 3 0 False 2 2 3 0 FN chr20 62349531 62349936 1 1 5 1 True 1 1 2 1 FN,FP -chr20 62360300 62360712 0 0 8 2 True 4 4 2 1 FN,FP +chr20 62360300 62360712 0 0 7 2 True 4 4 2 1 FN,FP chr20 62830540 62830807 2 2 1 1 True 1 1 0 0 TP chr20 62875131 62875514 2 2 3 0 False 2 2 3 0 FN chr20 63027956 63029140 4 4 1 1 True 3 3 0 0 TP @@ -75,10 +66,9 @@ chr20 63048983 63049269 3 3 1 0 False 3 3 1 0 FN chr20 63154577 63155031 1 1 1 0 False 1 1 1 0 FN chr20 63167363 63167674 2 2 1 0 False 2 2 1 0 FN chr20 63221399 63221831 1 1 2 1 True 2 2 0 0 TP -chr20 63372104 63372510 2 2 1 0 False 2 2 1 0 FN chr20 63491847 63492500 1 1 3 1 True 4 4 0 0 TP chr20 63535641 63536112 1 1 2 0 False 1 1 2 0 FN -chr20 63559305 63559829 1 1 4 1 True 5 5 0 0 TP +chr20 63559305 63559829 1 1 2 1 True 5 5 0 0 TP chr20 63641737 63642125 1 1 2 1 True 3 3 0 0 TP chr20 63693339 63693842 1 1 6 1 True 10 10 1 0 FN chr20 63770826 63771124 0 0 0 2 False 0 0 0 2 FP @@ -87,7 +77,7 @@ chr20 63964695 63966223 1 1 1 0 False 1 1 1 0 FN chr20 64065772 64065993 0 0 0 1 False 0 0 0 1 FP chr20 64090623 64091117 0 0 0 2 False 0 0 0 2 FP chr20 64096929 64097150 0 0 0 2 False 0 0 0 2 FP -chr20 64125250 64127985 3 3 3 0 False 3 3 3 0 FN +chr20 64125250 64127985 3 3 2 0 False 3 3 2 0 FN chr20 64131803 64133966 5 5 8 1 True 5 5 6 5 FN,FP chr20 64134880 64136440 3 3 1 0 False 3 3 1 0 FN chr20 64173328 64176440 4 4 7 3 True 9 9 3 6 FN,FP diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json index abb55304..13ae86d6 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json @@ -2,10 +2,10 @@ "TP-base": 452, "TP-comp": 452, "FP": 43, - "FN": 107, + "FN": 95, "precision": 0.9131313131313131, - "recall": 0.8085867620751341, - "f1": 0.857685009487666, - "base cnt": 559, + "recall": 0.8263254113345521, + "f1": 0.8675623800383877, + "base cnt": 547, "comp cnt": 495 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt index 0902bf25..8e0d4009 100644 --- a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt @@ -18,15 +18,15 @@ chr20 13848064 13848749 3 3 1 0 True 3 3 0 0 TP chr20 14861837 14862841 5 5 5 1 True 15 15 0 0 TP chr20 16226854 16228587 3 3 0 0 False 3 3 0 0 TP chr20 16395049 16395521 3 3 1 0 True 3 3 0 0 TP -chr20 17081116 17081510 2 2 1 0 True 2 2 0 0 TP +chr20 17081116 17081510 2 2 0 0 False 2 2 0 0 TP chr20 17197023 17197341 2 2 0 0 False 2 2 0 0 TP chr20 18208997 18210827 3 3 2 1 True 5 5 0 0 TP chr20 18675550 18676015 2 2 0 0 False 2 2 0 0 TP chr20 19663266 19663626 2 2 0 0 False 2 2 0 0 TP chr20 20337100 20337807 1 1 6 2 True 3 3 0 0 TP -chr20 20354470 20358423 7 7 9 1 True 16 16 0 0 TP +chr20 20354470 20358423 7 7 8 1 True 16 16 0 0 TP chr20 20458540 20459037 2 2 0 0 False 2 2 0 0 TP -chr20 21120112 21120639 2 2 1 0 True 1 1 0 0 TP +chr20 21120112 21120639 2 2 0 0 False 2 2 0 0 TP chr20 21721074 21721835 2 2 1 0 True 3 3 0 0 TP chr20 22471731 22472229 2 2 0 0 False 2 2 0 0 TP chr20 22882602 22882930 2 2 0 0 False 2 2 0 0 TP @@ -61,11 +61,11 @@ chr20 50853539 50854028 2 2 0 0 False 2 2 0 0 TP chr20 51500492 51500980 2 2 0 0 False 2 2 0 0 TP chr20 53203887 53204573 2 2 2 1 True 4 4 0 0 TP chr20 53415542 53415960 2 2 0 0 False 2 2 0 0 TP -chr20 55627244 55628550 7 7 4 0 True 8 8 0 0 TP +chr20 55627244 55628550 7 7 3 0 True 8 8 0 0 TP chr20 55943819 55945907 2 2 2 1 True 5 5 0 0 TP chr20 56284158 56284507 2 2 0 0 False 2 2 0 0 TP chr20 56710455 56711293 2 2 0 0 False 2 2 0 0 TP -chr20 57110112 57110885 2 2 1 0 True 2 2 0 0 TP +chr20 57110112 57110885 2 2 0 0 False 2 2 0 0 TP chr20 57417171 57418334 2 2 0 0 False 2 2 0 0 TP chr20 57974704 57975302 2 2 0 0 False 2 2 0 0 TP chr20 58196600 58197036 2 2 0 0 False 2 2 0 0 TP @@ -82,8 +82,8 @@ chr20 61329158 61329677 0 0 0 2 False 0 0 0 2 FP chr20 61331428 61331853 2 2 0 0 False 2 2 0 0 TP chr20 61337105 61337690 2 2 0 0 False 2 2 0 0 TP chr20 61475306 61475826 2 2 0 0 False 2 2 0 0 TP -chr20 61744088 61744754 2 2 1 0 True 2 2 0 0 TP -chr20 61783303 61784939 3 3 1 0 True 4 4 0 0 TP +chr20 61744088 61744754 2 2 0 0 False 2 2 0 0 TP +chr20 61783303 61784939 3 3 0 0 False 3 3 0 0 TP chr20 61919576 61921474 2 2 0 0 False 2 2 0 0 TP chr20 62057473 62059239 1 1 3 1 True 7 7 0 0 TP chr20 62212744 62213974 4 4 0 0 False 4 4 0 0 TP @@ -110,11 +110,11 @@ chr20 63293979 63294366 2 2 0 0 False 2 2 0 0 TP chr20 63303555 63304958 2 2 0 0 False 2 2 0 0 TP chr20 63334792 63335604 2 2 0 0 False 2 2 0 0 TP chr20 63361174 63361571 2 2 0 0 False 2 2 0 0 TP -chr20 63371965 63372791 2 2 1 0 True 2 2 0 0 TP +chr20 63371965 63372791 2 2 0 0 False 2 2 0 0 TP chr20 63450391 63450713 2 2 0 0 False 2 2 0 0 TP chr20 63486663 63487516 2 2 0 0 False 2 2 0 0 TP chr20 63491489 63493164 1 1 3 1 True 4 4 0 0 TP -chr20 63559188 63560063 1 1 4 1 True 4 4 0 0 TP +chr20 63559188 63560063 1 1 2 1 True 4 4 0 0 TP chr20 63641679 63642235 1 1 2 1 True 2 2 0 0 TP chr20 63669479 63670596 2 2 0 0 False 2 2 0 0 TP chr20 63693225 63693984 1 1 6 1 True 10 10 0 0 TP @@ -123,7 +123,7 @@ chr20 63824531 63825244 2 2 0 0 False 2 2 0 0 TP chr20 63948414 63948858 2 2 1 1 True 3 3 0 0 TP chr20 64090604 64091489 0 0 0 2 False 0 0 0 2 FP chr20 64096558 64097264 0 0 0 2 False 0 0 0 2 FP -chr20 64125009 64128074 3 3 3 0 True 12 12 0 0 TP +chr20 64125009 64128074 3 3 2 0 True 12 12 0 0 TP chr20 64131704 64134055 5 5 8 1 True 24 24 0 0 TP chr20 64134783 64136486 3 3 1 0 True 4 4 0 0 TP chr20 64173309 64176629 4 4 7 3 True 17 17 0 0 TP