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fixed CI tests
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@leonschuetz
leonschuetz committed Nov 25, 2024
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Showing 3 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion Test/CFDNA03_01_combined.GSvar.out
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Original file line number Diff line number Diff line change
Expand Up @@ -107,4 +107,4 @@ chr1 892745 892745 G A 0 0 0 0-0-0-0 False No_Coverage 0 0 0 0-0-0-0 False No_
chr1 894573 894573 G A 10958 952 0.07993 1.99e-10 485-900-5925-9475 False 6329 733 0.1038 1.55e-12 341-680-3348-5349 False 9074 1329 0.12775 1.04e-13 598-1237-4745-7679 False 3664 1078 0.22733 0 813-1398-2580-4346 False
chr1 897325 897325 G C 12550 383 0.02961 5.77e-08 228-342-8508-9051 False 6797 288 0.04065 1.04e-09 176-233-4721-4647 False 10729 452 0.04043 1.71e-09 249-374-6896-7650 False 3938 390 0.09011 2.79e-25 261-513-3581-3938 False
mean -1 -1 6552.4 464.3 0.039753667 1.1894172e-08 False 3798.4667 381.13333 0.054437 2.7160127e-10 False 5572.2333 644.5 0.062406333 1.8236444e-10 False 2256.0417 498.20833 0.10300208 1.5571429e-25 True
median -1 -1 8758 419 0.03763 1.53e-10 False 5414 350 0.05379 1.04e-12 False 7480 578 0.062406333 9.74e-14 False 3246 447 0.10300208 0 True
median -1 -1 8758 419 0.03763 1.53e-10 True 5414 350 0.05379 1.04e-12 True 7480 578 0.062406333 9.74e-14 True 3246 447 0.10300208 0 True
10 changes: 5 additions & 5 deletions Test/data_output/mrdCalculation01/mrdCalculation01_monitoring_counts.tsv
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@@ -1,7 +1,7 @@
chr pos REF ALT m_REF_1-fold m_ALT_1-fold m_OTHER_1-fold m_AF_1-fold p_value_1-fold outlier_1-fold fold-change_1-fold z_stats_mean-1-fold z_stats_median-1-fold z_stats_median_wo0-1-fold m_REF_2-fold m_ALT_2-fold m_OTHER_2-fold m_AF_2-fold p_value_2-fold outlier_2-fold fold-change_2-fold z_stats_mean-2-fold z_stats_median-2-fold z_stats_median_wo0-2-fold m_REF_3-fold m_ALT_3-fold m_OTHER_3-fold m_AF_3-fold p_value_3-fold outlier_3-fold fold-change_3-fold z_stats_mean-3-fold z_stats_median-3-fold z_stats_median_wo0-3-fold m_REF_4-fold m_ALT_4-fold m_OTHER_4-fold m_AF_4-fold p_value_4-fold outlier_4-fold fold-change_4-fold z_stats_mean-4-fold z_stats_median-4-fold z_stats_median_wo0-4-fold
chr1 114713909 G T 2504 29 0 0.011448874851954205 3.5191583e-50 0 -0.14602992697764838 -0.041697352293483925 -0.000793391372297312 -0.000793391372297312 1775 20 0 0.011142061281337047 3.8298849e-38 0 -0.12810767075739427 -0.03570219750938549 -0.00021755299087738468 -0.00021755299087738468 1484 18 0 0.011984021304926764 2.0500571e-35 0 -0.10787456861606037 -0.030833282075897844 0.0012130644821915812 0.0012130644821915812 1324 15 0 0.011202389843166542 2.0404597e-29 0 -0.14899673293201587 -0.04215213242371618 -0.010179693345230006 -0.010179693345230006
chr1 114713915 C T 2534 44 0 0.017067494181536073 1.0687688e-82 0 0.2730621516075964 0.0779701049589748 0.12838155699981205 0.12838155699981205 1765 31 0 0.017260579064587972 5.5542937e-64 0 0.3506806420018038 0.09773083430091052 0.14250496146979452 0.14250496146979452 1467 28 0 0.018729096989966554 1.6474266e-59 0 0.3942485002706415 0.11268620002652405 0.15338824501538553 0.15338824501538553 1303 22 0 0.01660377358490566 4.1548757e-46 0 0.26132599956169456 0.07393080319627321 0.11312898757785017 0.11312898757785017
chr3 179218303 G A 1734 36 0 0.020338983050847456 8.2016623e-71 0 0.5170820771237521 0.14764749925387335 0.20359476882362806 0.20359476882362806 1615 33 0 0.020024271844660196 4.1199532e-70 0 0.5669460595475047 0.15800162531613687 0.2069717484828962 0.2069717484828962 1528 33 0 0.02114029468289558 1.6765537e-71 0 0.573745075520548 0.16399086439126306 0.20778710743831044 0.20778710743831044 1416 31 0 0.021423635107118175 1.3263199e-67 0 0.6274726842996985 0.17751605126089456 0.22316204483746527 0.22316204483746527
chr7 55181378 C T 2373 22 0 0.00918580375782881 2.0904165e-36 0 -0.31483210295524344 -0.08989708741162718 -0.05282255985625937 -0.05282255985625937 2248 17 0 0.0075055187637969095 9.0979123e-30 0 -0.41267561971659794 -0.11500815209053071 -0.08504471382176473 -0.08504471382176473 2174 16 0 0.0073059360730593605 3.1118005e-28 0 -0.4561248511664425 -0.130372027237456 -0.1043288890777989 -0.1043288890777989 2085 16 0 0.007615421227986673 1.3647109e-28 0 -0.42148519772601967 -0.11924086870609348 -0.09206692624675787 -0.09206692624675787
chr1 114713909 G T 2504 29 0 0.011448874851954205 3.5191583e-50 0 -0.14602992697764838 -0.041697352293483925 -0.000793391372297312 -0.000793391372297312 1775 20 0 0.011142061281337047 3.829885e-38 0 -0.12810767075739427 -0.03570219750938549 -0.00021755299087738468 -0.00021755299087738468 1484 18 0 0.011984021304926764 2.0500571e-35 0 -0.10787456861606037 -0.030833282075897844 0.0012130644821915812 0.0012130644821915812 1324 15 0 0.011202389843166542 2.0404598e-29 0 -0.14899673293201587 -0.04215213242371618 -0.010179693345230006 -0.010179693345230006
chr1 114713915 C T 2534 44 0 0.017067494181536073 1.0687688e-82 0 0.2730621516075964 0.0779701049589748 0.12838155699981205 0.12838155699981205 1765 31 0 0.017260579064587972 5.5542938e-64 0 0.3506806420018038 0.09773083430091052 0.14250496146979452 0.14250496146979452 1467 28 0 0.018729096989966554 1.6474266e-59 0 0.3942485002706415 0.11268620002652405 0.15338824501538553 0.15338824501538553 1303 22 0 0.01660377358490566 4.1548757e-46 0 0.26132599956169456 0.07393080319627321 0.11312898757785017 0.11312898757785017
chr3 179218303 G A 1734 36 0 0.020338983050847456 8.2016624e-71 0 0.5170820771237521 0.14764749925387335 0.20359476882362806 0.20359476882362806 1615 33 0 0.020024271844660196 4.1199532e-70 0 0.5669460595475047 0.15800162531613687 0.2069717484828962 0.2069717484828962 1528 33 0 0.02114029468289558 1.6765537e-71 0 0.573745075520548 0.16399086439126306 0.20778710743831044 0.20778710743831044 1416 31 0 0.021423635107118175 1.3263199e-67 0 0.6274726842996985 0.17751605126089456 0.22316204483746527 0.22316204483746527
chr7 55181378 C T 2373 22 0 0.00918580375782881 2.0904165e-36 0 -0.31483210295524344 -0.08989708741162718 -0.05282255985625937 -0.05282255985625937 2248 17 0 0.0075055187637969095 9.0979127e-30 0 -0.41267561971659794 -0.11500815209053071 -0.08504471382176473 -0.08504471382176473 2174 16 0 0.0073059360730593605 3.1118005e-28 0 -0.4561248511664425 -0.130372027237456 -0.1043288890777989 -0.1043288890777989 2085 16 0 0.007615421227986673 1.3647109e-28 0 -0.42148519772601967 -0.11924086870609348 -0.09206692624675787 -0.09206692624675787
chr7 55191822 T G 2403 28 1 0.011517893870835048 1.3771379e-48 0 -0.14088180741517942 -0.04022735939895825 0.0007933913722973519 0.0007933913722973519 2274 22 0 0.009581881533101045 2.4374929e-40 0 -0.25019538149410936 -0.0697266984344352 -0.03661080779000761 -0.03661080779000761 2175 21 0 0.009562841530054645 5.7455622e-39 0 -0.2881142391036171 -0.08235034186771173 -0.05341100299293995 -0.05341100299293995 2070 21 0 0.010043041606886656 1.6737228e-39 0 -0.23706804187200237 -0.06706807121052313 -0.03664655972272296 -0.03664655972272296
chr12 25245350 C T 1909 21 0 0.010880829015544042 2.28567e-36 0 -0.18840039138327758 -0.05379580510877886 -0.013853057330612937 -0.013853057330612937 1772 20 0 0.011160714285714286 3.7038998e-38 0 -0.1266480295812069 -0.035295411582696036 0.00021755299087738468 0.00021755299087738468 1664 20 0 0.011876484560570071 4.4518517e-39 0 -0.11587991690506905 -0.033121413236721436 -0.0012130644821915812 -0.0012130644821915812 1552 19 0 0.0120942075111394 1.9153135e-37 0 -0.08124871133135658 -0.0229857821168354 0.010179693345230044 0.010179693345230044
chr12 25245350 C T 1909 21 0 0.010880829015544042 2.28567e-36 0 -0.18840039138327758 -0.05379580510877886 -0.013853057330612937 -0.013853057330612937 1772 20 0 0.011160714285714286 3.7038998e-38 0 -0.1266480295812069 -0.035295411582696036 0.00021755299087738468 0.00021755299087738468 1664 20 0 0.011876484560570071 4.4518516e-39 0 -0.11587991690506905 -0.033121413236721436 -0.0012130644821915812 -0.0012130644821915812 1552 19 0 0.0120942075111394 1.9153135e-37 0 -0.08124871133135658 -0.0229857821168354 0.010179693345230044 0.010179693345230044
14 changes: 7 additions & 7 deletions Test/data_output/mrdCalculation01/mrdCalculation01_monitoring_counts_unfiltered.tsv
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
chr pos REF ALT m_REF_1-fold m_ALT_1-fold m_OTHER_1-fold m_AF_1-fold p_value_1-fold outlier_1-fold fold-change_1-fold z_stats_mean-1-fold z_stats_median-1-fold z_stats_median_wo0-1-fold m_REF_2-fold m_ALT_2-fold m_OTHER_2-fold m_AF_2-fold p_value_2-fold outlier_2-fold fold-change_2-fold z_stats_mean-2-fold z_stats_median-2-fold z_stats_median_wo0-2-fold m_REF_3-fold m_ALT_3-fold m_OTHER_3-fold m_AF_3-fold p_value_3-fold outlier_3-fold fold-change_3-fold z_stats_mean-3-fold z_stats_median-3-fold z_stats_median_wo0-3-fold m_REF_4-fold m_ALT_4-fold m_OTHER_4-fold m_AF_4-fold p_value_4-fold outlier_4-fold fold-change_4-fold z_stats_mean-4-fold z_stats_median-4-fold z_stats_median_wo0-4-fold
chr1 114713909 G T 2504 29 0 0.011448874851954205 3.2725341e-20 0 0.050621893129207285 0.015028680413008413 0.0076455713808351285 0.0 1775 20 0 0.011142061281337047 1.1770734e-14 0 0.06280272603625559 0.01828388348207656 0.021788646433384965 0.0 1484 18 0 0.011984021304926764 6.7920596e-14 0 0.09310064177317856 0.02772443360045362 0.03472680975350795 0.0026263725616405944 1324 15 0 0.011202389843166542 2.0244069e-11 0 0.0358744484963236 0.010609456120366676 0.01599300806711816 0.0
chr1 114713915 C T 2534 44 0 0.017067494181536073 6.6419743e-37 0 0.5662222951905567 0.168100665366646 0.15889236307473736 0.13973257345407947 1765 31 0 0.017260579064587972 2.3476196e-27 0 0.6464269958320554 0.18819558667945344 0.1926846227801652 0.1542217131199983 1467 28 0 0.018729096989966554 7.3953545e-26 0 0.7083404158458861 0.2109366428803136 0.21998676934662553 0.16736152249902214 1303 22 0 0.01660377358490566 1.467424e-19 0 0.5353353209461484 0.15831927277830143 0.1650153139662061 0.13578287744768225
chr3 179218303 G A 1734 36 0 0.020338983050847456 4.0560309e-33 0 0.8664350124813198 0.2572281298920798 0.24695709330846918 0.22109305223370795 1615 33 0 0.020024271844660196 4.7717457e-31 0 0.9100461006297815 0.26494354492872463 0.2698771705024083 0.22388260979122554 1528 33 0 0.02114029468289558 7.5905296e-32 0 0.9282734148384004 0.27643047526411174 0.28621262180871165 0.2262502632665008 1416 31 0 0.021423635107118175 3.4686634e-30 0 0.9810233809091866 0.2901263977305857 0.29799362332127 0.2569471378811878
chr7 55174771 AGGAATTAAGAGAAGC A 2506 17 0 0.006738010305192232 5.1365806e-09 0 -0.381677131219856 -0.1133127046714011 -0.11916550212453454 -0.11715711417694909 2346 17 0 0.007194244604316547 8.6499012e-10 0 -0.31376586574277743 -0.0913472852529041 -0.08847759930743443 -0.09950760504128318 2235 16 0 0.007107952021323856 2.996611e-09 0 -0.35166112288136064 -0.1047211411811558 -0.09919910014503866 -0.11646198790271603 2108 16 0 0.007532956685499058 1.3349425e-09 0 -0.3034345830324785 -0.08973729294862202 -0.08524538132421111 -0.09224417604323037
chr1 114713909 G T 2504 29 0 0.011448874851954205 3.2725341e-20 0 0.050621893129207285 0.015028680413008413 0.0076455713808351285 0.0 1775 20 0 0.011142061281337047 1.1770734e-14 0 0.06280272603625559 0.01828388348207656 0.021788646433384965 0.0 1484 18 0 0.011984021304926764 6.7920597e-14 0 0.09310064177317856 0.02772443360045362 0.03472680975350795 0.0026263725616405944 1324 15 0 0.011202389843166542 2.0244068e-11 0 0.0358744484963236 0.010609456120366676 0.01599300806711816 0.0
chr1 114713915 C T 2534 44 0 0.017067494181536073 6.6419743e-37 0 0.5662222951905567 0.168100665366646 0.15889236307473736 0.13973257345407947 1765 31 0 0.017260579064587972 2.3476197e-27 0 0.6464269958320554 0.18819558667945344 0.1926846227801652 0.1542217131199983 1467 28 0 0.018729096989966554 7.3953546e-26 0 0.7083404158458861 0.2109366428803136 0.21998676934662553 0.16736152249902214 1303 22 0 0.01660377358490566 1.467424e-19 0 0.5353353209461484 0.15831927277830143 0.1650153139662061 0.13578287744768225
chr3 179218303 G A 1734 36 0 0.020338983050847456 4.0560309e-33 0 0.8664350124813198 0.2572281298920798 0.24695709330846918 0.22109305223370795 1615 33 0 0.020024271844660196 4.7717457e-31 0 0.9100461006297815 0.26494354492872463 0.2698771705024083 0.22388260979122554 1528 33 0 0.02114029468289558 7.5905297e-32 0 0.9282734148384004 0.27643047526411174 0.28621262180871165 0.2262502632665008 1416 31 0 0.021423635107118175 3.4686635e-30 0 0.9810233809091866 0.2901263977305857 0.29799362332127 0.2569471378811878
chr7 55174771 AGGAATTAAGAGAAGC A 2506 17 0 0.006738010305192232 5.1365806e-09 0 -0.381677131219856 -0.1133127046714011 -0.11916550212453454 -0.11715711417694909 2346 17 0 0.007194244604316547 8.6499009e-10 0 -0.31376586574277743 -0.0913472852529041 -0.08847759930743443 -0.09950760504128318 2235 16 0 0.007107952021323856 2.996611e-09 0 -0.35166112288136064 -0.1047211411811558 -0.09919910014503866 -0.11646198790271603 2108 16 0 0.007532956685499058 1.3349425e-09 0 -0.3034345830324785 -0.08973729294862202 -0.08524538132421111 -0.09224417604323037
chr7 55181316 GG GGCCAGCGTGG 2490 0 0 0.0 1.0 0 -1.0 -0.2968810426478762 -0.30054501571699865 -0.2847284452595773 2347 0 0 0.0 1.0 0 -1.0 -0.2911320039120821 -0.28941964103816625 -0.28084379899976375 2267 0 0 0.0 1.0 0 -1.0 -0.2977899300415002 -0.29442580563344534 -0.2900596755576607 2179 0 0 0.0 1.0 0 -1.0 -0.2957385148779066 -0.2930770461689637 -0.2816116758084821
chr7 55181378 C T 2373 22 0 0.00918580375782881 8.2089657e-14 0 -0.15705196722311998 -0.046625751779099944 -0.05327370830048603 -0.056281575480076854 2248 17 0 0.0075055187637969095 4.6124268e-10 0 -0.284074499227454 -0.08270317822040987 -0.07978341825241822 -0.09166171232254983 2174 16 0 0.0073059360730593605 2.042838e-09 0 -0.33360236876983695 -0.09934342605764848 -0.09376127866796431 -0.11162661852054633 2085 16 0 0.007615421227986673 1.1455881e-09 0 -0.2958091643793357 -0.08748216296081929 -0.08297021317027045 -0.09017113820667598
chr7 55191822 T G 2403 28 1 0.011517893870835048 1.2282736e-19 0 0.056955519203051086 0.01690901392555294 0.009503484252174862 0.0017164724213864148 2274 22 0 0.009581881533101045 1.1810273e-14 0 -0.08601742919922195 -0.025042426534135135 -0.021788646433384965 -0.03932547098363418 2175 21 0 0.009562841530054645 4.5052666e-14 0 -0.12774285461420765 -0.03804053573886641 -0.03177321014327934 -0.05650616083951149 2070 21 0 0.010043041606886656 1.7820928e-14 0 -0.07132939208454903 -0.021094848482228427 -0.01599300806711816 -0.029144316903374254
chr12 25245350 C T 1909 21 0 0.010880829015544042 1.1998693e-14 0 -0.0015056215611591872 -0.0004469904989100509 -0.0076455713808351285 -0.014127048284542542 1772 20 0 0.011160714285714286 1.1414564e-14 0 0.06458197167136093 0.018801878829276607 0.022309642450357433 0.0004701626099326456 1664 20 0 0.011876484560570071 3.3881159e-15 0 0.08329187380794023 0.024803481274291998 0.031773210143279294 0.0 1552 19 0 0.0120942075111394 1.1923061e-14 0 0.11833998914470478 0.034997692640322556 0.04059794851892759 0.022418990189548578
chr7 55181378 C T 2373 22 0 0.00918580375782881 8.2089656e-14 0 -0.15705196722311998 -0.046625751779099944 -0.05327370830048603 -0.056281575480076854 2248 17 0 0.0075055187637969095 4.6124268e-10 0 -0.284074499227454 -0.08270317822040987 -0.07978341825241822 -0.09166171232254983 2174 16 0 0.0073059360730593605 2.0428379e-09 0 -0.33360236876983695 -0.09934342605764848 -0.09376127866796431 -0.11162661852054633 2085 16 0 0.007615421227986673 1.1455882e-09 0 -0.2958091643793357 -0.08748216296081929 -0.08297021317027045 -0.09017113820667598
chr7 55191822 T G 2403 28 1 0.011517893870835048 1.2282736e-19 0 0.056955519203051086 0.01690901392555294 0.009503484252174862 0.0017164724213864148 2274 22 0 0.009581881533101045 1.1810273e-14 0 -0.08601742919922195 -0.025042426534135135 -0.021788646433384965 -0.03932547098363418 2175 21 0 0.009562841530054645 4.5052667e-14 0 -0.12774285461420765 -0.03804053573886641 -0.03177321014327934 -0.05650616083951149 2070 21 0 0.010043041606886656 1.7820928e-14 0 -0.07132939208454903 -0.021094848482228427 -0.01599300806711816 -0.029144316903374254
chr12 25245350 C T 1909 21 0 0.010880829015544042 1.1998693e-14 0 -0.0015056215611591872 -0.0004469904989100509 -0.0076455713808351285 -0.014127048284542542 1772 20 0 0.011160714285714286 1.1414563e-14 0 0.06458197167136093 0.018801878829276607 0.022309642450357433 0.0004701626099326456 1664 20 0 0.011876484560570071 3.3881159e-15 0 0.08329187380794023 0.024803481274291998 0.031773210143279294 0.0 1552 19 0 0.0120942075111394 1.1923061e-14 0 0.11833998914470478 0.034997692640322556 0.04059794851892759 0.022418990189548578

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