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Update ModelSegments expected results for Java 17.0.1+12.
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@cmnbroad
cmnbroad committed Jan 30, 2023
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Showing 23 changed files with 847 additions and 839 deletions.
6 changes: 3 additions & 3 deletions ...ols/copynumber/model-segments-expected/multiple-sample-ac-nac-tumor-1.modelBegin.af.param
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@HD VN:1.6
@RG ID:GATKCopyNumber SM:SM-74P4M-1
PARAMETER_NAME POSTERIOR_10 POSTERIOR_20 POSTERIOR_30 POSTERIOR_40 POSTERIOR_50 POSTERIOR_60 POSTERIOR_70 POSTERIOR_80 POSTERIOR_90
MEAN_BIAS 1.092482 1.106161 1.113179 1.124902 1.131327 1.144333 1.154568 1.164827 1.180697
BIAS_VARIANCE 0.434015 0.446432 0.459002 0.467580 0.475156 0.484281 0.487932 0.492417 0.495571
OUTLIER_PROBABILITY 0.057314 0.069014 0.076118 0.079128 0.082268 0.089037 0.093737 0.100190 0.110147
MEAN_BIAS 1.070124 1.081592 1.099740 1.106582 1.112816 1.119808 1.130594 1.135492 1.150073
BIAS_VARIANCE 0.388637 0.426262 0.437928 0.448314 0.464513 0.477831 0.482795 0.487486 0.492007
OUTLIER_PROBABILITY 0.062308 0.070366 0.083632 0.092903 0.099303 0.105473 0.110069 0.119230 0.132290
382 changes: 191 additions & 191 deletions ...er/tools/copynumber/model-segments-expected/multiple-sample-ac-nac-tumor-1.modelBegin.seg
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6 changes: 3 additions & 3 deletions ...r/tools/copynumber/model-segments-expected/multiple-sample-ac-tumor-1.modelBegin.af.param
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@HD VN:1.6
@RG ID:GATKCopyNumber SM:SM-74P4M-1
PARAMETER_NAME POSTERIOR_10 POSTERIOR_20 POSTERIOR_30 POSTERIOR_40 POSTERIOR_50 POSTERIOR_60 POSTERIOR_70 POSTERIOR_80 POSTERIOR_90
MEAN_BIAS 1.116663 1.123408 1.127238 1.130430 1.140573 1.156446 1.161426 1.170822 1.176871
BIAS_VARIANCE 0.470922 0.474828 0.481765 0.486072 0.492303 0.493527 0.495814 0.497711 0.498807
OUTLIER_PROBABILITY 0.014787 0.020051 0.024841 0.028065 0.029756 0.035209 0.036907 0.040733 0.046803
MEAN_BIAS 1.114452 1.117621 1.129473 1.134714 1.140738 1.149446 1.152084 1.158532 1.179227
BIAS_VARIANCE 0.459764 0.470122 0.476033 0.481435 0.487104 0.493330 0.495130 0.496575 0.498652
OUTLIER_PROBABILITY 0.019421 0.025365 0.028088 0.033099 0.036928 0.042074 0.044188 0.046482 0.051940
576 changes: 288 additions & 288 deletions ...bender/tools/copynumber/model-segments-expected/multiple-sample-ac-tumor-1.modelBegin.seg
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6 changes: 3 additions & 3 deletions .../copynumber/model-segments-expected/multiple-sample-cr-ac-nac-tumor-1.modelBegin.af.param
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@HD VN:1.6
@RG ID:GATKCopyNumber SM:SM-74P4M-1
PARAMETER_NAME POSTERIOR_10 POSTERIOR_20 POSTERIOR_30 POSTERIOR_40 POSTERIOR_50 POSTERIOR_60 POSTERIOR_70 POSTERIOR_80 POSTERIOR_90
MEAN_BIAS 1.092310 1.098678 1.111646 1.117541 1.120565 1.125976 1.133225 1.136642 1.148982
BIAS_VARIANCE 0.451935 0.459585 0.465554 0.471289 0.475876 0.479446 0.482660 0.491585 0.495789
OUTLIER_PROBABILITY 0.045637 0.051060 0.054284 0.057989 0.064227 0.068471 0.077494 0.083395 0.093476
MEAN_BIAS 1.071919 1.083975 1.094159 1.107253 1.114895 1.126273 1.131272 1.146231 1.159403
BIAS_VARIANCE 0.411686 0.418478 0.431803 0.440233 0.451278 0.460688 0.476434 0.486997 0.495994
OUTLIER_PROBABILITY 0.050319 0.058925 0.064151 0.067747 0.070172 0.077448 0.084848 0.089142 0.098892
156 changes: 78 additions & 78 deletions ...tools/copynumber/model-segments-expected/multiple-sample-cr-ac-nac-tumor-1.modelBegin.seg
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@SQ SN:20 LN:63025520 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens
@RG ID:GATKCopyNumber SM:SM-74P4M-1
CONTIG START END NUM_POINTS_COPY_RATIO NUM_POINTS_ALLELE_FRACTION LOG2_COPY_RATIO_POSTERIOR_10 LOG2_COPY_RATIO_POSTERIOR_50 LOG2_COPY_RATIO_POSTERIOR_90 MINOR_ALLELE_FRACTION_POSTERIOR_10 MINOR_ALLELE_FRACTION_POSTERIOR_50 MINOR_ALLELE_FRACTION_POSTERIOR_90
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20 45890779 45891424 1 1 -0.268258 -0.088095 0.101311 0.465602 0.493225 0.498821
20 45904807 62905205 1317 245 0.092592 0.100428 0.105982 0.485187 0.495274 0.499313
6 changes: 3 additions & 3 deletions ...ools/copynumber/model-segments-expected/multiple-sample-cr-ac-tumor-1.modelBegin.af.param
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@HD VN:1.6
@RG ID:GATKCopyNumber SM:SM-74P4M-1
PARAMETER_NAME POSTERIOR_10 POSTERIOR_20 POSTERIOR_30 POSTERIOR_40 POSTERIOR_50 POSTERIOR_60 POSTERIOR_70 POSTERIOR_80 POSTERIOR_90
MEAN_BIAS 1.107480 1.127598 1.130514 1.139511 1.142812 1.148875 1.156153 1.165459 1.169052
BIAS_VARIANCE 0.452167 0.463604 0.476934 0.482244 0.485483 0.490797 0.492643 0.494530 0.498252
OUTLIER_PROBABILITY 0.005022 0.010228 0.012933 0.015383 0.017580 0.020834 0.025056 0.034416 0.041315
MEAN_BIAS 1.101501 1.111624 1.117474 1.127434 1.134135 1.139207 1.144321 1.159496 1.171021
BIAS_VARIANCE 0.439194 0.451545 0.458149 0.463372 0.471589 0.479536 0.483401 0.485951 0.491700
OUTLIER_PROBABILITY 0.003480 0.005827 0.009182 0.011244 0.014605 0.017407 0.020466 0.024670 0.028342
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