| Previous changeset 0:f64acbe71392 (2023-05-14) Next changeset 2:09cf7e38022a (2024-04-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22 |
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modified:
fix.xml macros.xml test-data/ref-tas.cnn test-data/sample-diagram.pdf test-data/sample-heatmap.png test-data/tumor-diagram.pdf test-data/tumor-scatter.png test-data/tumor.call.cns test-data/tumor.cnr test-data/tumor.cns test-data/tumor.targetcoverage.cnn |
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added:
test-data/gene-breaks.txt test-data/gene-sex.txt test-data/gene_genemetrics.txt test-data/gene_segmetrics.cns test-data/normal.bam.bai test-data/reference.cnn.1 test-data/reference.cnn.2 test-data/sample-scatter.pdf test-data/test.targetcoverage.cnn test-data/tumor-scatter.pdf test-data/tumor.bam.bai |
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| diff -r f64acbe71392 -r dc0fb5f07231 fix.xml --- a/fix.xml Sun May 14 20:11:33 2023 +0000 +++ b/fix.xml Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -4,6 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="xrefs"/> + <expand macro="creators"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input_target_file' ./tumor.targetcoverage.cnn && @@ -31,9 +32,9 @@ $no_rmask ]]></command> <inputs> - <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" /> - <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" /> - <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" /> + <param name="input_target_file" type="data" format="bam" label="Sample Target coverage cnn file" help="" /> + <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Sample Antitarget coverage cnn file" help="" /> + <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage cnn file" help="TAS-on-target coverage cnn file is also accepted" /> <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" /> <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" /> <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" /> @@ -41,7 +42,7 @@ <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" /> </inputs> <outputs> - <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" /> + <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="sample.cnr" /> </outputs> <tests> <test expect_num_outputs="1"> |
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| diff -r f64acbe71392 -r dc0fb5f07231 macros.xml --- a/macros.xml Sun May 14 20:11:33 2023 +0000 +++ b/macros.xml Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">0.1</token> <token name="@TOOL_VERSION@">0.9.10</token> <xml name="requirements"> <requirements> @@ -30,6 +30,25 @@ <xref type="bio.tools">cnvkit</xref> </xrefs> </xml> + <xml name="creators"> + <creator> + <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" /> + <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" /> + <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" /> + <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" /> + <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" /> + </creator> + </xml> + <xml name="creators_and_zahra"> + <creator> + <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" /> + <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" /> + <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" /> + <person givenName="zahra" familyName="Karimi" url="https://github.com/zahraK20" /> + <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" /> + <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" /> + </creator> + </xml> <xml name="shared"> <param argument="--method" type="select" label="Select the sequencing method of the input files" help=""> <option value="hybrid" selected="True">hybridization capture </option> @@ -168,7 +187,7 @@ <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label="skip repeat master correction" help="" /> </xml> <xml name="scatter_optional"> - <param argument="--segment" optional="true" type="data" format="cns" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" /> + <param argument="--segment" optional="true" type="data" format="tabular" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" /> <param argument="--chromosome" optional="true" type="text" label="Chromosome range" value="" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" /> <param argument="--gene" optional="true" type="text" label="Name of gene or genes comma-separated to display" value="" help="" /> <param argument="--range-list" optional="true" type="data" format="bed" label="Range list" help="File listing the chromosomal ranges to display, as BED"/> @@ -213,9 +232,25 @@ </when> </conditional> </xml> - <xml name="citations"> + <xml name="genemetrics_segmetrics_statistics"> + <param argument="--mean" type="boolean" checked="true" truevalue="--mean" falsevalue="" label="Mean log2-ratio" help="" /> + <param argument="--median" type="boolean" checked="false" truevalue="--median" falsevalue="" label="Median" help="" /> + <param argument="--mode" type="boolean" checked="false" truevalue="--mode" falsevalue="" label="mode" help="peak density of log2 ratios" /> + <param argument="--ttest" type="boolean" checked="false" truevalue="--ttest" falsevalue="" label="One-sample t-test" help="bin log2 ratios versus 0.0" /> + <param argument="--stdev" type="boolean" checked="false" truevalue="--stdev" falsevalue="" label="Standard deviation" help="" /> + <param argument="--sem" type="boolean" checked="false" truevalue="--sem" falsevalue="" label="Standard error of the mean" help="" /> + <param argument="--mad" type="boolean" checked="false" truevalue="--mad" falsevalue="" label="Median absolute deviation" help="" /> + <param argument="--mse" type="boolean" checked="false" truevalue="--mse" falsevalue="" label="mean squared error" help="" /> + <param argument="--iqr" type="boolean" checked="false" truevalue="--iqr" falsevalue="" label="Inter-quartile range" help="" /> + <param argument="--bivar" type="boolean" checked="false" truevalue="--bivar" falsevalue="" label="Tukeys biweight midvariance" help="" /> + <param argument="--ci" type="boolean" checked="false" truevalue="--ci" falsevalue="" label="confidence interval" help="" /> + <param argument="--pi" type="boolean" checked="false" truevalue="--pi" falsevalue="" label="prediction interval" help="" /> + <param argument="--alpha" type="boolean" checked="false" truevalue="--alpha" falsevalue="" label="alpha" help="" /> + <param argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="estimate confidence interval" help="number of bootstrp interations" /> + </xml> + <xml name="citations"> <citations> <citation type="doi">10.1371/journal.pcbi.1004873</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/gene-breaks.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene-breaks.txt Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,1 @@ +gene chromosome location change probes_left probes_right |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/gene-sex.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene-sex.txt Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,2 @@ +sample sex X_logratio Y_logratio +./sample.cnr Female NA NA |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/gene_genemetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_genemetrics.txt Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,1 @@ +gene chromosome start end log2 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/gene_segmetrics.cns --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_segmetrics.cns Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,2 @@ +chromosome start end gene log2 depth probes weight iqr +chrM 848 16023 - -1.39012 2.05471 54 42.33 1.01226 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/normal.bam.bai |
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| Binary file test-data/normal.bam.bai has changed |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/ref-tas.cnn --- a/test-data/ref-tas.cnn Sun May 14 20:11:33 2023 +0000 +++ b/test-data/ref-tas.cnn Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -1,38 +1,62 @@ chromosome start end gene log2 depth spread -chrM 576 647 - 13.2947 96.2958 19.7107 -chrM 647 1601 - 1.74063 22.022 2.58065 -chrM 1601 1670 - 0.474375 3.10145 0.703308 -chrM 1670 3229 - -0.147713 1.6068 0.218999 -chrM 3229 3304 - 0 1.57333 0 -chrM 3306 4262 - 0.0246175 1.8295 0.0364979 -chrM 4262 4331 - -10.4357 0 15.472 -chrM 4328 4400 - -2.11465 0.0972222 3.13518 -chrM 4401 4469 - 0.106455 1.82353 0.157829 -chrM 4469 5511 - 0.501029 3.54127 0.742825 -chrM 5511 5579 - 0.394622 3.20588 0.585067 -chrM 5586 5655 - -10.4457 0 15.4869 +chrM 576 848 - 3.256 91.9926 4.82735 +chrM 848 1121 - 0.884565 5.9011 1.31146 +chrM 1121 1394 - -0.165367 1.4359 0.245173 +chrM 1394 1667 - 0.909286 3.78022 1.34811 +chrM 1667 1940 - 0 1.80586 0 +chrM 1940 2212 - -2.82466 0.0404412 4.18784 +chrM 2212 2485 - -0.0642305 1.65201 0.0952281 +chrM 2485 2758 - 0.01695 4.0696 0.0251301 +chrM 2758 3031 - -0.315323 0.717949 0.467498 +chrM 3031 3304 - 0.157569 1.33333 0.233612 +chrM 3306 3579 - -0.387402 0.626374 0.574362 +chrM 3579 3853 - 0 2.30292 0 +chrM 3853 4126 - 0.202715 2.74359 0.300545 +chrM 4126 4400 - -0.259225 0.748175 0.384327 +chrM 4401 4695 - -0.0877248 0.94898 0.130061 +chrM 4695 4990 - 0.16791 5.01695 0.248943 +chrM 4990 5284 - -0.25963 1.73129 0.384927 +chrM 5284 5579 - 0.810516 5.97966 1.20167 +chrM 5586 5655 - -10.4795 0 15.5369 chrM 5656 5729 - 0 0 0 -chrM 5760 5826 - 0 1.06061 0 -chrM 5825 5891 - 0.627211 2.5303 0.929902 -chrM 5903 7445 - 0.845795 2.01297 1.25398 -chrM 7445 7514 - 0.118826 1.85507 0.176171 -chrM 7517 7585 - -0.884742 0.544118 1.31172 -chrM 7585 8269 - 0 1.85088 0 -chrM 8294 8364 - -10.0424 0 14.8889 -chrM 8365 8572 - -0.774496 0.623188 1.14827 -chrM 8526 9207 - 2.12113 2.88693 3.14479 -chrM 9206 9990 - 0 1.97194 0 -chrM 9990 10058 - -10.5541 0 15.6474 -chrM 10058 10404 - -0.412764 1.11272 0.611965 -chrM 10404 10469 - -10.5842 0 15.6921 -chrM 10469 10766 - 0 1.69024 0 -chrM 10759 12137 - 0.227328 2.3164 0.337036 -chrM 12137 12206 - -0.173094 1.76812 0.256628 -chrM 12206 12265 - 0 0.152542 0 -chrM 12265 12336 - -8.64364 0 12.8151 -chrM 12336 14148 - 0.0642475 2.15563 0.0952533 -chrM 14148 14673 - 0.148476 2.24762 0.220131 -chrM 14673 14742 - 1.10758 8.5942 1.64209 -chrM 14746 15887 - 0.490853 3.49167 0.727739 -chrM 15887 15953 - -10.4334 0 15.4685 +chrM 5760 5891 - 0.415822 1.79389 0.616498 +chrM 5903 6171 - 0.131623 2.15299 0.195144 +chrM 6171 6440 - 0 2.02974 0 +chrM 6440 6708 - -0.0963015 1.51493 0.142777 +chrM 6708 6977 - 0 2.03717 0 +chrM 6977 7245 - 0.40989 3.05597 0.607703 +chrM 7245 7514 - -0.047091 1.24907 0.0698171 +chrM 7517 7767 - 0.271996 1.944 0.403261 +chrM 7767 8018 - 0.07072 2.24701 0.104849 +chrM 8018 8269 - -0.415822 1.00797 0.616498 +chrM 8294 8364 - -10.0057 0 14.8345 +chrM 8365 8630 - 0 1.0717 0 +chrM 8630 8896 - 0.485791 2.07895 0.720233 +chrM 8896 9162 - 0.280695 3.66165 0.416158 +chrM 9162 9427 - 0.563397 3.60755 0.835292 +chrM 9427 9693 - -0.195679 0.808271 0.290114 +chrM 9693 9959 - 0 2.07143 0 +chrM 9959 10224 - -4.10122 0.00377358 6.08048 +chrM 10224 10490 - -0.248445 1.44361 0.368345 +chrM 10490 10756 - -0.0920355 1.82331 0.136452 +chrM 10756 11022 - -0.51737 1.12406 0.767054 +chrM 11022 11287 - 0.26621 4.27925 0.394683 +chrM 11287 11553 - 0.350607 2.93609 0.519809 +chrM 11553 11819 - -0.0341651 1.06015 0.0506531 +chrM 11819 12084 - 0.590516 2.40377 0.875498 +chrM 12084 12350 - -1.0261 0.736842 1.5213 +chrM 12350 12616 - -0.64663 0.736842 0.958694 +chrM 12616 12882 - 0.295587 2.48872 0.438237 +chrM 12882 13147 - 0.50247 4.50943 0.744962 +chrM 13147 13413 - -0.322016 1.47368 0.477422 +chrM 13413 13679 - 0.356127 2.95865 0.527993 +chrM 13679 13944 - -0.0012925 1.64906 0.00191626 +chrM 13944 14210 - -0.865739 0.890977 1.28355 +chrM 14210 14476 - -0.4233 2.21053 0.627585 +chrM 14476 14742 - 0.598181 4.45489 0.886863 +chrM 14746 14987 - 1.03347 8.14523 1.53222 +chrM 14987 15228 - 0.355932 2.48133 0.527704 +chrM 15228 15470 - 0 1.11157 0 +chrM 15470 15711 - 0.393765 3.9751 0.583796 +chrM 15711 15953 - -0.312504 0.809917 0.463318 chrM 15955 16023 - 0 0 0 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/reference.cnn.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.cnn.1 Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,62 @@ +chromosome start end gene log2 depth gc rmask spread +chrM 576 848 - 2.75864 493.485 0.444853 4.08996 +chrM 848 1121 - 0.525695 22.4469 0.428571 0.779395 +chrM 1121 1394 - -0.84681 4.59341 0.483516 1.25548 +chrM 1394 1667 - 0.38341 11.022 0.450549 0.568444 +chrM 1667 1940 - -0.04005 7.45055 0.406593 0.0593781 +chrM 1940 2212 - -1.22672 1.36029 0.411765 1.81873 +chrM 2212 2485 - 0.21482 10.6081 0.388278 0.318492 +chrM 2485 2758 - 0.64779 31.7436 0.479853 0.960413 +chrM 2758 3031 - -0.27752 5.35531 0.457875 0.411451 +chrM 3031 3304 - 0.359575 7.55678 0.424908 0.533106 +chrM 3306 3579 - 0.03537 10.9817 0.509158 0.0524396 +chrM 3579 3853 - 0.026615 12.719 0.485401 0.0394594 +chrM 3853 4126 - 0 7.17949 0.450549 0 +chrM 4126 4400 - -0.485607 1.65693 0.423358 0.719961 +chrM 4401 4695 - -0.343535 5.18707 0.442177 0.509325 +chrM 4695 4990 - 0.603865 17.7458 0.427119 0.89529 +chrM 4990 5284 - -0.43303 5.94218 0.428571 0.64201 +chrM 5284 5579 - 0.5605 20.8136 0.410169 0.830997 +chrM 5586 5655 - -0.008305 9.37681 0.449275 0.012313 +chrM 5656 5729 - -0.462405 4.76712 0.410959 0.685562 +chrM 5760 5891 - 0.02536 10.5954 0.442748 0.0375987 +chrM 5903 6171 - 0.008305 13.8097 0.473881 0.012313 +chrM 6171 6440 - 0.19261 13.5353 0.498141 0.285564 +chrM 6440 6708 - 0 11.3657 0.470149 0 +chrM 6708 6977 - -0.132195 7.80669 0.457249 0.195992 +chrM 6977 7245 - 0.107015 15.3321 0.458955 0.15866 +chrM 7245 7514 - -0.50723 2.52045 0.420074 0.752019 +chrM 7517 7767 - 0.316705 8.152 0.372 0.469547 +chrM 7767 8018 - 0.49084 19.2311 0.501992 0.727719 +chrM 8018 8269 - -0.371965 6.7251 0.446215 0.551475 +chrM 8294 8364 - -11.0488 0 0.342857 16.381 +chrM 8365 8630 - -0.331755 2.89811 0.426415 0.49186 +chrM 8630 8896 - 0.13461 7.87594 0.406015 0.199573 +chrM 8896 9162 - -0.03223 13.5451 0.466165 0.0477842 +chrM 9162 9427 - -0.31024 9.68302 0.498113 0.459962 +chrM 9427 9693 - -0.712625 3.43233 0.466165 1.05654 +chrM 9693 9959 - -0.272205 5.87594 0.443609 0.403571 +chrM 9959 10224 - -0.26954 3.59623 0.377358 0.39962 +chrM 10224 10490 - -0.09971 2.99624 0.349624 0.14783 +chrM 10490 10756 - -0.241135 7.1015 0.43985 0.357507 +chrM 10756 11022 - -0.2582 4.00376 0.424812 0.382807 +chrM 11022 11287 - 0.01037 11.2377 0.430189 0.0153746 +chrM 11287 11553 - 0.06726 10.2932 0.443609 0.0997197 +chrM 11553 11819 - 0 11.109 0.466165 0 +chrM 11819 12084 - 0.28666 11.1509 0.441509 0.425002 +chrM 12084 12350 - 0.40266 10.1353 0.417293 0.596984 +chrM 12350 12616 - 0 9.23684 0.428571 0 +chrM 12616 12882 - 0.16725 9.39474 0.406015 0.247965 +chrM 12882 13147 - 0.13976 15.834 0.520755 0.207208 +chrM 13147 13413 - -0.026615 8.90226 0.432331 0.0394594 +chrM 13413 13679 - 0.00138 12.218 0.462406 0.00204599 +chrM 13679 13944 - -0.82452 4.30943 0.467925 1.22243 +chrM 13944 14210 - 0.317015 8.87218 0.413534 0.470006 +chrM 14210 14476 - -0.24388 9.2218 0.477444 0.361576 +chrM 14476 14742 - 0.87922 33.8872 0.383459 1.30353 +chrM 14746 14987 - 0.43224 28.1369 0.481328 0.640839 +chrM 14987 15228 - 0.289845 14.2531 0.46888 0.429724 +chrM 15228 15470 - -0.008065 9.3719 0.466942 0.0119572 +chrM 15470 15711 - 0.01195 11.2946 0.46473 0.0177171 +chrM 15711 15953 - -0.03537 6.29752 0.404959 0.0524396 +chrM 15955 16023 - 0 4.13235 0.323529 0 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/reference.cnn.2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.cnn.2 Fri Sep 29 15:42:57 2023 +0000 |
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| @@ -0,0 +1,62 @@ +chromosome start end gene log2 depth spread +chrM 576 848 - 3.09865 493.485 4.59406 +chrM 848 1121 - 0.49908 22.4469 0.739936 +chrM 1121 1394 - -0.516145 4.59341 0.765237 +chrM 1394 1667 - 0.24243 11.022 0.359427 +chrM 1667 1940 - -0.16725 7.45055 0.247965 +chrM 1940 2212 - -1.38174 1.36029 2.04857 +chrM 2212 2485 - 0.08762 10.6081 0.129905 +chrM 2485 2758 - 0.65974 31.7436 0.978131 +chrM 2758 3031 - -0.403685 5.35531 0.598503 +chrM 3031 3304 - 0.131495 7.55678 0.194954 +chrM 3306 3579 - 0.401125 10.9817 0.594708 +chrM 3579 3853 - 0.25737 12.719 0.381577 +chrM 3853 4126 - 0 7.17949 0 +chrM 4126 4400 - -1.09463 1.65693 1.62289 +chrM 4401 4695 - -0.271425 5.18707 0.402415 +chrM 4695 4990 - 0.32592 17.7458 0.483209 +chrM 4990 5284 - -0.46781 5.94218 0.693575 +chrM 5284 5579 - 0.575175 20.8136 0.852754 +chrM 5586 5655 - 0 9.37681 0 +chrM 5656 5729 - -0.24822 4.76712 0.368011 +chrM 5760 5891 - 0.327905 10.5954 0.486152 +chrM 5903 6171 - 0.19112 13.8097 0.283355 +chrM 6171 6440 - 0.45739 13.5353 0.678126 +chrM 6440 6708 - 0 11.3657 0 +chrM 6708 6977 - -0.121345 7.80669 0.179906 +chrM 6977 7245 - 0.215935 15.3321 0.320145 +chrM 7245 7514 - -0.846735 2.52045 1.25537 +chrM 7517 7767 - -0.100975 8.152 0.149706 +chrM 7767 8018 - 0.710745 19.2311 1.05375 +chrM 8018 8269 - -0.327905 6.7251 0.486152 +chrM 8294 8364 - -11.6145 0 17.2197 +chrM 8365 8630 - -0.559835 2.89811 0.830011 +chrM 8630 8896 - 0 7.87594 0 +chrM 8896 9162 - 0.126545 13.5451 0.187616 +chrM 9162 9427 - 0 9.68302 0 +chrM 9427 9693 - -0.59913 3.43233 0.88827 +chrM 9693 9959 - -0.204945 5.87594 0.303851 +chrM 9959 10224 - -0.69093 3.59623 1.02437 +chrM 10224 10490 - -0.69078 2.99624 1.02415 +chrM 10490 10756 - -0.163025 7.1015 0.241701 +chrM 10756 11022 - -0.601845 4.00376 0.892295 +chrM 11022 11287 - 0.07448 11.2377 0.110424 +chrM 11287 11553 - 0.07811 10.2932 0.115806 +chrM 11553 11819 - 0.12266 11.109 0.181856 +chrM 11819 12084 - 0.25082 11.1509 0.371866 +chrM 12084 12350 - 0 10.1353 0 +chrM 12350 12616 - 0 9.23684 0 +chrM 12616 12882 - 0.13357 9.39474 0.198031 +chrM 12882 13147 - 0.41539 15.834 0.615857 +chrM 13147 13413 - -0.171695 8.90226 0.254555 +chrM 13413 13679 - 0.16774 12.218 0.248691 +chrM 13679 13944 - -0.61691 4.30943 0.914631 +chrM 13944 14210 - -0.096015 8.87218 0.142352 +chrM 14210 14476 - -0.146255 9.2218 0.216838 +chrM 14476 14742 - 0.926785 33.8872 1.37405 +chrM 14746 14987 - 0.792645 28.1369 1.17518 +chrM 14987 15228 - 0.179775 14.2531 0.266534 +chrM 15228 15470 - 0 9.3719 0 +chrM 15470 15711 - 0 11.2946 0 +chrM 15711 15953 - -0.131495 6.29752 0.194954 +chrM 15955 16023 - -0.10308 4.13235 0.152826 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/sample-diagram.pdf --- a/test-data/sample-diagram.pdf Sun May 14 20:11:33 2023 +0000 +++ b/test-data/sample-diagram.pdf Fri Sep 29 15:42:57 2023 +0000 |
| [ |
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| @@ -0,0 +1,62 @@ +chromosome start end gene depth log2 +chrM 576 848 - 91.9926 6.52345 +chrM 848 1121 - 5.9011 2.56098 +chrM 1121 1394 - 1.4359 0.521953 +chrM 1394 1667 - 3.78022 1.91847 +chrM 1667 1940 - 1.80586 0.852687 +chrM 1940 2212 - 0.0404412 -4.62803 +chrM 2212 2485 - 1.65201 0.724226 +chrM 2485 2758 - 4.0696 2.02489 +chrM 2758 3031 - 0.717949 -0.478047 +chrM 3031 3304 - 1.33333 0.415037 +chrM 3306 3579 - 0.626374 -0.674905 +chrM 3579 3853 - 2.30292 1.20346 +chrM 3853 4126 - 2.74359 1.45606 +chrM 4126 4400 - 0.748175 -0.418552 +chrM 4401 4695 - 0.94898 -0.075551 +chrM 4695 4990 - 5.01695 2.32681 +chrM 4990 5284 - 1.73129 0.79185 +chrM 5284 5579 - 5.97966 2.58006 +chrM 5586 5655 - 0 -20 +chrM 5656 5729 - 0 -20 +chrM 5760 5891 - 1.79389 0.843094 +chrM 5903 6171 - 2.15299 1.10634 +chrM 6171 6440 - 2.02974 1.02129 +chrM 6440 6708 - 1.51493 0.599247 +chrM 6708 6977 - 2.03717 1.02657 +chrM 6977 7245 - 3.05597 1.61163 +chrM 7245 7514 - 1.24907 0.320855 +chrM 7517 7767 - 1.944 0.959028 +chrM 7767 8018 - 2.24701 1.16801 +chrM 8018 8269 - 1.00797 0.01145 +chrM 8294 8364 - 0 -20 +chrM 8365 8630 - 1.0717 0.0998986 +chrM 8630 8896 - 2.07895 1.05585 +chrM 8896 9162 - 3.66165 1.8725 +chrM 9162 9427 - 3.60755 1.85102 +chrM 9427 9693 - 0.808271 -0.30709 +chrM 9693 9959 - 2.07143 1.05063 +chrM 9959 10224 - 0.00377358 -8.04985 +chrM 10224 10490 - 1.44361 0.52968 +chrM 10490 10756 - 1.82331 0.866559 +chrM 10756 11022 - 1.12406 0.168719 +chrM 11022 11287 - 4.27925 2.09736 +chrM 11287 11553 - 2.93609 1.5539 +chrM 11553 11819 - 1.06015 0.0842689 +chrM 11819 12084 - 2.40377 1.2653 +chrM 12084 12350 - 0.736842 -0.440573 +chrM 12350 12616 - 0.736842 -0.440573 +chrM 12616 12882 - 2.48872 1.3154 +chrM 12882 13147 - 4.50943 2.17295 +chrM 13147 13413 - 1.47368 0.559427 +chrM 13413 13679 - 2.95865 1.56494 +chrM 13679 13944 - 1.64906 0.721641 +chrM 13944 14210 - 0.890977 -0.166539 +chrM 14210 14476 - 2.21053 1.14439 +chrM 14476 14742 - 4.45489 2.15539 +chrM 14746 14987 - 8.14523 3.02596 +chrM 14987 15228 - 2.48133 1.31111 +chrM 15228 15470 - 1.11157 0.152599 +chrM 15470 15711 - 3.9751 1.99099 +chrM 15711 15953 - 0.809917 -0.304153 +chrM 15955 16023 - 0 -20 |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor-scatter.pdf |
| b |
| Binary file test-data/tumor-scatter.pdf has changed |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor-scatter.png |
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| Binary file test-data/tumor-scatter.png has changed |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor.bam.bai |
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| Binary file test-data/tumor.bam.bai has changed |
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| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor.call.cns --- a/test-data/tumor.call.cns Sun May 14 20:11:33 2023 +0000 +++ b/test-data/tumor.call.cns Fri Sep 29 15:42:57 2023 +0000 |
| b |
| @@ -1,2 +1,2 @@ -chromosome start end gene log2 cn depth probes weight -chrM 848 16023 - 0 2 2.05471 54 42.33 +chromosome start end gene log2 cn depth p_ttest probes weight +chrM 848 16023 - 0 2 2.06481 0.0731783 51 39.1851 |
| b |
| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor.cnr --- a/test-data/tumor.cnr Sun May 14 20:11:33 2023 +0000 +++ b/test-data/tumor.cnr Fri Sep 29 15:42:57 2023 +0000 |
| b |
| @@ -1,55 +1,52 @@ chromosome start end gene depth log2 weight -chrM 848 1121 - 5.9011 -0.545691 0.408064 -chrM 1394 1667 - 3.78022 0.488494 0.663959 -chrM 1667 1940 - 1.80586 0.0200539 0.951602 -chrM 2212 2485 - 1.65201 -0.234816 0.863481 -chrM 2485 2758 - 4.0696 0.153636 0.124621 -chrM 2758 3031 - 0.717949 -1.35597 0.802412 -chrM 3031 3304 - 1.33333 0.385198 0.698993 -chrM 3306 3579 - 0.626374 -1.37983 0.9523 -chrM 3579 3853 - 2.30292 0.471839 0.953456 -chrM 3853 4126 - 2.74359 0.444955 0.954775 -chrM 4126 4400 - 0.748175 0.465611 0.488348 -chrM 4401 4695 - 0.94898 -0.583114 0.722949 -chrM 4695 4990 - 5.01695 1.13235 0.235104 -chrM 4990 5284 - 1.73129 0.209867 0.585461 -chrM 5284 5579 - 5.97966 1.18493 0.334994 -chrM 5586 5655 - 0 -21.0389 0.909906 -chrM 5656 5729 - 0 -19.8096 0.489546 -chrM 5760 5891 - 1.79389 0 0.933441 -chrM 5903 6171 - 2.15299 -0.0283011 0.954219 -chrM 6171 6440 - 2.02974 -0.212606 0.881048 -chrM 6440 6708 - 1.51493 -0.38297 0.954355 -chrM 6708 6977 - 2.03717 -0.317296 0.919868 -chrM 6977 7245 - 3.05597 -0.127011 0.931699 -chrM 7245 7514 - 1.24907 0.72831 0.445461 -chrM 7517 7767 - 1.944 0.680162 0.754313 -chrM 7767 8018 - 2.24701 -0.510836 0.476217 -chrM 8018 8269 - 1.00797 -0.663743 0.679122 -chrM 8365 8630 - 1.0717 0.28099 0.736364 -chrM 8630 8896 - 2.07895 -0.154606 0.918337 -chrM 8896 9162 - 3.66165 0.147562 0.952129 -chrM 9162 9427 - 3.60755 0.937798 0.763689 -chrM 9693 9959 - 2.07143 0.459741 0.807601 -chrM 9959 10224 - 0.00377358 -8.75948 0.810371 -chrM 10224 10490 - 1.44361 0.509209 0.934515 -chrM 10490 10756 - 1.82331 0.0655732 0.839154 -chrM 10756 11022 - 1.12406 0.238204 0.822297 -chrM 11022 11287 - 4.27925 1.20043 0.953885 -chrM 11287 11553 - 2.93609 0.224804 0.945234 -chrM 11553 11819 - 1.06015 -1.50066 0.954184 -chrM 11819 12084 - 2.40377 0.0920864 0.791533 -chrM 12084 12350 - 0.736842 -1.15941 0.633433 -chrM 12350 12616 - 0.736842 -1.25242 0.954184 -chrM 12616 12882 - 2.48872 -0.187246 0.898846 -chrM 12882 13147 - 4.50943 0.419127 0.915456 -chrM 13147 13413 - 1.47368 -0.730007 0.952782 -chrM 13413 13679 - 2.95865 -0.0213761 0.95418 -chrM 13944 14210 - 0.890977 -0.337011 0.755369 -chrM 14210 14476 - 2.21053 -0.0427224 0.83652 -chrM 14746 14987 - 8.14523 0.722701 0.582259 -chrM 14987 15228 - 2.48133 -0.105067 0.78567 -chrM 15228 15470 - 1.11157 -0.96567 0.951837 -chrM 15470 15711 - 3.9751 0.576278 0.951583 -chrM 15711 15953 - 0.809917 -1.38778 0.949491 -chrM 15955 16023 - 0 -21.1972 0.909384 +chrM 848 1121 - 5.9011 1.10765 0.461544 +chrM 1121 1394 - 1.4359 0.5119 0.42727 +chrM 1394 1667 - 3.78022 1.00545 0.83803 +chrM 1667 1940 - 1.80586 -0.141849 0.898961 +chrM 2212 2485 - 1.65201 -0.341112 0.939111 +chrM 2485 2758 - 4.0696 0.227416 0.0932326 +chrM 2758 3031 - 0.717949 -0.74495 0.631914 +chrM 3031 3304 - 1.33333 -0.242655 0.920093 +chrM 3306 3579 - 0.626374 -1.60223 0.635989 +chrM 3579 3853 - 2.30292 0.419897 0.823341 +chrM 3853 4126 - 2.74359 0.492218 0.954299 +chrM 4401 4695 - 0.94898 -0.75838 0.810217 +chrM 4695 4990 - 5.01695 0.833877 0.745894 +chrM 4990 5284 - 1.73129 -0.166905 0.52302 +chrM 5284 5579 - 5.97966 1.47869 0.301566 +chrM 5586 5655 - 0 -20.2111 0.909096 +chrM 5656 5729 - 0 -19.9628 0.789733 +chrM 5760 5891 - 1.79389 -0.439065 0.721317 +chrM 5903 6171 - 2.15299 0.879609 0.881613 +chrM 6171 6440 - 2.02974 -0.56855 0.540091 +chrM 6440 6708 - 1.51493 -0.533208 0.953875 +chrM 6708 6977 - 2.03717 0.010185 0.924831 +chrM 6977 7245 - 3.05597 0.140146 0.861631 +chrM 7517 7767 - 1.944 -0.010185 0.932072 +chrM 8018 8269 - 1.00797 -0.730833 0.739629 +chrM 8365 8630 - 1.0717 -0.175653 0.333588 +chrM 8630 8896 - 2.07895 -0.906325 0.953701 +chrM 8896 9162 - 3.66165 0.578937 0.922022 +chrM 9162 9427 - 3.60755 0.713289 0.953614 +chrM 9427 9693 - 0.808271 -0.874973 0.24358 +chrM 9693 9959 - 2.07143 0.093785 0.870609 +chrM 10490 10756 - 1.82331 0.051865 0.901124 +chrM 10756 11022 - 1.12406 -0.367165 0.23713 +chrM 11022 11287 - 4.27925 0.646415 0.94264 +chrM 11287 11553 - 2.93609 0.0993253 0.941632 +chrM 11553 11819 - 1.06015 -0.671504 0.923937 +chrM 11819 12084 - 2.40377 -0.123249 0.829158 +chrM 12084 12350 - 0.736842 -1.27337 0.953701 +chrM 12350 12616 - 0.736842 -1.07369 0.953701 +chrM 12616 12882 - 2.48872 -0.24473 0.918407 +chrM 12882 13147 - 4.50943 0.330991 0.612262 +chrM 13147 13413 - 1.47368 0.0980097 0.895383 +chrM 13413 13679 - 2.95865 0.764085 0.898039 +chrM 13679 13944 - 1.64906 0.200821 0.200719 +chrM 13944 14210 - 0.890977 -1.20825 0.935464 +chrM 14210 14476 - 2.21053 0.220457 0.911385 +chrM 14987 15228 - 2.48133 0.0611491 0.887423 +chrM 15228 15470 - 1.11157 -0.517988 0.95146 +chrM 15470 15711 - 3.9751 0.858538 0.951359 +chrM 15711 15953 - 0.809917 -0.698856 0.917254 +chrM 15955 16023 - 0 -20.8746 0.88741 |
| b |
| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor.cns --- a/test-data/tumor.cns Sun May 14 20:11:33 2023 +0000 +++ b/test-data/tumor.cns Fri Sep 29 15:42:57 2023 +0000 |
| b |
| @@ -1,2 +1,2 @@ -chromosome start end gene log2 depth probes weight -chrM 848 16023 - -1.39012 2.05471 54 42.33 +chromosome start end gene log2 depth probes weight ci_lo ci_hi +chrM 848 16023 - -1.4129 2.06481 51 39.1851 -1.84016 -0.943 |
| b |
| diff -r f64acbe71392 -r dc0fb5f07231 test-data/tumor.targetcoverage.cnn --- a/test-data/tumor.targetcoverage.cnn Sun May 14 20:11:33 2023 +0000 +++ b/test-data/tumor.targetcoverage.cnn Fri Sep 29 15:42:57 2023 +0000 |
| b |
| @@ -1,38 +1,62 @@ chromosome start end gene depth log2 -chrM 576 647 - 96.2958 6.5894 -chrM 647 1601 - 22.022 4.46087 -chrM 1601 1670 - 3.10145 1.63294 -chrM 1670 3229 - 1.6068 0.68419 -chrM 3229 3304 - 1.57333 0.653824 -chrM 3306 4262 - 1.8295 0.871448 -chrM 4262 4331 - 0 -20 -chrM 4328 4400 - 0.0972222 -3.36257 -chrM 4401 4469 - 1.82353 0.866733 -chrM 4469 5511 - 3.54127 1.82427 -chrM 5511 5579 - 3.20588 1.68072 +chrM 576 848 - 91.9926 6.52345 +chrM 848 1121 - 5.9011 2.56098 +chrM 1121 1394 - 1.4359 0.521953 +chrM 1394 1667 - 3.78022 1.91847 +chrM 1667 1940 - 1.80586 0.852687 +chrM 1940 2212 - 0.0404412 -4.62803 +chrM 2212 2485 - 1.65201 0.724226 +chrM 2485 2758 - 4.0696 2.02489 +chrM 2758 3031 - 0.717949 -0.478047 +chrM 3031 3304 - 1.33333 0.415037 +chrM 3306 3579 - 0.626374 -0.674905 +chrM 3579 3853 - 2.30292 1.20346 +chrM 3853 4126 - 2.74359 1.45606 +chrM 4126 4400 - 0.748175 -0.418552 +chrM 4401 4695 - 0.94898 -0.075551 +chrM 4695 4990 - 5.01695 2.32681 +chrM 4990 5284 - 1.73129 0.79185 +chrM 5284 5579 - 5.97966 2.58006 chrM 5586 5655 - 0 -20 chrM 5656 5729 - 0 -20 -chrM 5760 5826 - 1.06061 0.0848889 -chrM 5825 5891 - 2.5303 1.33931 -chrM 5903 7445 - 2.01297 1.00933 -chrM 7445 7514 - 1.85507 0.891476 -chrM 7517 7585 - 0.544118 -0.878009 -chrM 7585 8269 - 1.85088 0.888209 +chrM 5760 5891 - 1.79389 0.843094 +chrM 5903 6171 - 2.15299 1.10634 +chrM 6171 6440 - 2.02974 1.02129 +chrM 6440 6708 - 1.51493 0.599247 +chrM 6708 6977 - 2.03717 1.02657 +chrM 6977 7245 - 3.05597 1.61163 +chrM 7245 7514 - 1.24907 0.320855 +chrM 7517 7767 - 1.944 0.959028 +chrM 7767 8018 - 2.24701 1.16801 +chrM 8018 8269 - 1.00797 0.01145 chrM 8294 8364 - 0 -20 -chrM 8365 8572 - 0.623188 -0.68226 -chrM 8526 9207 - 2.88693 1.52954 -chrM 9206 9990 - 1.97194 0.979615 -chrM 9990 10058 - 0 -20 -chrM 10058 10404 - 1.11272 0.154086 -chrM 10404 10469 - 0 -20 -chrM 10469 10766 - 1.69024 0.757224 -chrM 10759 12137 - 2.3164 1.21188 -chrM 12137 12206 - 1.76812 0.822213 -chrM 12206 12265 - 0.152542 -2.71272 -chrM 12265 12336 - 0 -20 -chrM 12336 14148 - 2.15563 1.10811 -chrM 14148 14673 - 2.24762 1.1684 -chrM 14673 14742 - 8.5942 3.10336 -chrM 14746 15887 - 3.49167 1.80392 -chrM 15887 15953 - 0 -20 +chrM 8365 8630 - 1.0717 0.0998986 +chrM 8630 8896 - 2.07895 1.05585 +chrM 8896 9162 - 3.66165 1.8725 +chrM 9162 9427 - 3.60755 1.85102 +chrM 9427 9693 - 0.808271 -0.30709 +chrM 9693 9959 - 2.07143 1.05063 +chrM 9959 10224 - 0.00377358 -8.04985 +chrM 10224 10490 - 1.44361 0.52968 +chrM 10490 10756 - 1.82331 0.866559 +chrM 10756 11022 - 1.12406 0.168719 +chrM 11022 11287 - 4.27925 2.09736 +chrM 11287 11553 - 2.93609 1.5539 +chrM 11553 11819 - 1.06015 0.0842689 +chrM 11819 12084 - 2.40377 1.2653 +chrM 12084 12350 - 0.736842 -0.440573 +chrM 12350 12616 - 0.736842 -0.440573 +chrM 12616 12882 - 2.48872 1.3154 +chrM 12882 13147 - 4.50943 2.17295 +chrM 13147 13413 - 1.47368 0.559427 +chrM 13413 13679 - 2.95865 1.56494 +chrM 13679 13944 - 1.64906 0.721641 +chrM 13944 14210 - 0.890977 -0.166539 +chrM 14210 14476 - 2.21053 1.14439 +chrM 14476 14742 - 4.45489 2.15539 +chrM 14746 14987 - 8.14523 3.02596 +chrM 14987 15228 - 2.48133 1.31111 +chrM 15228 15470 - 1.11157 0.152599 +chrM 15470 15711 - 3.9751 1.99099 +chrM 15711 15953 - 0.809917 -0.304153 chrM 15955 16023 - 0 -20 |
