Repository 'cnvkit_scatter'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_scatter

Changeset 1:3323a7867128 (2023-09-29)
Previous changeset 0:ec9731970f8b (2023-05-14) Next changeset 2:76f9a071da54 (2024-04-22)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
modified:
macros.xml
scatter.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
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
b
diff -r ec9731970f8b -r 3323a7867128 macros.xml
--- a/macros.xml Sun May 14 20:10:25 2023 +0000
+++ b/macros.xml Fri Sep 29 15:44:52 2023 +0000
b
@@ -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>
b
diff -r ec9731970f8b -r 3323a7867128 scatter.xml
--- a/scatter.xml Sun May 14 20:10:25 2023 +0000
+++ b/scatter.xml Fri Sep 29 15:44:52 2023 +0000
[
@@ -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_cnr_file' ./tumor.cnr &&
@@ -18,7 +19,7 @@
         #end if
         cnvkit.py scatter
             ./tumor.cnr
-            --output sample-scatter.png
+            --output sample-scatter.pdf
             #if $advanced_settings.segment
                 --segment ./segment.cns
             #end if
@@ -71,7 +72,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="input_cnr_file" type="data" format="tabular" label="cnn file" help="" />
+        <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
             <expand macro="scatter_optional" />
             <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
@@ -83,14 +84,14 @@
         </section>   
     </inputs>
     <outputs>
-        <data name="out_scatter_file" format="png" label="${tool.name} on ${on_string}: diagram pdf file" from_work_dir="sample-scatter.png" />
+        <data name="out_scatter_file" format="pdf" label="${tool.name} on ${on_string}: Sample Scatter pdf file" from_work_dir="sample-scatter.pdf" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
             <param name="zygosity_freq" value="0.25" />
             <param name="by_bin" value="1" />
-            <output name="out_scatter_file" file="sample-scatter.png" ftype="png" compare="sim_size">
+            <output name="out_scatter_file" file="sample-scatter.pdf" ftype="pdf" compare="sim_size">
                 <assert_contents><has_size value="12000" delta="5000" /></assert_contents>
             </output>
         </test>
b
diff -r ec9731970f8b -r 3323a7867128 test-data/gene-breaks.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene-breaks.txt Fri Sep 29 15:44:52 2023 +0000
b
@@ -0,0 +1,1 @@
+gene chromosome location change probes_left probes_right
b
diff -r ec9731970f8b -r 3323a7867128 test-data/gene-sex.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene-sex.txt Fri Sep 29 15:44:52 2023 +0000
b
@@ -0,0 +1,2 @@
+sample sex X_logratio Y_logratio
+./sample.cnr Female NA NA
b
diff -r ec9731970f8b -r 3323a7867128 test-data/gene_genemetrics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_genemetrics.txt Fri Sep 29 15:44:52 2023 +0000
b
@@ -0,0 +1,1 @@
+gene chromosome start end log2
b
diff -r ec9731970f8b -r 3323a7867128 test-data/gene_segmetrics.cns
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_segmetrics.cns Fri Sep 29 15:44:52 2023 +0000
b
@@ -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
b
diff -r ec9731970f8b -r 3323a7867128 test-data/normal.bam.bai
b
Binary file test-data/normal.bam.bai has changed
b
diff -r ec9731970f8b -r 3323a7867128 test-data/ref-tas.cnn
--- a/test-data/ref-tas.cnn Sun May 14 20:10:25 2023 +0000
+++ b/test-data/ref-tas.cnn Fri Sep 29 15:44:52 2023 +0000
b
@@ -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
b
diff -r ec9731970f8b -r 3323a7867128 test-data/reference.cnn.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.cnn.1 Fri Sep 29 15:44:52 2023 +0000
b
@@ -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
b
diff -r ec9731970f8b -r 3323a7867128 test-data/reference.cnn.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.cnn.2 Fri Sep 29 15:44:52 2023 +0000
b
@@ -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
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+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
b
diff -r ec9731970f8b -r 3323a7867128 test-data/sample-diagram.pdf
--- a/test-data/sample-diagram.pdf Sun May 14 20:10:25 2023 +0000
+++ b/test-data/sample-diagram.pdf Fri Sep 29 15:44:52 2023 +0000
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diff -r ec9731970f8b -r 3323a7867128 test-data/sample-heatmap.png
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diff -r ec9731970f8b -r 3323a7867128 test-data/sample-scatter.pdf
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diff -r ec9731970f8b -r 3323a7867128 test-data/test.targetcoverage.cnn
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+++ b/test-data/test.targetcoverage.cnn Fri Sep 29 15:44:52 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
b
diff -r ec9731970f8b -r 3323a7867128 test-data/tumor-diagram.pdf
--- a/test-data/tumor-diagram.pdf Sun May 14 20:10:25 2023 +0000
+++ b/test-data/tumor-diagram.pdf Fri Sep 29 15:44:52 2023 +0000
[
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diff -r ec9731970f8b -r 3323a7867128 test-data/tumor-scatter.pdf
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Binary file test-data/tumor-scatter.pdf has changed
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diff -r ec9731970f8b -r 3323a7867128 test-data/tumor-scatter.png
b
Binary file test-data/tumor-scatter.png has changed
b
diff -r ec9731970f8b -r 3323a7867128 test-data/tumor.bam.bai
b
Binary file test-data/tumor.bam.bai has changed
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diff -r ec9731970f8b -r 3323a7867128 test-data/tumor.call.cns
--- a/test-data/tumor.call.cns Sun May 14 20:10:25 2023 +0000
+++ b/test-data/tumor.call.cns Fri Sep 29 15:44:52 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 ec9731970f8b -r 3323a7867128 test-data/tumor.cnr
--- a/test-data/tumor.cnr Sun May 14 20:10:25 2023 +0000
+++ b/test-data/tumor.cnr Fri Sep 29 15:44:52 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
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+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 ec9731970f8b -r 3323a7867128 test-data/tumor.cns
--- a/test-data/tumor.cns Sun May 14 20:10:25 2023 +0000
+++ b/test-data/tumor.cns Fri Sep 29 15:44:52 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 ec9731970f8b -r 3323a7867128 test-data/tumor.targetcoverage.cnn
--- a/test-data/tumor.targetcoverage.cnn Sun May 14 20:10:25 2023 +0000
+++ b/test-data/tumor.targetcoverage.cnn Fri Sep 29 15:44:52 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