# HG changeset patch
# User iuc
# Date 1696001999 0
# Node ID 4653aeb60243d732ed405890e649564b161ecf30
# Parent  e3bbe8171af95b45e8319f9c07b49a71ea4aca1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22

diff -r e3bbe8171af9 -r 4653aeb60243 batch.xml
--- a/batch.xml	Sun May 14 20:10:48 2023 +0000
+++ b/batch.xml	Fri Sep 29 15:39:59 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 '$CNV_reference.input_sample_file' ./tumor.bam &&
@@ -112,35 +113,35 @@
     <outputs>
         <data name="out_sample_bintest" format="tabular" label="${tool.name} on ${on_string}: Sample Bintest" from_work_dir="tumor.bintest.cns" />
         <data name="out_sample_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Sample Antitarget Coverage" from_work_dir="tumor.antitargetcoverage.cnn" />
-        <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: rounded absolute scale copy numbers integer (not log2 ratios) " from_work_dir="tumor.call.cns" />
+        <data name="out_sample_call" format="tabular" label="${tool.name} on ${on_string}: Rounded absolute scale copy numbers integer (not log2 ratios)" from_work_dir="tumor.call.cns" />
         <data name="out_sample_targetcoverage_cnn" format="tabular" label="${tool.name} on ${on_string}: Sample Target Coverage" from_work_dir="tumor.targetcoverage.cnn" />
         <data name="out_sample_cns" format="tabular" label="${tool.name} on ${on_string}: CN segmentation calls" from_work_dir="tumor.cns" />
         <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Bin-Level log2 Ratios/Coverages" from_work_dir="tumor.cnr" />
         <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: Capture Antitarget" from_work_dir="capture.antitarget.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
+        <data name="out_control_targetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Target Coverage" from_work_dir="normal.targetcoverage.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Output Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
+        <data name="out_control_antitargetcoverage" format="tabular" label="${tool.name} on ${on_string}: Normal Sample Antitarget Coverage" from_work_dir="normal.antitargetcoverage.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Output Copy Number Reference Profile" from_work_dir="reference.cnn">
+        <data name="out_reference_cnn" format="tabular" label="${tool.name} on ${on_string}: Copy Number Reference Profile" from_work_dir="reference.cnn">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Output Capture Target" from_work_dir="capture.target.bed">
+        <data name="out_capture_target" format="bed" label="${tool.name} on ${on_string}: Capture Target" from_work_dir="capture.target.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'no'</filter>
         </data>
-        <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Output Reference Target" from_work_dir="reference.target-tmp.bed">
+        <data name="out_reference_target_bed" format="tabular" label="${tool.name} on ${on_string}: Reference Target" from_work_dir="reference.target-tmp.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
         </data>
-        <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Output Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
+        <data name="out_reference_antitarget_bed" format="bed" label="${tool.name} on ${on_string}: Reference Antitarget" from_work_dir="reference.antitarget-tmp.bed">
             <filter>(CNV_reference['CNV_reference_availabel']) == 'yes'</filter>
         </data>
-        <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Output Sample Diagram" from_work_dir="tumor-diagram.pdf">
+        <data name="out_sample_diagram_pdf" format="pdf" label="${tool.name} on ${on_string}: Sample Diagram" from_work_dir="tumor-diagram.pdf">
             <filter>output_section['diagram']</filter>
         </data>
-        <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Output Sample Scatter " from_work_dir="tumor-scatter.png">
+        <data name="out_sample_scatter_png" format="png" label="${tool.name} on ${on_string}: Sample Scatter pdf plot " from_work_dir="tumor-scatter.png">
             <filter>output_section['scatter']</filter>
         </data>
     </outputs>
diff -r e3bbe8171af9 -r 4653aeb60243 macros.xml
--- a/macros.xml	Sun May 14 20:10:48 2023 +0000
+++ b/macros.xml	Fri Sep 29 15:39:59 2023 +0000
@@ -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>
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/gene-breaks.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene-breaks.txt	Fri Sep 29 15:39:59 2023 +0000
@@ -0,0 +1,1 @@
+gene	chromosome	location	change	probes_left	probes_right
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/gene-sex.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene-sex.txt	Fri Sep 29 15:39:59 2023 +0000
@@ -0,0 +1,2 @@
+sample	sex	X_logratio	Y_logratio
+./sample.cnr	Female	NA	NA
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/gene_genemetrics.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_genemetrics.txt	Fri Sep 29 15:39:59 2023 +0000
@@ -0,0 +1,1 @@
+gene	chromosome	start	end	log2
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/gene_segmetrics.cns
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_segmetrics.cns	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/normal.bam.bai
Binary file test-data/normal.bam.bai has changed
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/ref-tas.cnn
--- a/test-data/ref-tas.cnn	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/ref-tas.cnn	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/reference.cnn.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.cnn.1	Fri Sep 29 15:39:59 2023 +0000
@@ -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
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/reference.cnn.2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.cnn.2	Fri Sep 29 15:39:59 2023 +0000
@@ -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	2485	2758	-	0.65974	31.7436	0.978131
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+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
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+chrM	8018	8269	-	-0.327905	6.7251	0.486152
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+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
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/sample-diagram.pdf
--- a/test-data/sample-diagram.pdf	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/sample-diagram.pdf	Fri Sep 29 15:39:59 2023 +0000
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/sample-heatmap.png
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/sample-scatter.pdf
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/test.targetcoverage.cnn
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.targetcoverage.cnn	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor-diagram.pdf
--- a/test-data/tumor-diagram.pdf	Sun May 14 20:10:48 2023 +0000
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diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor-scatter.pdf
Binary file test-data/tumor-scatter.pdf has changed
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor-scatter.png
Binary file test-data/tumor-scatter.png has changed
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor.bam.bai
Binary file test-data/tumor.bam.bai has changed
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor.call.cns
--- a/test-data/tumor.call.cns	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/tumor.call.cns	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor.cnr
--- a/test-data/tumor.cnr	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/tumor.cnr	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor.cns
--- a/test-data/tumor.cns	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/tumor.cns	Fri Sep 29 15:39:59 2023 +0000
@@ -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
diff -r e3bbe8171af9 -r 4653aeb60243 test-data/tumor.targetcoverage.cnn
--- a/test-data/tumor.targetcoverage.cnn	Sun May 14 20:10:48 2023 +0000
+++ b/test-data/tumor.targetcoverage.cnn	Fri Sep 29 15:39:59 2023 +0000
@@ -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