# HG changeset patch
# User iuc
# Date 1573237544 18000
# Node ID 45af4a9748cff0804e0fabc757cd64a03aecc110
# Parent  165732ee5a48a8c9db651cc4433afe08a7cb9d81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth commit 91a0182476a7fc26be7bef1677790518c4e88348"

diff -r 165732ee5a48 -r 45af4a9748cf exomedepth-a9701c421408/exomedepth.R
--- a/exomedepth-a9701c421408/exomedepth.R	Mon Jun 11 09:34:25 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-# Load ExomeDepth library (without warnings)
-suppressMessages(library(ExomeDepth))
-
-# Import parameters from xml wrapper (args_file)
-args  <- commandArgs(trailingOnly=TRUE)
-param <- read.table(args[1],sep="=", as.is=TRUE)
-
-# Set common parameters
-target      <- param[match("target",param[,1]),2]
-trans_prob  <- as.numeric(param[match("trans_prob",param[,1]),2])
-output      <- param[match("output",param[,1]),2]
-test_vs_ref <- as.logical(param[match("test_vs_ref",param[,1]),2])
-
-# Create symbolic links for multiple bam and bai 
-bam         <- param[param[,1]=="bam",2]
-bam_bai     <- param[param[,1]=="bam_bai",2]
-bam_label   <- param[param[,1]=="bam_label",2]
-bam_label   <- gsub(" ", "_", bam_label)
-
-for(i in 1:length(bam)){
-  stopifnot(file.symlink(bam[i], paste(bam_label[i], "bam", sep=".")))
-  stopifnot(file.symlink(bam_bai[i], paste(bam_label[i], "bam.bai", sep=".")))
-}
-
-# Generate read count data
-BAMFiles <- paste(bam_label, "bam", sep=".")
-sink("/dev/null")
-ExomeCount <- suppressMessages(getBamCounts(bed.file=target, bam.files = BAMFiles))
-sink()
-
-# Convert counts in a data frame
-ExomeCount.dafr <- as(ExomeCount[, colnames(ExomeCount)], 'data.frame')
-
-# Prepare the main matrix of read count data
-ExomeCount.mat <- as.matrix(ExomeCount.dafr[, grep(names(ExomeCount.dafr), pattern='.bam')])
-
-# Remove .bam from sample name
-colnames(ExomeCount.mat) <- gsub(".bam", "", colnames(ExomeCount.mat))
-
-# Set nsamples == 1 if mode is test vs reference, assuming test is sample 1
-nsamples <- ifelse(test_vs_ref, 1, ncol(ExomeCount.mat))
-
-# Loop over samples
-for (i in 1:nsamples){
-
-	# Create the aggregate reference set for this sample
-	my.choice <- suppressWarnings(suppressMessages(
-					select.reference.set(test.counts = ExomeCount.mat[,i],  
-                           				 reference.counts = subset(ExomeCount.mat, select=-i),  
-                           			     bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000,
-                           		         n.bins.reduced = 10000)))
-
-	my.reference.selected <- apply(X = ExomeCount.mat[, my.choice$reference.choice, drop=FALSE],
-                               	   MAR = 1,
-                               	   FUN = sum)
-                               
-	# Now create the ExomeDepth object for the CNVs call
-	all.exons<-suppressWarnings(suppressMessages(new('ExomeDepth',
-               test = ExomeCount.mat[,i],
-               reference = my.reference.selected,
-               formula = 'cbind(test,reference)~1')))
-
-
-	# Now call the CNVs
-	result <- try(all.exons<-suppressMessages(CallCNVs(x=all.exons,
-                            transition.probability = trans_prob,
-                            chromosome = ExomeCount.dafr$space,
-                            start = ExomeCount.dafr$start,
-                            end = ExomeCount.dafr$end,
-                            name = ExomeCount.dafr$names)), silent=T)
-
-	# Next if CNVs are not detected
-	if (class(result)=="try-error"){
-		next
-	}
-
-	# Compute correlation between ref and test
-	my.cor <- cor(all.exons@reference, all.exons@test)
-	n.call <- nrow(all.exons@CNV.calls)
-
-	# Write results
-	my.results <- cbind(all.exons@CNV.calls[,c(7,5,6,3)], 
-            		 	sample=colnames(ExomeCount.mat)[i],
-            			corr=my.cor,
-            			all.exons@CNV.calls[,c(4,9,12)])
-            			
-    	# Re-order by chr and position
-    	chrOrder<-c(paste("chr",1:22,sep=""),"chrX","chrY","chrM")
-    	my.results[,1] <- factor(my.results[,1], levels=chrOrder)
-    	my.results <- my.results[order(my.results[,1], my.results[,2], my.results[,3]),]
-    
-	write.table(sep='\t', quote=FALSE, file = output,
-            		x = my.results,
-       			row.names = FALSE, col.names = FALSE, dec=".", append=TRUE)
-}
diff -r 165732ee5a48 -r 45af4a9748cf exomedepth.R
--- a/exomedepth.R	Mon Jun 11 09:34:25 2018 -0400
+++ b/exomedepth.R	Fri Nov 08 13:25:44 2019 -0500
@@ -3,8 +3,7 @@
 
 # Import parameters from xml wrapper (args_file)
 args  <- commandArgs(trailingOnly=TRUE)
-eval(parse(text=args[[1]]))
-param <- read.table(mypars,sep="=", as.is=TRUE)
+param <- read.table(args[1],sep="=", as.is=TRUE)
 
 # Set common parameters
 target      <- param[match("target",param[,1]),2]
diff -r 165732ee5a48 -r 45af4a9748cf exomedepth.xml
--- a/exomedepth.xml	Mon Jun 11 09:34:25 2018 -0400
+++ b/exomedepth.xml	Fri Nov 08 13:25:44 2019 -0500
@@ -1,31 +1,17 @@
-<tool id="exomedepth" name="ExomeDepth" version="1.0.0">
-  <description>cnv caller</description>
-  <requirements>
-	  <requirement type="package" version="1.1.10">r-exomedepth</requirement>
-  </requirements>
-  <command>
-    R CMD BATCH --no-save --no-restore '--args mypars="$args_file"' $__tool_directory__/exomedepth.R
-  </command>
-  <inputs>
-    <param format="bed" name="targetFile" type="data" label="Target regions (BED)">
-      <validator type="unspecified_build" />
-    </param>
-    <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" />
-    <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
-      <param format="bam" name="input" type="data" label="BAM file">
-        <options>
-          <filter type="data_meta" ref="targetFile" key="dbkey"/>
-        </options>
-      </param>
-      <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
-           <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
-      </param>  
-    </repeat>
-    <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
-  </inputs>
-
-  <configfiles>
-    <configfile name="args_file">target=$targetFile
+<tool id="exomedepth" name="ExomeDepth" version="1.1.0">
+    <description>Calls copy number variants (CNVs) from targeted sequence data</description>
+    <requirements>
+        <requirement type="package" version="1.1.10">r-exomedepth</requirement>
+    </requirements>
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", ExomeDepth version" $(R --vanilla --slave -e "library(ExomeDepth); cat(sessionInfo()\$otherPkgs\$ExomeDepth\$Version)")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '${__tool_directory__}/exomedepth.R' '$args_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="args_file"><![CDATA[
+target=$targetFile
 test_vs_ref=$test_vs_ref
 #for $i in $inputs
 bam=${i.input}
@@ -38,13 +24,51 @@
 #end for
 trans_prob=$transition_probability
 output=$output
-</configfile>
-  </configfiles>
-  <outputs>
-    <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
-  </outputs>
-  <help>
-
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="targetFile" type="data" format="bed" label="Target regions (BED)">
+            <validator type="unspecified_build" />
+        </param>
+        <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" />
+        <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
+            <param name="input" type="data" format="bam" label="BAM file">
+                <options>
+                    <filter type="data_meta" ref="targetFile" key="dbkey"/>
+                </options>
+            </param>
+            <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
+                <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
+            </param>  
+        </repeat>
+        <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="targetFile" value="CNV_TruSeq_Chr2.bed" dbkey="hg19" ftype="bed"/>
+            <param name="test_vs_ref" value="True"/>
+            <repeat name="inputs">
+                <param name="input" value="CNV_case_small.bam"/>
+            </repeat>
+            <repeat name="inputs">
+                <param name="input" value="CNV_control_small.bam"/>
+            </repeat>
+            <param name="transition_probability" value="0.5"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="chr2" />
+                    <has_text text="97890544" />
+                    <has_text text="97890616" />
+                    <has_text text="deletion" />
+                    <has_text text="CNV_case_small" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: warningmark
 
 **Warning about counts for chromosome X**
@@ -92,30 +116,9 @@
 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often 
 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high 
 number in order to equalize the representation of each amplicon, which can discard the CNV information.
-
-**License and citation**
-
-This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
-
-.. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-You can use this tool only if you agree to the license terms of: `ExomeDepth`_.
-
-.. _ExomeDepth: http://cran.r-project.org/web/packages/ExomeDepth/
-
-If you use this tool, please cite:
-
-- |Cuccuru2014|_
-- |Plagnol2012|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
-.. |Plagnol2012| replace:: Plagnol, V., *et al.* (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. *Bioinformatics* 28(21), 2747-2754
-.. _Plagnol2012: http://bioinformatics.oxfordjournals.org/content/28/21/2747
-  </help>
+    ]]></help>
     <citations>
-    <citation type="doi">10.1093/bioinformatics/btu135</citation>
-    <citation type="doi">10.1093/bioinformatics/bts526</citation>
-  </citations>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+        <citation type="doi">10.1093/bioinformatics/bts526</citation>
+    </citations>
 </tool>
diff -r 165732ee5a48 -r 45af4a9748cf test-data/CNV_TruSeq_Chr2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CNV_TruSeq_Chr2.bed	Fri Nov 08 13:25:44 2019 -0500
@@ -0,0 +1,746 @@
+chr2	91824709	91825059	LOC654342
+chr2	91842946	91843023	LOC654342
+chr2	91843394	91843528	LOC654342
+chr2	91963368	91964133	GGT8P
+chr2	91968436	91970153	GGT8P
+chr2	92129159	92130494	FKSG73
+chr2	95426675	95426777	ANKRD20B
+chr2	95426875	95426910	ANKRD20B
+chr2	95455916	95455995	ANKRD20B
+chr2	95456835	95456888	ANKRD20B
+chr2	95458058	95458103	ANKRD20B
+chr2	95461541	95461763	ANKRD20B
+chr2	95463672	95463886	ANKRD20B
+chr2	95464479	95464758	ANKRD20B
+chr2	95472086	95472215	ANKRD20B
+chr2	95474216	95474328	ANKRD20B
+chr2	95479136	95479285	ANKRD20B
+chr2	95480827	95481750	ANKRD20B
+chr2	95482918	95483098	ANKRD20B
+chr2	95484506	95484669	ANKRD20B
+chr2	95488749	95488819	ANKRD20B
+chr2	95494751	95494823	ANKRD20B
+chr2	95494915	95494943	ANKRD20B
+chr2	95497752	95497833	ANKRD20B
+chr2	95511110	95511180	ANKRD20B
+chr2	95513762	95513899	ANKRD20B
+chr2	95514946	95515052	ANKRD20B
+chr2	95518947	95519120	ANKRD20B
+chr2	95519283	95519397	ANKRD20B
+chr2	95522712	95522820	ANKRD20B
+chr2	95537232	95537822	TEKT4
+chr2	95539265	95539335	TEKT4
+chr2	95539710	95539853	TEKT4
+chr2	95540521	95540743	TEKT4
+chr2	95541333	95541487	TEKT4
+chr2	95542298	95542568	TEKT4
+chr2	95691479	95691630	MAL
+chr2	95713704	95713871	MAL
+chr2	95715326	95715451	MAL
+chr2	95719126	95719735	MAL
+chr2	95752953	95753326	MRPS5
+chr2	95756131	95756267	MRPS5
+chr2	95766219	95766281	MRPS5
+chr2	95766582	95766639	MRPS5
+chr2	95767422	95767468	MRPS5
+chr2	95770385	95770475	MRPS5
+chr2	95772168	95772202	MRPS5
+chr2	95773920	95774153	MRPS5
+chr2	95775661	95775786	MRPS5
+chr2	95780811	95780948	MRPS5
+chr2	95783610	95783690	MRPS5
+chr2	95787479	95787754	MRPS5
+chr2	95813400	95816012	ZNF514
+chr2	95818419	95818514	ZNF514
+chr2	95818878	95819004	ZNF514
+chr2	95823096	95823184	ZNF514
+chr2	95824985	95825263	ZNF514
+chr2	95831183	95831605	ZNF2
+chr2	95841933	95842004	ZNF2
+chr2	95843228	95843354	ZNF2
+chr2	95845904	95846017	ZNF2
+chr2	95846848	95850062	ZNF2
+chr2	95940201	95940577	PROM2
+chr2	95941209	95941258	PROM2
+chr2	95941678	95941880	PROM2
+chr2	95941975	95942095	PROM2
+chr2	95942342	95942405	PROM2
+chr2	95942720	95942809	PROM2
+chr2	95943112	95943314	PROM2
+chr2	95943678	95943752	PROM2
+chr2	95944469	95944532	PROM2
+chr2	95944733	95944892	PROM2
+chr2	95945593	95945745	PROM2
+chr2	95946990	95947113	PROM2
+chr2	95947673	95947764	PROM2
+chr2	95947890	95947974	PROM2
+chr2	95950717	95950863	PROM2
+chr2	95951387	95951458	PROM2
+chr2	95952227	95952319	PROM2
+chr2	95952552	95952605	PROM2
+chr2	95952881	95952961	PROM2
+chr2	95953144	95953212	PROM2
+chr2	95953959	95954048	PROM2
+chr2	95954231	95954337	PROM2
+chr2	95954681	95954754	PROM2
+chr2	95954972	95957053	PROM2
+chr2	95963072	95963201	KCNIP3
+chr2	95976103	95976268	KCNIP3
+chr2	96012768	96012870	KCNIP3
+chr2	96040044	96040168	KCNIP3
+chr2	96040596	96040665	KCNIP3
+chr2	96040886	96040956	KCNIP3
+chr2	96047344	96047451	KCNIP3
+chr2	96048125	96048229	KCNIP3
+chr2	96048980	96049042	KCNIP3
+chr2	96049750	96051824	KCNIP3
+chr2	96068448	96068620	FAHD2A
+chr2	96071301	96071551	FAHD2A
+chr2	96072689	96072905	FAHD2A
+chr2	96076275	96076334	FAHD2A
+chr2	96076612	96076774	FAHD2A
+chr2	96078182	96078290	FAHD2A
+chr2	96078425	96078512	FAHD2A
+chr2	96078643	96078878	FAHD2A
+chr2	96146053	96146283	TRIM43B
+chr2	96147343	96147438	TRIM43B
+chr2	96148052	96148466	TRIM43B
+chr2	96150354	96150479	TRIM43B
+chr2	96257766	96257897	TRIM43
+chr2	96259768	96260182	TRIM43
+chr2	96260798	96260893	TRIM43
+chr2	96261950	96262180	TRIM43
+chr2	96263077	96263099	TRIM43
+chr2	96264840	96265467	TRIM43
+chr2	96676299	96676480	LOC729234
+chr2	96686873	96686981	LOC729234
+chr2	96687116	96687213	LOC729234
+chr2	96687695	96688023	GPAT2
+chr2	96688416	96688421	GPAT2
+chr2	96688472	96688705	LOC729234
+chr2	96688772	96688853	LOC729234
+chr2	96688883	96688974	GPAT2
+chr2	96689057	96689188	GPAT2
+chr2	96689671	96689748	GPAT2
+chr2	96689937	96690085	GPAT2
+chr2	96690175	96690415	GPAT2
+chr2	96690521	96690591	GPAT2
+chr2	96691233	96691351	GPAT2
+chr2	96691678	96691760	GPAT2
+chr2	96691931	96692053	GPAT2
+chr2	96696154	96696282	GPAT2
+chr2	96696492	96696596	GPAT2
+chr2	96697781	96697894	GPAT2
+chr2	96698045	96698167	GPAT2
+chr2	96778626	96781888	ADRA2B
+chr2	96789590	96790010	ASTL
+chr2	96795563	96795717	ASTL
+chr2	96795803	96795884	ASTL
+chr2	96798279	96798460	ASTL
+chr2	96799164	96799281	ASTL
+chr2	96799704	96799797	ASTL
+chr2	96801090	96801151	ASTL
+chr2	96803314	96803439	ASTL
+chr2	96804121	96804175	ASTL
+chr2	96808917	96809776	DUSP2
+chr2	96809893	96810112	DUSP2
+chr2	96810500	96810621	DUSP2
+chr2	96810706	96811179	DUSP2
+chr2	96850605	96852652	STARD7
+chr2	96852955	96853039	STARD7
+chr2	96858107	96858206	STARD7
+chr2	96858816	96858898	STARD7
+chr2	96858980	96859090	STARD7
+chr2	96860696	96860745	STARD7
+chr2	96861079	96861287	STARD7
+chr2	96873883	96874573	STARD7
+chr2	96905977	96906426	LOC285033
+chr2	96916314	96919853	TMEM127
+chr2	96920571	96920735	TMEM127
+chr2	96930876	96931250	TMEM127
+chr2	96931607	96931732	TMEM127
+chr2	96931884	96932227	CIAO1
+chr2	96933059	96933207	CIAO1
+chr2	96933363	96933474	CIAO1
+chr2	96933574	96933662	CIAO1
+chr2	96934195	96934396	CIAO1
+chr2	96935006	96935093	CIAO1
+chr2	96936849	96939892	CIAO1
+chr2	96940075	96940893	SNRNP200
+chr2	96940995	96941087	SNRNP200
+chr2	96942642	96942723	SNRNP200
+chr2	96942819	96942979	SNRNP200
+chr2	96943277	96943453	SNRNP200
+chr2	96943545	96943688	SNRNP200
+chr2	96943975	96944096	SNRNP200
+chr2	96944285	96944449	SNRNP200
+chr2	96944547	96944736	SNRNP200
+chr2	96945189	96945297	SNRNP200
+chr2	96947552	96947660	SNRNP200
+chr2	96948939	96949090	SNRNP200
+chr2	96949273	96949451	SNRNP200
+chr2	96949551	96949742	SNRNP200
+chr2	96950096	96950323	SNRNP200
+chr2	96950918	96951078	SNRNP200
+chr2	96952049	96952222	SNRNP200
+chr2	96952426	96952615	SNRNP200
+chr2	96952744	96952898	SNRNP200
+chr2	96953177	96953295	SNRNP200
+chr2	96953601	96953707	SNRNP200
+chr2	96954401	96954484	SNRNP200
+chr2	96954775	96954855	SNRNP200
+chr2	96954965	96955117	SNRNP200
+chr2	96955537	96955734	SNRNP200
+chr2	96956064	96956252	SNRNP200
+chr2	96956422	96956553	SNRNP200
+chr2	96957130	96957240	SNRNP200
+chr2	96957489	96957638	SNRNP200
+chr2	96958710	96958833	SNRNP200
+chr2	96959054	96959247	SNRNP200
+chr2	96961226	96961396	SNRNP200
+chr2	96962274	96962429	SNRNP200
+chr2	96962671	96962808	SNRNP200
+chr2	96963101	96963274	SNRNP200
+chr2	96963375	96963458	SNRNP200
+chr2	96964022	96964158	SNRNP200
+chr2	96964341	96964440	SNRNP200
+chr2	96964553	96964705	SNRNP200
+chr2	96965067	96965165	SNRNP200
+chr2	96966736	96966791	SNRNP200
+chr2	96967262	96967454	SNRNP200
+chr2	96968897	96969068	SNRNP200
+chr2	96970443	96970606	SNRNP200
+chr2	96971131	96971261	SNRNP200
+chr2	96991062	96991303	ITPRIPL1
+chr2	96991485	96991587	ITPRIPL1
+chr2	96991935	96994090	ITPRIPL1
+chr2	97001484	97001586	NCAPH
+chr2	97007380	97007632	NCAPH
+chr2	97007788	97007878	NCAPH
+chr2	97008494	97008586	NCAPH
+chr2	97008904	97009042	NCAPH
+chr2	97009843	97009967	NCAPH
+chr2	97017569	97017758	NCAPH
+chr2	97019044	97019135	NCAPH
+chr2	97019921	97020126	NCAPH
+chr2	97024783	97024931	NCAPH
+chr2	97025881	97025987	NCAPH
+chr2	97026326	97026448	NCAPH
+chr2	97030219	97030329	NCAPH
+chr2	97031614	97031796	NCAPH
+chr2	97032995	97033111	NCAPH
+chr2	97034710	97034801	NCAPH
+chr2	97035163	97035238	NCAPH
+chr2	97039030	97041274	NCAPH
+chr2	97163385	97164183	NEURL3
+chr2	97165115	97165186	NEURL3
+chr2	97166176	97166661	NEURL3
+chr2	97202464	97202567	ARID5A
+chr2	97213139	97213254	ARID5A
+chr2	97215058	97215196	ARID5A
+chr2	97215490	97215542	ARID5A
+chr2	97215925	97216022	ARID5A
+chr2	97216311	97216470	ARID5A
+chr2	97216836	97218370	ARID5A
+chr2	97258916	97261368	KIAA1310
+chr2	97267380	97267513	KIAA1310
+chr2	97267853	97268075	KIAA1310
+chr2	97268490	97268599	KIAA1310
+chr2	97269987	97270117	KIAA1310
+chr2	97270516	97270600	KIAA1310
+chr2	97271057	97271248	KIAA1310
+chr2	97274245	97274401	KIAA1310
+chr2	97274601	97274801	KIAA1310
+chr2	97275236	97275299	KIAA1310
+chr2	97276463	97276620	KIAA1310
+chr2	97276801	97276875	KIAA1310
+chr2	97278019	97278090	KIAA1310
+chr2	97278199	97278300	KIAA1310
+chr2	97278555	97278671	KIAA1310
+chr2	97279225	97279356	KIAA1310
+chr2	97285096	97285281	KIAA1310
+chr2	97285409	97285499	KIAA1310
+chr2	97297049	97297280	KIAA1310
+chr2	97302658	97302922	KIAA1310
+chr2	97304020	97304115	KIAA1310
+chr2	97308574	97308658	FER1L5
+chr2	97312138	97312190	FER1L5
+chr2	97312801	97312892	FER1L5
+chr2	97313515	97313623	FER1L5
+chr2	97315360	97315414	FER1L5
+chr2	97315917	97316026	FER1L5
+chr2	97317629	97317757	FER1L5
+chr2	97319377	97319439	FER1L5
+chr2	97326078	97326108	FER1L5
+chr2	97327062	97327177	FER1L5
+chr2	97327405	97327528	FER1L5
+chr2	97327952	97328004	FER1L5
+chr2	97329176	97329244	FER1L5
+chr2	97334488	97334531	FER1L5
+chr2	97334623	97334741	FER1L5
+chr2	97334780	97334874	FER1L5
+chr2	97335856	97335984	FER1L5
+chr2	97338814	97338991	FER1L5
+chr2	97350064	97350188	FER1L5
+chr2	97351066	97351166	FER1L5
+chr2	97351677	97351854	FER1L5
+chr2	97351932	97352087	FER1L5
+chr2	97353553	97353684	FER1L5
+chr2	97354950	97355113	FER1L5
+chr2	97355381	97355495	FER1L5
+chr2	97356224	97356320	FER1L5
+chr2	97356927	97357090	FER1L5
+chr2	97357182	97357349	FER1L5
+chr2	97357460	97357700	FER1L5
+chr2	97357841	97357918	FER1L5
+chr2	97359243	97359424	FER1L5
+chr2	97359648	97359809	FER1L5
+chr2	97360097	97360201	FER1L5
+chr2	97361194	97361398	FER1L5
+chr2	97361479	97361641	FER1L5
+chr2	97361789	97361814	FER1L5
+chr2	97363263	97363313	FER1L5
+chr2	97363397	97363498	FER1L5
+chr2	97363774	97363893	FER1L5
+chr2	97364408	97364569	FER1L5
+chr2	97364782	97364873	FER1L5
+chr2	97365287	97365457	FER1L5
+chr2	97365669	97365817	FER1L5
+chr2	97366069	97366208	FER1L5
+chr2	97367692	97367780	FER1L5
+chr2	97368016	97368138	FER1L5
+chr2	97368337	97368478	FER1L5
+chr2	97368715	97368814	FER1L5
+chr2	97368890	97369083	FER1L5
+chr2	97369260	97369369	FER1L5
+chr2	97369952	97370099	FER1L5
+chr2	97370205	97370480	FER1L5
+chr2	97371669	97373135	LMAN2L
+chr2	97373451	97373570	LMAN2L
+chr2	97377393	97377507	LMAN2L
+chr2	97377601	97377762	LMAN2L
+chr2	97378844	97378876	LMAN2L
+chr2	97399256	97399338	LMAN2L
+chr2	97400146	97400263	LMAN2L
+chr2	97403686	97403804	LMAN2L
+chr2	97405591	97405813	LMAN2L
+chr2	97426639	97428138	CNNM4
+chr2	97462749	97462892	CNNM4
+chr2	97463250	97463384	CNNM4
+chr2	97464794	97464963	CNNM4
+chr2	97465289	97465385	CNNM4
+chr2	97474298	97474479	CNNM4
+chr2	97475057	97477626	CNNM4
+chr2	97481991	97483239	CNNM3
+chr2	97490795	97490938	CNNM3
+chr2	97492570	97492719	CNNM3
+chr2	97493468	97493637	CNNM3
+chr2	97493836	97493932	CNNM3
+chr2	97494304	97494437	CNNM3
+chr2	97494733	97494871	CNNM3
+chr2	97498289	97501120	CNNM3
+chr2	97503652	97505381	ANKRD23
+chr2	97505464	97505562	ANKRD23
+chr2	97505734	97505832	ANKRD23
+chr2	97505969	97506067	ANKRD23
+chr2	97506153	97506251	ANKRD23
+chr2	97506524	97506649	ANKRD23
+chr2	97507797	97507922	ANKRD23
+chr2	97508102	97508248	ANKRD23
+chr2	97509703	97509758	ANKRD23
+chr2	97513731	97514181	ANKRD39
+chr2	97519138	97519341	ANKRD39
+chr2	97520075	97520178	ANKRD39
+chr2	97523625	97523756	ANKRD39
+chr2	97525474	97527192	SEMA4C
+chr2	97527316	97527386	SEMA4C
+chr2	97527474	97527631	SEMA4C
+chr2	97529419	97529531	SEMA4C
+chr2	97529663	97529885	SEMA4C
+chr2	97529975	97530119	SEMA4C
+chr2	97530442	97530617	SEMA4C
+chr2	97530701	97530852	SEMA4C
+chr2	97530941	97531057	SEMA4C
+chr2	97531178	97531274	SEMA4C
+chr2	97531403	97531501	SEMA4C
+chr2	97531604	97531666	SEMA4C
+chr2	97532020	97532168	SEMA4C
+chr2	97533515	97533660	SEMA4C
+chr2	97541620	97542045	FAM178B
+chr2	97543627	97543779	FAM178B
+chr2	97544153	97544230	FAM178B
+chr2	97559663	97559788	FAM178B
+chr2	97563651	97563831	FAM178B
+chr2	97568357	97568444	FAM178B
+chr2	97586902	97586999	FAM178B
+chr2	97587215	97587391	FAM178B
+chr2	97589227	97589320	FAM178B
+chr2	97594943	97595057	FAM178B
+chr2	97613555	97613639	FAM178B
+chr2	97617116	97617221	FAM178B
+chr2	97626025	97626177	FAM178B
+chr2	97633257	97633364	FAM178B
+chr2	97636453	97636514	FAM178B
+chr2	97637638	97638059	FAM178B
+chr2	97638275	97638343	FAM178B
+chr2	97651978	97652301	FAM178B
+chr2	97749324	97749554	FAHD2B
+chr2	97749685	97749772	FAHD2B
+chr2	97749906	97750014	FAHD2B
+chr2	97751436	97751598	FAHD2B
+chr2	97751876	97751935	FAHD2B
+chr2	97755846	97756062	FAHD2B
+chr2	97757199	97757449	FAHD2B
+chr2	97760438	97760582	FAHD2B
+chr2	97779233	97779673	ANKRD36
+chr2	97783801	97783915	ANKRD36
+chr2	97784081	97784254	ANKRD36
+chr2	97788624	97788730	ANKRD36
+chr2	97790197	97790334	ANKRD36
+chr2	97792804	97792871	ANKRD36
+chr2	97808377	97808405	ANKRD36
+chr2	97808500	97808572	ANKRD36
+chr2	97810255	97810283	ANKRD36
+chr2	97810377	97810449	ANKRD36
+chr2	97812223	97812253	ANKRD36
+chr2	97815032	97815098	ANKRD36
+chr2	97817616	97817676	ANKRD36
+chr2	97818241	97818271	ANKRD36
+chr2	97820412	97820478	ANKRD36
+chr2	97823844	97823904	ANKRD36
+chr2	97824325	97824392	ANKRD36
+chr2	97827836	97827875	ANKRD36
+chr2	97830020	97830048	ANKRD36
+chr2	97830134	97830206	ANKRD36
+chr2	97833314	97833342	ANKRD36
+chr2	97833432	97833504	ANKRD36
+chr2	97845475	97845503	ANKRD36
+chr2	97845598	97845670	ANKRD36
+chr2	97847335	97847363	ANKRD36
+chr2	97847458	97847530	ANKRD36
+chr2	97849196	97849224	ANKRD36
+chr2	97849319	97849391	ANKRD36
+chr2	97851053	97851081	ANKRD36
+chr2	97851175	97851247	ANKRD36
+chr2	97852935	97852963	ANKRD36
+chr2	97853066	97853138	ANKRD36
+chr2	97854824	97854852	ANKRD36
+chr2	97854955	97855027	ANKRD36
+chr2	97856715	97856743	ANKRD36
+chr2	97856846	97856918	ANKRD36
+chr2	97858595	97858623	ANKRD36
+chr2	97858718	97858790	ANKRD36
+chr2	97860463	97860491	ANKRD36
+chr2	97860582	97860654	ANKRD36
+chr2	97862330	97862358	ANKRD36
+chr2	97862453	97862525	ANKRD36
+chr2	97864200	97864228	ANKRD36
+chr2	97864323	97864395	ANKRD36
+chr2	97866071	97866099	ANKRD36
+chr2	97866190	97866262	ANKRD36
+chr2	97867939	97867967	ANKRD36
+chr2	97868058	97868130	ANKRD36
+chr2	97869805	97869833	ANKRD36
+chr2	97869928	97870000	ANKRD36
+chr2	97871677	97871705	ANKRD36
+chr2	97871800	97871872	ANKRD36
+chr2	97873548	97873576	ANKRD36
+chr2	97873671	97873743	ANKRD36
+chr2	97875418	97875446	ANKRD36
+chr2	97875537	97875609	ANKRD36
+chr2	97877283	97877311	ANKRD36
+chr2	97877406	97877478	ANKRD36
+chr2	97881038	97881066	ANKRD36
+chr2	97881162	97881312	ANKRD36
+chr2	97882914	97882942	ANKRD36
+chr2	97883037	97883109	ANKRD36
+chr2	97884787	97884815	ANKRD36
+chr2	97884911	97884983	ANKRD36
+chr2	97890543	97890616	ANKRD36
+chr2	97899467	97899608	ANKRD36
+chr2	97909583	97909766	ANKRD36
+chr2	97910894	97911808	ANKRD36
+chr2	97914881	97914951	ANKRD36
+chr2	97915881	97915910	ANKRD36
+chr2	98123499	98123528	ANKRD36B
+chr2	98124027	98124120	ANKRD36B
+chr2	98124458	98124528	ANKRD36B
+chr2	98127601	98128515	ANKRD36B
+chr2	98129643	98129826	ANKRD36B
+chr2	98139789	98139930	ANKRD36B
+chr2	98148774	98148847	ANKRD36B
+chr2	98152763	98152835	ANKRD36B
+chr2	98152931	98152959	ANKRD36B
+chr2	98154631	98154703	ANKRD36B
+chr2	98154798	98154826	ANKRD36B
+chr2	98156497	98156569	ANKRD36B
+chr2	98156664	98156692	ANKRD36B
+chr2	98158374	98158446	ANKRD36B
+chr2	98158542	98158570	ANKRD36B
+chr2	98162129	98162201	ANKRD36B
+chr2	98162296	98162324	ANKRD36B
+chr2	98163999	98164071	ANKRD36B
+chr2	98164166	98164194	ANKRD36B
+chr2	98165882	98165954	ANKRD36B
+chr2	98166049	98166077	ANKRD36B
+chr2	98167752	98167824	ANKRD36B
+chr2	98167915	98167943	ANKRD36B
+chr2	98169631	98169703	ANKRD36B
+chr2	98169806	98169834	ANKRD36B
+chr2	98171523	98171595	ANKRD36B
+chr2	98171689	98171717	ANKRD36B
+chr2	98173400	98173472	ANKRD36B
+chr2	98173567	98173595	ANKRD36B
+chr2	98175262	98175334	ANKRD36B
+chr2	98175429	98175457	ANKRD36B
+chr2	98177128	98177200	ANKRD36B
+chr2	98177295	98177323	ANKRD36B
+chr2	98192842	98192909	ANKRD36B
+chr2	98195369	98195506	ANKRD36B
+chr2	98196925	98197031	ANKRD36B
+chr2	98201407	98201580	ANKRD36B
+chr2	98201747	98201861	ANKRD36B
+chr2	98205988	98206428	ANKRD36B
+chr2	98262521	98262652	COX5B
+chr2	98263530	98263603	COX5B
+chr2	98263807	98263906	COX5B
+chr2	98264459	98264656	COX5B
+chr2	98272402	98273423	ACTR1B
+chr2	98273615	98273655	ACTR1B
+chr2	98273911	98273972	ACTR1B
+chr2	98274406	98274580	ACTR1B
+chr2	98274687	98274779	ACTR1B
+chr2	98274890	98275106	ACTR1B
+chr2	98275342	98275466	ACTR1B
+chr2	98275815	98275940	ACTR1B
+chr2	98277034	98277109	ACTR1B
+chr2	98278345	98278409	ACTR1B
+chr2	98280306	98280561	ACTR1B
+chr2	98330031	98330137	ZAP70
+chr2	98330379	98330457	ZAP70
+chr2	98340479	98340901	ZAP70
+chr2	98341555	98341715	ZAP70
+chr2	98349346	98349484	ZAP70
+chr2	98349588	98349675	ZAP70
+chr2	98349760	98349806	ZAP70
+chr2	98350007	98350058	ZAP70
+chr2	98350869	98351175	ZAP70
+chr2	98351713	98351919	ZAP70
+chr2	98353936	98354128	ZAP70
+chr2	98354220	98354360	ZAP70
+chr2	98354458	98354570	ZAP70
+chr2	98355838	98356323	ZAP70
+chr2	98372803	98373846	TMEM131
+chr2	98375356	98375516	TMEM131
+chr2	98376115	98376212	TMEM131
+chr2	98377056	98377152	TMEM131
+chr2	98377256	98377377	TMEM131
+chr2	98378498	98378663	TMEM131
+chr2	98382577	98382726	TMEM131
+chr2	98382941	98383065	TMEM131
+chr2	98388760	98388887	TMEM131
+chr2	98392306	98392481	TMEM131
+chr2	98408849	98409447	TMEM131
+chr2	98409858	98410016	TMEM131
+chr2	98411393	98411578	TMEM131
+chr2	98412681	98412867	TMEM131
+chr2	98413307	98413449	TMEM131
+chr2	98413828	98413979	TMEM131
+chr2	98418358	98418424	TMEM131
+chr2	98418891	98419000	TMEM131
+chr2	98419115	98419253	TMEM131
+chr2	98421551	98421668	TMEM131
+chr2	98421839	98421914	TMEM131
+chr2	98422014	98422166	TMEM131
+chr2	98426151	98426237	TMEM131
+chr2	98427591	98427695	TMEM131
+chr2	98428884	98429018	TMEM131
+chr2	98429102	98429212	TMEM131
+chr2	98430434	98430604	TMEM131
+chr2	98430698	98430851	TMEM131
+chr2	98431662	98431770	TMEM131
+chr2	98435076	98435184	TMEM131
+chr2	98449828	98449889	TMEM131
+chr2	98451084	98451140	TMEM131
+chr2	98451238	98451388	TMEM131
+chr2	98453540	98453620	TMEM131
+chr2	98458278	98458400	TMEM131
+chr2	98460608	98460724	TMEM131
+chr2	98475767	98475890	TMEM131
+chr2	98504515	98504583	TMEM131
+chr2	98525121	98525161	TMEM131
+chr2	98543889	98543950	TMEM131
+chr2	98611939	98612354	TMEM131
+chr2	98703595	98703826	VWA3B
+chr2	98709524	98709751	VWA3B
+chr2	98732115	98732209	VWA3B
+chr2	98735976	98736226	VWA3B
+chr2	98737762	98737921	VWA3B
+chr2	98744702	98744871	VWA3B
+chr2	98750287	98750402	VWA3B
+chr2	98779314	98779439	VWA3B
+chr2	98797479	98797675	VWA3B
+chr2	98804438	98804592	VWA3B
+chr2	98809361	98809499	VWA3B
+chr2	98810824	98810955	VWA3B
+chr2	98828393	98828491	VWA3B
+chr2	98834309	98834491	VWA3B
+chr2	98844665	98844795	VWA3B
+chr2	98846513	98846670	VWA3B
+chr2	98851111	98851230	VWA3B
+chr2	98852853	98852940	VWA3B
+chr2	98853037	98853193	VWA3B
+chr2	98866781	98866899	VWA3B
+chr2	98872587	98872637	VWA3B
+chr2	98887145	98887346	VWA3B
+chr2	98906974	98907085	VWA3B
+chr2	98914370	98914494	VWA3B
+chr2	98916542	98916679	VWA3B
+chr2	98920165	98920265	VWA3B
+chr2	98928282	98928495	VWA3B
+chr2	98928663	98929408	VWA3B
+chr2	98962618	98962997	CNGA3
+chr2	98986402	98986539	CNGA3
+chr2	98994150	98994263	CNGA3
+chr2	98996638	98996817	CNGA3
+chr2	98999851	98999904	CNGA3
+chr2	99006121	99006237	CNGA3
+chr2	99008327	99008433	CNGA3
+chr2	99012307	99015057	CNGA3
+chr2	99061321	99061548	INPP4A
+chr2	99135427	99135488	INPP4A
+chr2	99136409	99136617	INPP4A
+chr2	99137150	99137194	INPP4A
+chr2	99149840	99149958	INPP4A
+chr2	99152192	99152308	INPP4A
+chr2	99152592	99152671	INPP4A
+chr2	99154326	99154437	INPP4A
+chr2	99155354	99155444	INPP4A
+chr2	99155991	99156138	INPP4A
+chr2	99160340	99160470	INPP4A
+chr2	99162432	99162536	INPP4A
+chr2	99163049	99163157	INPP4A
+chr2	99165418	99165432	INPP4A
+chr2	99169249	99169432	INPP4A
+chr2	99170734	99170952	INPP4A
+chr2	99172016	99172154	INPP4A
+chr2	99175926	99175958	INPP4A
+chr2	99179928	99180100	INPP4A
+chr2	99181103	99181226	INPP4A
+chr2	99182103	99182229	INPP4A
+chr2	99182492	99182632	INPP4A
+chr2	99185034	99185131	INPP4A
+chr2	99189278	99189390	INPP4A
+chr2	99193452	99193606	INPP4A
+chr2	99198039	99198284	INPP4A
+chr2	99203939	99207495	INPP4A
+chr2	99215866	99217256	C2orf64
+chr2	99220571	99220654	C2orf64
+chr2	99224770	99224955	C2orf64
+chr2	99225042	99225189	UNC50
+chr2	99226219	99226502	UNC50
+chr2	99227238	99227358	UNC50
+chr2	99232670	99232809	UNC50
+chr2	99232895	99232996	UNC50
+chr2	99234631	99234975	UNC50
+chr2	99235571	99237968	MGAT4A
+chr2	99242186	99242298	MGAT4A
+chr2	99251685	99251751	MGAT4A
+chr2	99252980	99253058	MGAT4A
+chr2	99256271	99256464	MGAT4A
+chr2	99256584	99256691	MGAT4A
+chr2	99260386	99260516	MGAT4A
+chr2	99261891	99262005	MGAT4A
+chr2	99271908	99271983	MGAT4A
+chr2	99272815	99272928	MGAT4A
+chr2	99274681	99274727	MGAT4A
+chr2	99279509	99279642	MGAT4A
+chr2	99279804	99279936	MGAT4A
+chr2	99291498	99291638	MGAT4A
+chr2	99294767	99294934	MGAT4A
+chr2	99342702	99343030	MGAT4A
+chr2	99410309	99411134	C2orf55
+chr2	99412583	99412727	C2orf55
+chr2	99413813	99414000	C2orf55
+chr2	99438320	99440000	C2orf55
+chr2	99443438	99443632	C2orf55
+chr2	99448811	99448975	C2orf55
+chr2	99449325	99449460	C2orf55
+chr2	99454582	99454750	C2orf55
+chr2	99463194	99463273	C2orf55
+chr2	99552401	99552684	C2orf55
+chr2	99613725	99614684	TSGA10
+chr2	99634663	99634812	TSGA10
+chr2	99634999	99635103	TSGA10
+chr2	99636743	99636945	TSGA10
+chr2	99651693	99651902	TSGA10
+chr2	99681402	99681587	TSGA10
+chr2	99685351	99685461	TSGA10
+chr2	99688169	99688337	TSGA10
+chr2	99689481	99689536	TSGA10
+chr2	99695122	99695276	TSGA10
+chr2	99697745	99697860	TSGA10
+chr2	99720430	99720581	TSGA10
+chr2	99721822	99721899	TSGA10
+chr2	99721990	99722160	TSGA10
+chr2	99725296	99725454	TSGA10
+chr2	99725852	99725975	TSGA10
+chr2	99727313	99727378	TSGA10
+chr2	99734007	99734222	TSGA10
+chr2	99735014	99735149	TSGA10
+chr2	99743511	99743639	TSGA10
+chr2	99757891	99758037	TSGA10
+chr2	99758185	99758400	C2orf15
+chr2	99758748	99758864	C2orf15
+chr2	99763865	99763956	C2orf15
+chr2	99766946	99767926	C2orf15
+chr2	99771156	99771187	TSGA10
+chr2	99771418	99771514	LIPT1
+chr2	99771945	99772007	LIPT1
+chr2	99773190	99773317	LIPT1
+chr2	99778420	99779611	LIPT1
+chr2	99785726	99785933	MITD1
+chr2	99786013	99786073	MITD1
+chr2	99787000	99787115	MITD1
+chr2	99787806	99787892	MITD1
+chr2	99787973	99788109	MITD1
+chr2	99790378	99790479	MITD1
+chr2	99797294	99797492	MITD1
+chr2	99797578	99797712	MRPL30
+chr2	99802640	99802717	MRPL30
+chr2	99804640	99804720	MRPL30
+chr2	99811214	99811360	MRPL30
+chr2	99811579	99811652	MRPL30
+chr2	99812036	99814088	MRPL30
+chr2	99858711	99858945	LYG2
+chr2	99860462	99860600	LYG2
+chr2	99861725	99861921	LYG2
+chr2	99863143	99863283	LYG2
+chr2	99870681	99870748	LYG2
+chr2	99871483	99871570	LYG2
+chr2	99900702	99900974	LYG1
+chr2	99901151	99901283	LYG1
+chr2	99907700	99907884	LYG1
+chr2	99908999	99909103	LYG1
+chr2	99912091	99912165	LYG1
+chr2	99914922	99915012	LYG1
+chr2	99917513	99917639	LYG1
+chr2	99935489	99936262	TXNDC9
+chr2	99938418	99938672	TXNDC9
+chr2	99943998	99944116	TXNDC9
+chr2	99949485	99949705	TXNDC9
+chr2	99952702	99952860	TXNDC9
+chr2	99953834	99954052	EIF5B
+chr2	99976699	99976824	EIF5B
+chr2	99976928	99977012	EIF5B
+chr2	99977611	99978283	EIF5B
+chr2	99980108	99980325	EIF5B
+chr2	99980734	99980884	EIF5B
+chr2	99984956	99985054	EIF5B
+chr2	99985855	99985944	EIF5B
+chr2	99988119	99988193	EIF5B
+chr2	99992810	99993099	EIF5B
+chr2	99995482	99995589	EIF5B
+chr2	99995781	99995891	EIF5B
+chr2	99998622	99998689	EIF5B
+chr2	99999243	99999384	EIF5B
diff -r 165732ee5a48 -r 45af4a9748cf test-data/CNV_case_small.bam
Binary file test-data/CNV_case_small.bam has changed
diff -r 165732ee5a48 -r 45af4a9748cf test-data/CNV_control_small.bam
Binary file test-data/CNV_control_small.bam has changed