# HG changeset patch
# User rnateam
# Date 1437732339 14400
# Node ID f7f366ede872446c9d84fe86fcb601790673dda2

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty

diff -r 000000000000 -r f7f366ede872 piranha.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/piranha.xml	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,162 @@
+<tool id="piranha" name="Piranha" version="0.1.0">
+    <description>peak-caller for CLIP- and RIP-Seq data</description>
+    <requirements>
+        <requirement type="package" version="1.2.1">piranha</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        ln -s $input ./foo.$input.ext &&
+
+        Piranha
+        $sort
+        #if $p_threshold:
+            -p $p_threshold
+        #end if
+        $no_pval_correct
+        #if $background_thresh:
+            -a $background_thresh
+        #end if
+        #if $bin_size_reponse:
+            -b $bin_size_reponse
+        #end if
+        #if $bin_size_covars:
+            -i $bin_size_covars
+        #end if
+        #if $bin_size_both:
+            -z $bin_size_both
+        #end if
+        #if $merge_bins.merge=="yes":
+            -u $merge_bins.cluster_dist
+        #else:
+            -u $merge_bins.merge
+        #end if
+        $print_covars
+        $fit
+        #if $dist:
+            -d $dist
+        #end if
+        $fitMethod
+        #if $model:
+            -m $model
+        #end if
+        $stranded
+        $no_normalisation
+        $log_covars
+        ./foo.$input.ext
+        #for $covariate in $covariates:
+            $covariate.covariate_file
+        #end for
+
+        -o ./piranha.out
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/>
+        <repeat name="covariates" title="Choose covariate">
+            <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/>
+        </repeat>
+        <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/>
+        <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/>
+        <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c"
+            label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B &amp; H."/>
+        <param name="background_thresh" type="float" optional="true"
+            label="Indicates that this proportion of the lowest scores should be considered the background"/>
+        <param name="bin_size_reponse" type="integer" optional="true"
+            label="Indicates that input is raw reads and should be binned into bins of this size"/>
+        <param name="bin_size_covars" type="integer" optional="true"
+            label="Indicates that the covariates are raw reads and should be binned into bins of this size"/>
+        <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/>
+        <conditional name="merge_bins">
+            <param name="merge" type="select" label="Merge significant bins within certain distance?">
+                <option value="yes">Yes</option>
+                <option value="0" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance"
+                help="Default is 1 (merge adjacent)"/>
+            </when>
+        </conditional>
+        <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r"  label="Print covariate values in output" help="(-r)" />
+        <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />
+        <param name="dist" type="select" label="Select distribution type">
+            <option value="">None</option>
+            <option value="Poisson">Poisson</option>
+            <option value="NegativeBinomial">NegativeBinomial</option>
+            <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option>
+            <option value="ZeroTruncatedNegativeBinomial">ZeroTruncatedNegativeBinomial</option>
+            <option value="PoissonRegression">PoissonRegression</option>
+            <option value="NegativeBinomialRegression">NegativeBinomialRegression</option>
+            <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option>
+            <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>
+        </param>
+        <param name="fitMethod" type="boolean" checked="False" truevalue="-t"
+            falsevalue="" label="Use component fitting method"  help="(-t)"/>
+        <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>
+
+        <param name="stranded" type="boolean" checked="True" truevalue=""
+            falsevalue="-x" label="Preserve strand information"
+            help="If not set all the peaks will be associated to the positive strand. (-x)"/>
+        <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n" 
+            truevalue="" label="Normalise covariates?" help="(-n)"/>
+        <param name="log_covars" type="boolean" checked="False" truevalue="-l" 
+            falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_bed" from_work_dir="piranha.out"
+            label="${tool.name} on ${on_string}: BED with p-values">
+            <filter>fit is False</filter>
+        </data>
+        <data format="xml" name="output_xml" from_work_dir="piranha.out"
+            label="${tool.name} on ${on_string}: Model file">
+            <filter>fit is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/>
+            <repeat name="covariates">
+                <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/>
+            </repeat>
+            <repeat name="covariates">
+                <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/>
+            </repeat>
+            <param name="fit" value="True"/>
+            <param name="bin_size_reponse" value="1"/>
+            <param name="background_thresh" value="1"/>
+            <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/>
+        </test>
+        <test>
+            <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/>
+            <param name="fit" value="True"/>
+            <param name="bin_size_reponse" value="1"/>
+            <param name="background_thresh" value="1"/>
+            <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/>
+        </test>
+        <test>
+            <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/>
+            <param name="no_pval_correct" value="True"/>
+            <param name="p_threshold" value="1"/>
+            <param name="background_thresh" value="1"/>
+            <param name="-" value="ZeroTruncatedNegativeBinomial"/>
+            <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`Piranha <http://smithlabresearch.org/software/piranha/>`_  is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process. 
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{bgruening_galaxytools,
+                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+                url = {https://github.com/bgruening/galaxytools}
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r f7f366ede872 test-data/testPrianha_zntb_unbinned.bam
Binary file test-data/testPrianha_zntb_unbinned.bam has changed
diff -r 000000000000 -r f7f366ede872 test-data/zntbr_unbinned_response.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zntbr_unbinned_response.bed	Fri Jul 24 06:05:39 2015 -0400
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+chr2	531468	531504	read_18042	0	+
+chr2	531468	531504	read_18043	0	+
+chr2	531468	531504	read_18044	0	+
+chr2	531468	531504	read_18045	0	+
+chr2	531468	531504	read_18046	0	+
+chr2	531468	531504	read_18047	0	+
+chr2	531468	531504	read_18048	0	+
+chr2	531468	531504	read_18049	0	+
+chr2	531468	531504	read_18050	0	+
+chr2	531831	531867	read_18051	0	+
+chr2	532626	532662	read_18052	0	+
+chr2	532626	532662	read_18053	0	+
+chr2	536015	536051	read_18054	0	+
+chr2	536015	536051	read_18055	0	+
+chr2	536015	536051	read_18056	0	+
+chr2	536787	536823	read_18057	0	+
+chr2	536787	536823	read_18058	0	+
+chr2	536787	536823	read_18059	0	+
+chr2	536787	536823	read_18060	0	+
+chr2	536787	536823	read_18061	0	+
+chr2	536787	536823	read_18062	0	+
+chr2	536787	536823	read_18063	0	+
+chr2	536787	536823	read_18064	0	+
+chr2	536787	536823	read_18065	0	+
+chr2	536787	536823	read_18066	0	+
+chr2	536787	536823	read_18067	0	+
+chr2	536787	536823	read_18068	0	+
+chr2	536787	536823	read_18069	0	+
+chr2	536787	536823	read_18070	0	+
+chr2	536787	536823	read_18071	0	+
+chr2	536787	536823	read_18072	0	+
+chr2	536787	536823	read_18073	0	+
+chr2	536787	536823	read_18074	0	+
+chr2	537171	537207	read_18075	0	+
+chr2	537171	537207	read_18076	0	+
+chr2	537171	537207	read_18077	0	+
+chr2	537171	537207	read_18078	0	+
+chr2	537171	537207	read_18079	0	+
+chr2	537171	537207	read_18080	0	+
+chr2	537702	537738	read_18081	0	+
+chr2	537702	537738	read_18082	0	+
+chr2	539834	539870	read_18083	0	+
+chr2	539834	539870	read_18084	0	+
+chr2	539834	539870	read_18085	0	+
+chr2	539834	539870	read_18086	0	+
+chr2	539834	539870	read_18087	0	+
+chr2	541188	541224	read_18088	0	+
+chr2	541188	541224	read_18089	0	+
+chr2	541188	541224	read_18090	0	+
+chr2	541188	541224	read_18091	0	+
+chr2	541188	541224	read_18092	0	+
+chr2	541235	541271	read_18093	0	+
+chr2	541235	541271	read_18094	0	+
+chr2	541402	541438	read_18095	0	+
+chr2	541402	541438	read_18096	0	+
+chr2	541402	541438	read_18097	0	+
+chr2	541402	541438	read_18098	0	+
+chr2	542179	542215	read_18099	0	+
+chr2	542179	542215	read_18100	0	+
+chr2	542179	542215	read_18101	0	+
+chr2	542179	542215	read_18102	0	+
+chr2	542901	542937	read_18103	0	+
+chr2	544270	544306	read_18104	0	+
+chr2	544270	544306	read_18105	0	+
+chr2	544270	544306	read_18106	0	+
+chr2	544270	544306	read_18107	0	+
+chr2	544270	544306	read_18108	0	+
+chr2	544270	544306	read_18109	0	+
+chr2	544270	544306	read_18110	0	+
+chr2	544270	544306	read_18111	0	+
+chr2	544270	544306	read_18112	0	+
+chr2	545055	545091	read_18113	0	+
+chr2	545055	545091	read_18114	0	+
+chr2	545055	545091	read_18115	0	+
+chr2	546833	546869	read_18116	0	+
+chr2	546833	546869	read_18117	0	+
+chr2	546833	546869	read_18118	0	+
+chr2	546833	546869	read_18119	0	+
+chr2	546833	546869	read_18120	0	+
+chr2	546833	546869	read_18121	0	+
+chr2	546833	546869	read_18122	0	+
+chr2	546833	546869	read_18123	0	+
+chr2	546833	546869	read_18124	0	+
+chr2	546833	546869	read_18125	0	+
+chr2	546833	546869	read_18126	0	+
+chr2	546833	546869	read_18127	0	+
+chr2	546833	546869	read_18128	0	+
+chr2	546833	546869	read_18129	0	+
+chr2	546833	546869	read_18130	0	+
+chr2	546833	546869	read_18131	0	+
+chr2	546833	546869	read_18132	0	+
+chr2	546833	546869	read_18133	0	+
+chr2	546833	546869	read_18134	0	+
+chr2	546833	546869	read_18135	0	+
+chr2	546833	546869	read_18136	0	+
+chr2	546833	546869	read_18137	0	+
+chr2	546833	546869	read_18138	0	+
+chr2	546833	546869	read_18139	0	+
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+chr2	546833	546869	read_18141	0	+
+chr2	546833	546869	read_18142	0	+
+chr2	546833	546869	read_18143	0	+
+chr2	546833	546869	read_18144	0	+
+chr2	546833	546869	read_18145	0	+
+chr2	546833	546869	read_18146	0	+
+chr2	546833	546869	read_18147	0	+
+chr2	546833	546869	read_18148	0	+
+chr2	546833	546869	read_18149	0	+
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+chr2	549310	549346	read_18151	0	+
+chr2	549737	549773	read_18152	0	+
+chr2	549737	549773	read_18153	0	+
+chr2	549737	549773	read_18154	0	+
+chr2	549737	549773	read_18155	0	+
+chr2	549737	549773	read_18156	0	+
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+chr2	549737	549773	read_18158	0	+
+chr2	549737	549773	read_18159	0	+
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+chr2	549737	549773	read_18162	0	+
+chr2	549737	549773	read_18163	0	+
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+chr2	549737	549773	read_18167	0	+
+chr2	549737	549773	read_18168	0	+
+chr2	549737	549773	read_18169	0	+
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+chr2	549737	549773	read_18173	0	+
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+chr2	549737	549773	read_18175	0	+
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+chr2	549737	549773	read_18179	0	+
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+chr2	557126	557162	read_18208	0	+
+chr2	557126	557162	read_18209	0	+
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+chr2	557126	557162	read_18216	0	+
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+chr2	557126	557162	read_18234	0	+
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+chr2	560442	560478	read_18285	0	+
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+chr2	570146	570182	read_18430	0	+
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diff -r 000000000000 -r f7f366ede872 test-data/ztnbBinningTestModelOutput.expected.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbBinningTestModelOutput.expected.xml	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,5 @@
+<ZTNB>
+	<mean> 156.449 	</mean>
+
+	<alpha> 1.31103 	</alpha>
+</ZTNB>
diff -r 000000000000 -r f7f366ede872 test-data/ztnbSimpleTest_output.expected.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbSimpleTest_output.expected.bed	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,1000 @@
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diff -r 000000000000 -r f7f366ede872 test-data/ztnbSimpleTest_response.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbSimpleTest_response.bed	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,1000 @@
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diff -r 000000000000 -r f7f366ede872 test-data/ztnbrBinningTestModelOutput.expected.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbrBinningTestModelOutput.expected.xml	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,5 @@
+<ZeroTruncatedNegativeBinomialRegression>
+<coefficient> 0.2419 </coefficient>
+<coefficient> 2.67587 </coefficient>
+<alpha>3.82529</alpha>
+</ZeroTruncatedNegativeBinomialRegression>
diff -r 000000000000 -r f7f366ede872 test-data/ztnbr_binning_cov1.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbr_binning_cov1.bed	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,6000 @@
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+chr1	22632	22633	X	1.13912	+
+chr1	23061	23062	X	1.75873	+
+chr1	26296	26297	X	0.480598	+
+chr1	26547	26548	X	1.74772	+
+chr1	27872	27873	X	0.247971	+
+chr1	28869	28870	X	0.948629	+
+chr1	29180	29181	X	0.413779	+
+chr1	29318	29319	X	0.674768	+
+chr1	29901	29902	X	1.33647	+
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+chr1	32583	32584	X	0.0128481	+
+chr1	33062	33063	X	1.89563	+
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+chr1	34290	34291	X	1.50553	+
+chr1	35414	35415	X	1.66374	+
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+chr1	35889	35890	X	1.18951	+
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+chr1	36502	36503	X	1.72694	+
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+chr1	37546	37547	X	0.736448	+
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+chr1	38349	38350	X	1.15713	+
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+chr1	38832	38833	X	0.540252	+
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+chr1	44126	44127	X	1.23074	+
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+chr1	44429	44430	X	0.189879	+
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+chr1	45615	45616	X	0.0463213	+
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+chr1	62854	62855	X	1.81581	+
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+chr1	83420	83421	X	0.752991	+
+chr1	84786	84787	X	0.115763	+
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+chr1	88045	88046	X	0.449229	+
+chr1	90681	90682	X	0.719652	+
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+chr1	92273	92274	X	1.91486	+
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+chr1	94089	94090	X	0.0980611	+
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+chr1	100086	100087	X	1.87577	+
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+chr1	100786	100787	X	1.92829	+
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+chr1	103658	103659	X	0.176259	+
+chr1	105724	105725	X	1.34591	+
+chr1	106923	106924	X	1.74876	+
+chr1	107388	107389	X	0.492444	+
+chr1	107822	107823	X	0.0501172	+
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+chr1	110557	110558	X	1.44346	+
+chr1	111212	111213	X	1.90297	+
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+chr1	113671	113672	X	1.07209	+
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+chr1	119919	119920	X	1.24937	+
+chr1	120284	120285	X	1.54883	+
+chr1	120524	120525	X	0.729878	+
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+chr1	121828	121829	X	1.53059	+
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+chr1	143165	143166	X	1.04755	+
+chr1	143309	143310	X	1.22407	+
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+chr1	147700	147701	X	1.61725	+
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+chr1	151705	151706	X	1.47765	+
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+chr1	152860	152861	X	1.90027	+
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+chr1	153551	153552	X	0.952804	+
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+chr1	155551	155552	X	1.8986	+
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+chr1	158724	158725	X	1.73273	+
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+chr1	159833	159834	X	1.03548	+
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+chr1	161310	161311	X	1.93517	+
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+chr1	162652	162653	X	0.770699	+
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+chr1	164842	164843	X	1.50731	+
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+chr1	177776	177777	X	0.0153609	+
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+chr1	177985	177986	X	0.760104	+
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+chr1	179618	179619	X	0.587068	+
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+chr1	180217	180218	X	1.5058	+
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+chr1	183601	183602	X	0.860868	+
+chr1	183929	183930	X	1.79588	+
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+chr1	187091	187092	X	1.94613	+
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+chr1	192857	192858	X	1.39247	+
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+chr1	203275	203276	X	0.739381	+
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+chr1	206867	206868	X	1.96622	+
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+chr1	209938	209939	X	1.26814	+
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+chr1	211076	211077	X	0.793741	+
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+chr1	211205	211206	X	0.472129	+
+chr1	211279	211280	X	0.0298591	+
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+chr1	212086	212087	X	1.50349	+
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+chr1	215222	215223	X	1.15547	+
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+chr1	220036	220037	X	0.248944	+
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+chr1	224115	224116	X	1.50007	+
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+chr1	228213	228214	X	1.92999	+
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+chr1	228949	228950	X	0.981147	+
+chr1	229058	229059	X	0.693601	+
+chr1	231213	231214	X	1.1397	+
+chr1	232700	232701	X	1.56479	+
+chr1	233126	233127	X	1.66817	+
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+chr1	233220	233221	X	1.29043	+
+chr1	234475	234476	X	0.878088	+
+chr1	234873	234874	X	0.573784	+
+chr1	236794	236795	X	0.297754	+
+chr1	240353	240354	X	1.63646	+
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+chr1	243479	243480	X	0.248559	+
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+chr1	245013	245014	X	1.97537	+
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+chr1	246485	246486	X	0.102892	+
+chr1	246888	246889	X	1.05231	+
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+chr1	247697	247698	X	1.90089	+
+chr1	248781	248782	X	1.56606	+
+chr1	249698	249699	X	0.827492	+
+chr1	249889	249890	X	0.302125	+
+chr1	250730	250731	X	0.0833002	+
+chr1	251844	251845	X	0.357616	+
+chr1	251865	251866	X	0.43083	+
+chr1	252061	252062	X	1.7103	+
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+chr1	252304	252305	X	0.939812	+
+chr1	253424	253425	X	1.09624	+
+chr1	253722	253723	X	0.369712	+
+chr1	254175	254176	X	0.0757591	+
+chr1	255660	255661	X	0.062822	+
+chr1	257506	257507	X	1.08041	+
+chr1	257533	257534	X	1.8216	+
+chr1	258085	258086	X	1.49066	+
+chr1	258538	258539	X	0.243297	+
+chr1	258963	258964	X	1.22065	+
+chr1	259086	259087	X	1.8924	+
+chr1	259143	259144	X	0.746773	+
+chr1	259218	259219	X	0.876909	+
+chr1	260854	260855	X	0.805241	+
+chr1	260976	260977	X	0.538271	+
+chr1	262046	262047	X	0.268838	+
+chr1	262377	262378	X	1.17207	+
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+chr1	263269	263270	X	0.305599	+
+chr1	263526	263527	X	0.446437	+
+chr1	265277	265278	X	1.32457	+
+chr1	265477	265478	X	1.65464	+
+chr1	266586	266587	X	1.08797	+
+chr1	266859	266860	X	0.582619	+
+chr1	268078	268079	X	1.21578	+
+chr1	269238	269239	X	1.57224	+
+chr1	269434	269435	X	1.80161	+
+chr1	270218	270219	X	0.570883	+
+chr1	270410	270411	X	1.03522	+
+chr1	270664	270665	X	1.13864	+
+chr1	272909	272910	X	1.3163	+
+chr1	274186	274187	X	1.54185	+
+chr1	278115	278116	X	1.52191	+
+chr1	278389	278390	X	0.69232	+
+chr1	279046	279047	X	0.186515	+
+chr1	281420	281421	X	1.50058	+
+chr1	282748	282749	X	0.302664	+
+chr1	283639	283640	X	1.87169	+
+chr1	284042	284043	X	0.0649883	+
+chr1	285468	285469	X	1.08007	+
+chr1	285957	285958	X	0.91211	+
+chr1	286053	286054	X	0.632156	+
+chr1	286090	286091	X	0.629839	+
+chr1	286604	286605	X	0.482739	+
+chr1	287368	287369	X	1.47658	+
+chr1	288284	288285	X	1.31125	+
+chr1	289794	289795	X	1.12671	+
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+chr1	292391	292392	X	0.766159	+
+chr1	292990	292991	X	0.903466	+
+chr1	295066	295067	X	1.51951	+
+chr1	296150	296151	X	0.692055	+
+chr1	296303	296304	X	0.24362	+
+chr1	296780	296781	X	1.52989	+
+chr1	297574	297575	X	0.99552	+
+chr1	298502	298503	X	0.0912696	+
+chr1	300255	300256	X	1.21142	+
+chr1	300623	300624	X	0.368401	+
+chr1	300670	300671	X	0.402836	+
+chr1	300787	300788	X	0.94532	+
+chr1	302433	302434	X	1.25335	+
+chr1	302507	302508	X	1.62431	+
+chr1	302589	302590	X	0.907978	+
+chr1	303029	303030	X	0.962899	+
+chr1	303037	303038	X	0.77452	+
+chr1	303292	303293	X	0.959959	+
+chr1	304117	304118	X	0.346475	+
+chr1	305125	305126	X	0.462367	+
+chr1	305243	305244	X	1.37633	+
+chr1	306023	306024	X	0.151658	+
+chr1	306630	306631	X	1.754	+
+chr1	307208	307209	X	1.21748	+
+chr1	307439	307440	X	0.395423	+
+chr1	307837	307838	X	0.137924	+
+chr1	309257	309258	X	0.477256	+
+chr1	310827	310828	X	0.614415	+
+chr1	311745	311746	X	1.46978	+
+chr1	311775	311776	X	0.777659	+
+chr1	314308	314309	X	1.67463	+
+chr1	315080	315081	X	1.05024	+
+chr1	315462	315463	X	1.21842	+
+chr1	317187	317188	X	1.13926	+
+chr1	318106	318107	X	0.596113	+
+chr1	318432	318433	X	1.27569	+
+chr1	319159	319160	X	0.480077	+
+chr1	319515	319516	X	0.379643	+
+chr1	319535	319536	X	1.53266	+
+chr1	319775	319776	X	1.95296	+
+chr1	320166	320167	X	0.0398047	+
+chr1	320547	320548	X	0.662885	+
+chr1	321497	321498	X	1.3966	+
+chr1	322058	322059	X	0.841366	+
+chr1	322710	322711	X	1.52593	+
+chr1	322838	322839	X	0.410473	+
+chr1	322850	322851	X	0.610746	+
+chr1	323375	323376	X	0.891215	+
+chr1	323987	323988	X	0.130661	+
+chr1	324397	324398	X	1.818	+
+chr1	324407	324408	X	0.570435	+
+chr1	325786	325787	X	1.81021	+
+chr1	325916	325917	X	1.86473	+
+chr1	326162	326163	X	1.92261	+
+chr1	328294	328295	X	0.1173	+
+chr1	329199	329200	X	0.236917	+
+chr1	329377	329378	X	1.627	+
+chr1	330616	330617	X	1.60698	+
+chr1	331006	331007	X	1.07093	+
+chr1	331855	331856	X	0.390376	+
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+chr1	332728	332729	X	1.04814	+
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+chr1	333712	333713	X	0.516941	+
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+chr1	335358	335359	X	0.0229226	+
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+chr1	338219	338220	X	0.373335	+
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+chr1	339921	339922	X	1.92379	+
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+chr1	511711	511712	X	0.0169419	+
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+chr1	523028	523029	X	1.15598	+
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+chr1	533226	533227	X	1.90141	+
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+chr1	538720	538721	X	0.331674	+
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+chr1	540092	540093	X	0.501506	+
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+chr1	543888	543889	X	1.52881	+
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+chr1	551760	551761	X	1.20451	+
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+chr1	553731	553732	X	1.13308	+
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+chr1	557591	557592	X	1.12347	+
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+chr1	559316	559317	X	0.0512891	+
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+chr1	564311	564312	X	1.24047	+
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+chr1	564949	564950	X	1.03467	+
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+chr1	566004	566005	X	1.99824	+
+chr1	566306	566307	X	1.69116	+
+chr1	567730	567731	X	0.17171	+
+chr1	568070	568071	X	0.890241	+
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+chr1	571884	571885	X	1.77149	+
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+chr1	578632	578633	X	1.42863	+
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+chr1	582280	582281	X	1.38343	+
+chr1	583050	583051	X	1.71276	+
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+chr1	584181	584182	X	1.80531	+
+chr1	584935	584936	X	1.0692	+
+chr1	585560	585561	X	0.922901	+
+chr1	586086	586087	X	1.41279	+
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+chr1	589539	589540	X	0.582326	+
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+chr1	590705	590706	X	1.24191	+
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+chr1	594044	594045	X	0.616141	+
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+chr1	601440	601441	X	1.7431	+
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+chr1	604811	604812	X	0.664799	+
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+chr1	606535	606536	X	0.826486	+
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+chr1	612643	612644	X	0.366835	+
+chr1	613299	613300	X	1.46527	+
+chr1	616654	616655	X	1.11149	+
+chr1	617889	617890	X	1.65181	+
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+chr1	621477	621478	X	1.69285	+
+chr1	623210	623211	X	0.57834	+
+chr1	623790	623791	X	1.25656	+
+chr1	626093	626094	X	0.875073	+
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+chr1	626531	626532	X	0.40837	+
+chr1	628832	628833	X	0.18678	+
+chr1	629215	629216	X	1.61133	+
+chr1	629397	629398	X	1.28002	+
+chr1	630813	630814	X	0.190707	+
+chr1	631464	631465	X	1.56014	+
+chr1	631864	631865	X	1.73795	+
+chr1	632014	632015	X	1.92501	+
+chr1	634202	634203	X	0.774979	+
+chr1	634633	634634	X	0.129228	+
+chr1	635079	635080	X	1.99627	+
+chr1	635122	635123	X	0.159191	+
+chr1	636214	636215	X	1.68086	+
+chr1	637555	637556	X	0.309434	+
+chr1	638065	638066	X	1.84926	+
+chr1	638355	638356	X	0.571649	+
+chr1	638499	638500	X	1.63503	+
+chr1	639054	639055	X	1.50869	+
+chr1	639452	639453	X	1.34883	+
+chr1	641222	641223	X	1.35133	+
+chr1	641284	641285	X	0.968171	+
+chr1	642354	642355	X	0.895973	+
+chr1	642667	642668	X	0.914197	+
+chr1	643120	643121	X	0.852655	+
+chr1	645782	645783	X	1.51258	+
+chr1	646857	646858	X	0.0576972	+
+chr1	649253	649254	X	0.266818	+
+chr1	649394	649395	X	1.80992	+
+chr1	651673	651674	X	0.675571	+
+chr1	654455	654456	X	1.18731	+
+chr1	655634	655635	X	1.41963	+
+chr1	656468	656469	X	1.94159	+
+chr1	656709	656710	X	1.04382	+
+chr1	657415	657416	X	0.824768	+
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+chr1	658868	658869	X	0.148045	+
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+chr1	889038	889039	X	1.97718	+
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+chr1	894239	894240	X	0.172679	+
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+chr1	895090	895091	X	0.180922	+
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+chr1	900694	900695	X	1.45482	+
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+chr1	910144	910145	X	1.31147	+
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+chr1	926117	926118	X	0.326355	+
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+chr1	926487	926488	X	1.80498	+
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+chr1	928061	928062	X	0.429359	+
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+chr1	935446	935447	X	1.53451	+
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+chr1	935834	935835	X	0.5449	+
+chr1	936149	936150	X	1.42467	+
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+chr1	940173	940174	X	0.801913	+
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+chr1	944759	944760	X	1.12865	+
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+chr1	946711	946712	X	1.37035	+
+chr1	948504	948505	X	0.713161	+
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+chr1	951761	951762	X	1.37343	+
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+chr1	953903	953904	X	1.99625	+
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+chr1	954476	954477	X	1.6557	+
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+chr1	963440	963441	X	1.41423	+
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+chr1	964097	964098	X	1.17007	+
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+chr1	966471	966472	X	1.31292	+
+chr1	966610	966611	X	1.5937	+
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diff -r 000000000000 -r f7f366ede872 test-data/ztnbr_binning_cov2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ztnbr_binning_cov2.bed	Fri Jul 24 06:05:39 2015 -0400
@@ -0,0 +1,6000 @@
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+chr1	9045	9046	X	1.82473	+
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+chr1	12158	12159	X	0.830783	+
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+chr1	32583	32584	X	1.93859	+
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+chr1	66107	66108	X	1.19387	+
+chr1	66154	66155	X	0.0100984	+
+chr1	67064	67065	X	1.67506	+
+chr1	68397	68398	X	0.581221	+
+chr1	68486	68487	X	1.52365	+
+chr1	68899	68900	X	0.957973	+
+chr1	69144	69145	X	1.6432	+
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+chr1	70119	70120	X	0.463907	+
+chr1	71175	71176	X	1.98611	+
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+chr1	72533	72534	X	1.6018	+
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+chr1	92273	92274	X	1.11234	+
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+chr1	146365	146366	X	1.8492	+
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+chr1	147700	147701	X	1.19033	+
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+chr1	155551	155552	X	1.81738	+
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+chr1	159833	159834	X	1.27462	+
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+chr1	161310	161311	X	0.374554	+
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+chr1	162011	162012	X	0.779083	+
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+chr1	180917	180918	X	1.23909	+
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+chr1	243479	243480	X	1.52786	+
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+chr1	245899	245900	X	1.74725	+
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+chr1	247274	247275	X	1.31944	+
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+chr1	251844	251845	X	0.455431	+
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+chr1	252061	252062	X	1.05451	+
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+chr1	255660	255661	X	1.84989	+
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+chr1	258085	258086	X	1.58364	+
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+chr1	259086	259087	X	1.53476	+
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+chr1	259218	259219	X	0.205201	+
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+chr1	263075	263076	X	1.74917	+
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+chr1	263526	263527	X	1.27229	+
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+chr1	265477	265478	X	1.48695	+
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+chr1	266859	266860	X	0.081705	+
+chr1	268078	268079	X	1.67059	+
+chr1	269238	269239	X	0.689106	+
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+chr1	270218	270219	X	0.831858	+
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+chr1	278115	278116	X	0.768768	+
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+chr1	279046	279047	X	0.764771	+
+chr1	281420	281421	X	0.182561	+
+chr1	282748	282749	X	0.869868	+
+chr1	283639	283640	X	1.44226	+
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+chr1	285468	285469	X	0.653354	+
+chr1	285957	285958	X	1.84046	+
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+chr1	286090	286091	X	1.71122	+
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+chr1	287368	287369	X	0.915768	+
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+chr1	289794	289795	X	0.616708	+
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+chr1	292990	292991	X	0.548314	+
+chr1	295066	295067	X	0.487338	+
+chr1	296150	296151	X	1.36385	+
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+chr1	296780	296781	X	0.905991	+
+chr1	297574	297575	X	1.70882	+
+chr1	298502	298503	X	1.96866	+
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+chr1	300623	300624	X	1.71241	+
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+chr1	300787	300788	X	1.99865	+
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+chr1	302507	302508	X	1.75278	+
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+chr1	303029	303030	X	1.44052	+
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+chr1	303292	303293	X	0.0232252	+
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+chr1	306023	306024	X	0.918769	+
+chr1	306630	306631	X	1.54752	+
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+chr1	307439	307440	X	1.87768	+
+chr1	307837	307838	X	0.0809471	+
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+chr1	310827	310828	X	0.471082	+
+chr1	311745	311746	X	0.567786	+
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+chr1	314308	314309	X	1.4867	+
+chr1	315080	315081	X	1.30334	+
+chr1	315462	315463	X	0.0575438	+
+chr1	317187	317188	X	1.56093	+
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+chr1	318432	318433	X	0.585023	+
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+chr1	319515	319516	X	0.665409	+
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+chr1	319775	319776	X	1.47463	+
+chr1	320166	320167	X	0.996886	+
+chr1	320547	320548	X	1.11164	+
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+chr1	322058	322059	X	0.831411	+
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+chr1	323375	323376	X	0.651284	+
+chr1	323987	323988	X	0.0208138	+
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+chr1	325786	325787	X	0.262859	+
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+chr1	329199	329200	X	1.86277	+
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+chr1	330616	330617	X	0.554238	+
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+chr1	332728	332729	X	0.104556	+
+chr1	333014	333015	X	1.34518	+
+chr1	333712	333713	X	0.221361	+
+chr1	334098	334099	X	1.59793	+
+chr1	334625	334626	X	0.171629	+
+chr1	334695	334696	X	1.40025	+
+chr1	335358	335359	X	1.25988	+
+chr1	335930	335931	X	1.89531	+
+chr1	337640	337641	X	1.96571	+
+chr1	337808	337809	X	0.444242	+
+chr1	338219	338220	X	0.640959	+
+chr1	339041	339042	X	1.71226	+
+chr1	339921	339922	X	1.08802	+
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+chr1	340393	340394	X	0.358063	+
+chr1	341592	341593	X	1.28052	+
+chr1	341982	341983	X	0.810399	+
+chr1	342298	342299	X	1.18817	+
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+chr1	342703	342704	X	0.756426	+
+chr1	342758	342759	X	0.321901	+
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+chr1	343568	343569	X	1.57645	+
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+chr1	351948	351949	X	1.27869	+
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+chr1	352473	352474	X	0.31055	+
+chr1	352840	352841	X	1.0079	+
+chr1	353760	353761	X	0.890381	+
+chr1	356655	356656	X	0.788245	+
+chr1	357729	357730	X	1.32247	+
+chr1	358592	358593	X	0.368005	+
+chr1	358664	358665	X	1.26971	+
+chr1	359184	359185	X	0.946359	+
+chr1	361123	361124	X	0.182067	+
+chr1	361791	361792	X	0.262572	+
+chr1	362328	362329	X	0.510634	+
+chr1	362391	362392	X	1.44576	+
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+chr1	362692	362693	X	0.342838	+
+chr1	362982	362983	X	1.51333	+
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+chr1	364098	364099	X	0.64256	+
+chr1	364988	364989	X	1.77298	+
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+chr1	372203	372204	X	1.64516	+
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+chr1	373649	373650	X	1.61847	+
+chr1	374828	374829	X	0.1696	+
+chr1	375155	375156	X	1.07382	+
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+chr1	376551	376552	X	0.913095	+
+chr1	376910	376911	X	0.648173	+
+chr1	377188	377189	X	0.875609	+
+chr1	377961	377962	X	0.584842	+
+chr1	379097	379098	X	0.530543	+
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+chr1	382252	382253	X	0.305066	+
+chr1	383647	383648	X	1.74539	+
+chr1	383967	383968	X	1.73437	+
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+chr1	387934	387935	X	1.02934	+
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+chr1	395035	395036	X	0.85693	+
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+chr1	452886	452887	X	1.22413	+
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+chr1	456613	456614	X	0.101984	+
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+chr1	567730	567731	X	1.93627	+
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+chr1	584181	584182	X	1.88963	+
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+chr1	591711	591712	X	1.9146	+
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+chr1	604811	604812	X	1.28485	+
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+chr1	617889	617890	X	1.95939	+
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+chr1	623790	623791	X	1.02867	+
+chr1	626093	626094	X	1.35012	+
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+chr1	626531	626532	X	1.46845	+
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+chr1	629397	629398	X	1.21677	+
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+chr1	631464	631465	X	1.34228	+
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+chr1	634633	634634	X	1.93812	+
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+chr1	638355	638356	X	1.70796	+
+chr1	638499	638500	X	1.88942	+
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+chr1	641222	641223	X	1.87582	+
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+chr1	642354	642355	X	0.624913	+
+chr1	642667	642668	X	0.915979	+
+chr1	643120	643121	X	0.572233	+
+chr1	645782	645783	X	1.9668	+
+chr1	646857	646858	X	1.71716	+
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+chr1	651673	651674	X	0.318033	+
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+chr1	655634	655635	X	1.74796	+
+chr1	656468	656469	X	0.304459	+
+chr1	656709	656710	X	1.55393	+
+chr1	657415	657416	X	1.87391	+
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+chr1	658868	658869	X	0.18641	+
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+chr1	661516	661517	X	1.25537	+
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+chr1	663047	663048	X	1.07298	+
+chr1	663102	663103	X	0.33607	+
+chr1	665856	665857	X	1.33418	+
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+chr1	667296	667297	X	1.71984	+
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+chr1	668565	668566	X	0.357977	+
+chr1	668613	668614	X	1.06286	+
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+chr1	672750	672751	X	0.842955	+
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+chr1	673195	673196	X	0.755575	+
+chr1	674163	674164	X	1.38732	+
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+chr1	677019	677020	X	0.730428	+
+chr1	677357	677358	X	1.35305	+
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+chr1	679097	679098	X	0.484033	+
+chr1	683021	683022	X	0.00772518	+
+chr1	683152	683153	X	1.12858	+
+chr1	683695	683696	X	1.50707	+
+chr1	684079	684080	X	1.02384	+
+chr1	684087	684088	X	1.20478	+
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+chr1	687226	687227	X	0.593532	+
+chr1	687635	687636	X	0.596296	+
+chr1	687950	687951	X	0.000370413	+
+chr1	688402	688403	X	0.522805	+
+chr1	688911	688912	X	1.99934	+
+chr1	689152	689153	X	0.39852	+
+chr1	691151	691152	X	1.01222	+
+chr1	691743	691744	X	1.07223	+
+chr1	691781	691782	X	0.86966	+
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+chr1	692333	692334	X	1.19699	+
+chr1	694983	694984	X	1.56841	+
+chr1	697390	697391	X	0.0588876	+
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+chr1	698313	698314	X	1.29235	+
+chr1	698556	698557	X	0.657704	+
+chr1	699048	699049	X	1.76207	+
+chr1	699058	699059	X	0.265495	+
+chr1	701061	701062	X	1.00386	+
+chr1	702030	702031	X	1.93222	+
+chr1	702345	702346	X	1.88458	+
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+chr1	702785	702786	X	1.52047	+
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+chr1	704628	704629	X	0.421707	+
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+chr1	708730	708731	X	0.0710936	+
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+chr1	953903	953904	X	0.996929	+
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+chr1	955463	955464	X	0.644782	+
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+chr1	963440	963441	X	1.00094	+
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+chr1	978724	978725	X	1.0309	+
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+chr1	990250	990251	X	1.56491	+
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+chr1	996960	996961	X	1.76483	+
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+chr1	997471	997472	X	0.191673	+
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+chr1	999910	999911	X	0.435523	+
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+chr2	3147	3148	X	1.14718	+
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+chr2	6438	6439	X	0.906347	+
+chr2	6715	6716	X	1.11762	+
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+chr2	12780	12781	X	1.7149	+
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+chr2	13613	13614	X	0.85731	+
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