changeset 0:f7f366ede872 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty
author rnateam
date Fri, 24 Jul 2015 06:05:39 -0400
parents
children
files piranha.xml test-data/testPrianha_zntb_unbinned.bam test-data/zntbr_unbinned_response.bed test-data/ztnbBinningTestModelOutput.expected.xml test-data/ztnbSimpleTest_output.expected.bed test-data/ztnbSimpleTest_response.bed test-data/ztnbrBinningTestModelOutput.expected.xml test-data/ztnbr_binning_cov1.bed test-data/ztnbr_binning_cov2.bed
diffstat 9 files changed, 74211 insertions(+), 0 deletions(-) [+]
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--- /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>
Binary file test-data/testPrianha_zntb_unbinned.bam has changed
--- /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_18040	0	+
+chr2	531468	531504	read_18041	0	+
+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	+
+chr2	546833	546869	read_18150	0	+
+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	+
+chr2	549737	549773	read_18157	0	+
+chr2	549737	549773	read_18158	0	+
+chr2	549737	549773	read_18159	0	+
+chr2	549737	549773	read_18160	0	+
+chr2	549737	549773	read_18161	0	+
+chr2	549737	549773	read_18162	0	+
+chr2	549737	549773	read_18163	0	+
+chr2	549737	549773	read_18164	0	+
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+chr2	549737	549773	read_18167	0	+
+chr2	549737	549773	read_18168	0	+
+chr2	549737	549773	read_18169	0	+
+chr2	549737	549773	read_18170	0	+
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+chr2	549737	549773	read_18173	0	+
+chr2	549737	549773	read_18174	0	+
+chr2	549737	549773	read_18175	0	+
+chr2	549737	549773	read_18176	0	+
+chr2	549737	549773	read_18177	0	+
+chr2	549737	549773	read_18178	0	+
+chr2	549737	549773	read_18179	0	+
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+chr2	550695	550731	read_18182	0	+
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+chr2	552786	552822	read_18194	0	+
+chr2	552786	552822	read_18195	0	+
+chr2	553968	554004	read_18196	0	+
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+chr2	553968	554004	read_18199	0	+
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+chr2	556363	556399	read_18206	0	+
+chr2	556363	556399	read_18207	0	+
+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_18231	0	+
+chr2	557126	557162	read_18232	0	+
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+chr2	557126	557162	read_18234	0	+
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+chr2	557126	557162	read_18237	0	+
+chr2	557126	557162	read_18238	0	+
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+chr2	557126	557162	read_18242	0	+
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+chr2	557126	557162	read_18246	0	+
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+chr2	558950	558986	read_18250	0	+
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+chr2	560228	560264	read_18279	0	+
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+chr2	560419	560455	read_18281	0	+
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+chr2	560442	560478	read_18283	0	+
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+chr2	560442	560478	read_18285	0	+
+chr2	560442	560478	read_18286	0	+
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+chr2	570146	570182	read_18427	0	+
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--- /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>
--- /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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--- /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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--- /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>
--- /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	29318	29319	X	0.674768	+
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+chr1	106923	106924	X	1.74876	+
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+chr1	107822	107823	X	0.0501172	+
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+chr1	113671	113672	X	1.07209	+
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+chr1	147700	147701	X	1.61725	+
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+chr1	187091	187092	X	1.94613	+
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+chr1	209938	209939	X	1.26814	+
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+chr1	212086	212087	X	1.50349	+
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+chr1	228949	228950	X	0.981147	+
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+chr1	231213	231214	X	1.1397	+
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+chr1	233220	233221	X	1.29043	+
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+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	+
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+chr1	248781	248782	X	1.56606	+
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+chr1	250730	250731	X	0.0833002	+
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+chr1	251865	251866	X	0.43083	+
+chr1	252061	252062	X	1.7103	+
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+chr1	252304	252305	X	0.939812	+
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+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	+
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+chr1	259086	259087	X	1.8924	+
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+chr1	259218	259219	X	0.876909	+
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+chr1	260976	260977	X	0.538271	+
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+chr1	263526	263527	X	0.446437	+
+chr1	265277	265278	X	1.32457	+
+chr1	265477	265478	X	1.65464	+
+chr1	266586	266587	X	1.08797	+
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+chr1	268078	268079	X	1.21578	+
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+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	+
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+chr1	279046	279047	X	0.186515	+
+chr1	281420	281421	X	1.50058	+
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+chr1	283639	283640	X	1.87169	+
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+chr1	285468	285469	X	1.08007	+
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+chr1	286090	286091	X	0.629839	+
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+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	+
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+chr1	295066	295067	X	1.51951	+
+chr1	296150	296151	X	0.692055	+
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+chr1	296780	296781	X	1.52989	+
+chr1	297574	297575	X	0.99552	+
+chr1	298502	298503	X	0.0912696	+
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+chr1	300623	300624	X	0.368401	+
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+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	+
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+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	+
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+chr1	314308	314309	X	1.67463	+
+chr1	315080	315081	X	1.05024	+
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+chr1	317187	317188	X	1.13926	+
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+chr1	318432	318433	X	1.27569	+
+chr1	319159	319160	X	0.480077	+
+chr1	319515	319516	X	0.379643	+
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+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	+
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+chr1	322850	322851	X	0.610746	+
+chr1	323375	323376	X	0.891215	+
+chr1	323987	323988	X	0.130661	+
+chr1	324397	324398	X	1.818	+
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+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	+
+chr1	331946	331947	X	1.5035	+
+chr1	332728	332729	X	1.04814	+
+chr1	333014	333015	X	1.27776	+
+chr1	333712	333713	X	0.516941	+
+chr1	334098	334099	X	0.41397	+
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+chr1	335358	335359	X	0.0229226	+
+chr1	335930	335931	X	0.84845	+
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+chr1	337808	337809	X	1.75525	+
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+chr1	339921	339922	X	1.92379	+
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+chr1	340393	340394	X	0.0342927	+
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+chr1	342298	342299	X	0.378841	+
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+chr1	349049	349050	X	0.786544	+
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+chr1	353760	353761	X	1.73957	+
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+chr1	357729	357730	X	0.0323272	+
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+chr1	406738	406739	X	1.53644	+
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+chr1	412922	412923	X	0.784904	+
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+chr1	413899	413900	X	1.41762	+
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+chr1	513540	513541	X	1.47699	+
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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	551760	551761	X	1.20451	+
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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	566004	566005	X	1.99824	+
+chr1	566306	566307	X	1.69116	+
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+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	+
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+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	+
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+chr1	623790	623791	X	1.25656	+
+chr1	626093	626094	X	0.875073	+
+chr1	626096	626097	X	1.3893	+
+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	+
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+chr1	632014	632015	X	1.92501	+
+chr1	634202	634203	X	0.774979	+
+chr1	634633	634634	X	0.129228	+
+chr1	635079	635080	X	1.99627	+
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+chr1	636214	636215	X	1.68086	+
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+chr1	638355	638356	X	0.571649	+
+chr1	638499	638500	X	1.63503	+
+chr1	639054	639055	X	1.50869	+
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+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	+
+chr1	658112	658113	X	0.786407	+
+chr1	658477	658478	X	1.50169	+
+chr1	658868	658869	X	0.148045	+
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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	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	+
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+chr1	940173	940174	X	0.801913	+
+chr1	942524	942525	X	1.39578	+
+chr1	944759	944760	X	1.12865	+
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+chr1	946711	946712	X	1.37035	+
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+chr1	948695	948696	X	1.46706	+
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+chr1	954476	954477	X	1.6557	+
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+chr1	955463	955464	X	1.78501	+
+chr1	955608	955609	X	0.849001	+
+chr1	959557	959558	X	1.22438	+
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+chr1	963440	963441	X	1.41423	+
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+chr1	966610	966611	X	1.5937	+
+chr1	967745	967746	X	1.65376	+
+chr1	968360	968361	X	0.19328	+
+chr1	970572	970573	X	0.0363319	+
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+chr5	775411	775412	X	1.19805	+
+chr5	775422	775423	X	1.38904	+
+chr5	776256	776257	X	0.466852	+
+chr5	776612	776613	X	1.84903	+
+chr5	777204	777205	X	0.957169	+
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+chr5	778096	778097	X	0.502009	+
+chr5	778151	778152	X	1.8554	+
+chr5	778305	778306	X	0.488685	+
+chr5	778554	778555	X	1.20147	+
+chr5	778947	778948	X	0.828708	+
+chr5	779707	779708	X	1.98061	+
+chr5	779933	779934	X	0.841993	+
+chr5	780837	780838	X	0.232548	+
+chr5	781022	781023	X	1.29691	+
+chr5	781237	781238	X	0.747016	+
+chr5	781256	781257	X	1.23464	+
+chr5	781937	781938	X	1.9184	+
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+chr5	783088	783089	X	1.43148	+
+chr5	783155	783156	X	0.0392823	+
+chr5	784933	784934	X	1.15373	+
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+chr5	785500	785501	X	0.412755	+
+chr5	786497	786498	X	1.6392	+
+chr5	787705	787706	X	0.0994616	+
+chr5	788016	788017	X	0.081912	+
+chr5	788806	788807	X	1.68501	+
+chr5	790902	790903	X	0.552965	+
+chr5	790967	790968	X	1.50002	+
+chr5	793656	793657	X	0.670484	+
+chr5	794032	794033	X	0.228034	+
+chr5	794478	794479	X	0.657012	+
+chr5	795791	795792	X	1.49647	+
+chr5	796513	796514	X	1.97458	+
+chr5	798953	798954	X	1.75187	+
+chr5	800087	800088	X	1.08541	+
+chr5	801864	801865	X	0.877776	+
+chr5	803836	803837	X	0.909069	+
+chr5	803844	803845	X	0.696964	+
+chr5	805249	805250	X	1.20101	+
+chr5	806534	806535	X	1.25385	+
+chr5	807896	807897	X	0.487304	+
+chr5	809992	809993	X	0.841552	+
+chr5	810451	810452	X	1.33588	+
+chr5	810836	810837	X	0.120978	+
+chr5	811128	811129	X	0.499484	+
+chr5	811323	811324	X	1.93543	+
+chr5	811414	811415	X	0.414563	+
+chr5	814173	814174	X	0.249189	+
+chr5	814240	814241	X	0.816488	+
+chr5	814344	814345	X	0.300546	+
+chr5	815858	815859	X	1.02216	+
+chr5	816268	816269	X	1.26407	+
+chr5	816932	816933	X	0.457501	+
+chr5	821566	821567	X	1.60178	+
+chr5	821584	821585	X	0.713107	+
+chr5	822442	822443	X	0.804919	+
+chr5	822930	822931	X	1.32788	+
+chr5	823256	823257	X	0.0970424	+
+chr5	823680	823681	X	1.91265	+
+chr5	825385	825386	X	0.850441	+
+chr5	826044	826045	X	0.0364801	+
+chr5	826737	826738	X	0.0920297	+
+chr5	828331	828332	X	0.659949	+
+chr5	828476	828477	X	0.136536	+
+chr5	828724	828725	X	1.35182	+
+chr5	829308	829309	X	0.814452	+
+chr5	830005	830006	X	0.29599	+
+chr5	830262	830263	X	0.424777	+
+chr5	831892	831893	X	1.99597	+
+chr5	832396	832397	X	1.75687	+
+chr5	832640	832641	X	0.308323	+
+chr5	832785	832786	X	1.67268	+
+chr5	832848	832849	X	0.215225	+
+chr5	833727	833728	X	1.90049	+
+chr5	833787	833788	X	0.465973	+
+chr5	834119	834120	X	1.76409	+
+chr5	835461	835462	X	1.52798	+
+chr5	836078	836079	X	1.73611	+
+chr5	836975	836976	X	1.39214	+
+chr5	837432	837433	X	1.67468	+
+chr5	837721	837722	X	0.133981	+
+chr5	838307	838308	X	0.697158	+
+chr5	839397	839398	X	0.790558	+
+chr5	839551	839552	X	0.413139	+
+chr5	839600	839601	X	0.806161	+
+chr5	840290	840291	X	1.72441	+
+chr5	840357	840358	X	1.33635	+
+chr5	841633	841634	X	1.32279	+
+chr5	842298	842299	X	1.33415	+
+chr5	842316	842317	X	0.31673	+
+chr5	842575	842576	X	1.70224	+
+chr5	843158	843159	X	1.8357	+
+chr5	843366	843367	X	0.127112	+
+chr5	846850	846851	X	0.489901	+
+chr5	848758	848759	X	0.351355	+
+chr5	849087	849088	X	1.42668	+
+chr5	849814	849815	X	1.94709	+
+chr5	849971	849972	X	1.3136	+
+chr5	851419	851420	X	0.149585	+
+chr5	851869	851870	X	0.326058	+
+chr5	852194	852195	X	1.29501	+
+chr5	853099	853100	X	0.207155	+
+chr5	853757	853758	X	0.523022	+
+chr5	854609	854610	X	0.129384	+
+chr5	855469	855470	X	0.664245	+
+chr5	855753	855754	X	1.50374	+
+chr5	861876	861877	X	1.40906	+
+chr5	862938	862939	X	0.470495	+
+chr5	864237	864238	X	0.409806	+
+chr5	865336	865337	X	0.250001	+
+chr5	865721	865722	X	1.88148	+
+chr5	866795	866796	X	0.606937	+
+chr5	866853	866854	X	1.48985	+
+chr5	866925	866926	X	1.70833	+
+chr5	867730	867731	X	1.6449	+
+chr5	870636	870637	X	1.76591	+
+chr5	870646	870647	X	0.418633	+
+chr5	871124	871125	X	1.65883	+
+chr5	872053	872054	X	0.264152	+
+chr5	872901	872902	X	0.0485646	+
+chr5	873122	873123	X	0.908935	+
+chr5	873624	873625	X	0.790518	+
+chr5	873878	873879	X	1.39359	+
+chr5	874158	874159	X	1.81492	+
+chr5	874774	874775	X	0.401734	+
+chr5	874853	874854	X	0.0624721	+
+chr5	875178	875179	X	1.48805	+
+chr5	875752	875753	X	1.05925	+
+chr5	877239	877240	X	0.772913	+
+chr5	877810	877811	X	1.24577	+
+chr5	877918	877919	X	1.95023	+
+chr5	878361	878362	X	1.16848	+
+chr5	880230	880231	X	1.45481	+
+chr5	881432	881433	X	1.162	+
+chr5	881571	881572	X	1.09483	+
+chr5	881797	881798	X	0.0515042	+
+chr5	883738	883739	X	1.87495	+
+chr5	884626	884627	X	0.876604	+
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+chr5	886088	886089	X	1.73894	+
+chr5	886837	886838	X	0.0337518	+
+chr5	889489	889490	X	1.66828	+
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+chr5	890088	890089	X	0.747105	+
+chr5	891161	891162	X	0.666514	+
+chr5	893162	893163	X	0.361703	+
+chr5	893990	893991	X	0.218734	+
+chr5	893992	893993	X	1.66343	+
+chr5	895649	895650	X	0.187207	+
+chr5	895772	895773	X	1.46801	+
+chr5	896853	896854	X	0.291323	+
+chr5	897272	897273	X	1.40914	+
+chr5	897972	897973	X	0.357695	+
+chr5	898139	898140	X	0.0383098	+
+chr5	898502	898503	X	0.952347	+
+chr5	899105	899106	X	1.97599	+
+chr5	900399	900400	X	0.237619	+
+chr5	900481	900482	X	1.35314	+
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+chr5	901588	901589	X	0.124649	+
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+chr5	902860	902861	X	1.96621	+
+chr5	902906	902907	X	0.68492	+
+chr5	903179	903180	X	0.0100725	+
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+chr5	904588	904589	X	0.385787	+
+chr5	904988	904989	X	0.706646	+
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+chr5	906395	906396	X	0.326339	+
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+chr5	907561	907562	X	0.461994	+
+chr5	909164	909165	X	1.83356	+
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+chr5	910969	910970	X	1.57445	+
+chr5	911922	911923	X	1.06162	+
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+chr5	915000	915001	X	0.258766	+
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+chr5	918484	918485	X	1.73239	+
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+chr5	922841	922842	X	0.787163	+
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+chr5	926572	926573	X	1.59726	+
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+chr5	926947	926948	X	1.2063	+
+chr5	928787	928788	X	0.439252	+
+chr5	930071	930072	X	1.05369	+
+chr5	930698	930699	X	0.870024	+
+chr5	931636	931637	X	1.91354	+
+chr5	932071	932072	X	1.49651	+
+chr5	932346	932347	X	0.811263	+
+chr5	934744	934745	X	1.90298	+
+chr5	934954	934955	X	1.14743	+
+chr5	935139	935140	X	0.865671	+
+chr5	935760	935761	X	0.0204511	+
+chr5	936333	936334	X	0.0347518	+
+chr5	936765	936766	X	1.80367	+
+chr5	936962	936963	X	0.514709	+
+chr5	937504	937505	X	1.48227	+
+chr5	938899	938900	X	1.08512	+
+chr5	940442	940443	X	1.00468	+
+chr5	942165	942166	X	1.57674	+
+chr5	943367	943368	X	0.515381	+
+chr5	943730	943731	X	0.421601	+
+chr5	944885	944886	X	1.60003	+
+chr5	946337	946338	X	0.402714	+
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+chr5	948701	948702	X	0.557612	+
+chr5	949463	949464	X	1.46497	+
+chr5	949637	949638	X	0.0204203	+
+chr5	950561	950562	X	1.96697	+
+chr5	950950	950951	X	1.10505	+
+chr5	951098	951099	X	1.61955	+
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+chr5	954289	954290	X	1.58268	+
+chr5	954373	954374	X	0.0776612	+
+chr5	955379	955380	X	1.46136	+
+chr5	955387	955388	X	1.5604	+
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+chr5	956109	956110	X	1.59023	+
+chr5	956823	956824	X	0.870337	+
+chr5	957195	957196	X	0.489102	+
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+chr5	957714	957715	X	1.51231	+
+chr5	960901	960902	X	0.535719	+
+chr5	961311	961312	X	0.912848	+
+chr5	962998	962999	X	1.32854	+
+chr5	963049	963050	X	0.288613	+
+chr5	966196	966197	X	1.21976	+
+chr5	966761	966762	X	0.489067	+
+chr5	968861	968862	X	1.46246	+
+chr5	968886	968887	X	1.66972	+
+chr5	970159	970160	X	1.03466	+
+chr5	971246	971247	X	1.41681	+
+chr5	973013	973014	X	1.23073	+
+chr5	974071	974072	X	1.09954	+
+chr5	974282	974283	X	0.380615	+
+chr5	974507	974508	X	0.0339671	+
+chr5	974529	974530	X	0.113886	+
+chr5	976758	976759	X	0.635588	+
+chr5	977058	977059	X	0.454781	+
+chr5	977612	977613	X	0.540581	+
+chr5	978608	978609	X	0.626268	+
+chr5	978961	978962	X	0.485206	+
+chr5	979460	979461	X	0.488413	+
+chr5	979751	979752	X	0.705387	+
+chr5	980716	980717	X	0.370287	+
+chr5	981025	981026	X	1.7251	+
+chr5	982067	982068	X	1.18116	+
+chr5	982104	982105	X	0.870954	+
+chr5	983267	983268	X	1.3199	+
+chr5	983289	983290	X	0.304294	+
+chr5	983545	983546	X	1.19256	+
+chr5	983603	983604	X	1.44016	+
+chr5	983840	983841	X	0.387686	+
+chr5	985162	985163	X	0.798185	+
+chr5	985794	985795	X	1.71795	+
+chr5	986466	986467	X	1.16394	+
+chr5	988990	988991	X	0.893724	+
+chr5	988995	988996	X	0.100857	+
+chr5	989039	989040	X	0.984503	+
+chr5	989298	989299	X	0.607637	+
+chr5	989734	989735	X	1.12427	+
+chr5	990227	990228	X	0.0125343	+
+chr5	994522	994523	X	0.684804	+
+chr5	995636	995637	X	1.27112	+
+chr5	996389	996390	X	0.41321	+
+chr5	996409	996410	X	1.59288	+
+chr5	996641	996642	X	0.785893	+
+chr5	996686	996687	X	0.807039	+
+chr5	997183	997184	X	0.971826	+
+chr5	998263	998264	X	1.24186	+
+chr5	999924	999925	X	0.187548	+
--- /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 @@
+chr1	15	16	X	0.285884	+
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+chr1	1414	1415	X	1.98967	+
+chr1	1757	1758	X	0.83515	+
+chr1	3314	3315	X	1.62779	+
+chr1	3707	3708	X	0.000849908	+
+chr1	4549	4550	X	0.0355585	+
+chr1	5999	6000	X	1.70938	+
+chr1	6457	6458	X	0.424355	+
+chr1	8507	8508	X	1.4421	+
+chr1	9045	9046	X	1.82473	+
+chr1	9631	9632	X	0.063309	+
+chr1	10117	10118	X	1.77154	+
+chr1	11176	11177	X	1.72367	+
+chr1	11911	11912	X	0.452338	+
+chr1	11939	11940	X	0.0455983	+
+chr1	12158	12159	X	0.830783	+
+chr1	12683	12684	X	1.19446	+
+chr1	13639	13640	X	1.43541	+
+chr1	14015	14016	X	1.34891	+
+chr1	15396	15397	X	1.83012	+
+chr1	18695	18696	X	0.422904	+
+chr1	19215	19216	X	0.521697	+
+chr1	19316	19317	X	1.2931	+
+chr1	22632	22633	X	1.18818	+
+chr1	23061	23062	X	0.989616	+
+chr1	26296	26297	X	1.41059	+
+chr1	26547	26548	X	1.9492	+
+chr1	27872	27873	X	1.65687	+
+chr1	28869	28870	X	1.60162	+
+chr1	29180	29181	X	0.386784	+
+chr1	29318	29319	X	0.819143	+
+chr1	29901	29902	X	0.0682755	+
+chr1	31735	31736	X	0.947939	+
+chr1	32583	32584	X	1.93859	+
+chr1	33062	33063	X	1.83032	+
+chr1	33816	33817	X	1.02466	+
+chr1	34290	34291	X	1.43902	+
+chr1	35414	35415	X	0.46227	+
+chr1	35570	35571	X	0.413351	+
+chr1	35889	35890	X	0.157111	+
+chr1	36167	36168	X	0.419452	+
+chr1	36502	36503	X	0.697678	+
+chr1	36956	36957	X	1.79965	+
+chr1	37546	37547	X	1.48405	+
+chr1	37832	37833	X	1.61137	+
+chr1	38184	38185	X	0.370391	+
+chr1	38349	38350	X	1.83134	+
+chr1	38606	38607	X	1.98277	+
+chr1	38673	38674	X	1.86473	+
+chr1	38832	38833	X	0.0157611	+
+chr1	39976	39977	X	1.57853	+
+chr1	41920	41921	X	0.683479	+
+chr1	44126	44127	X	1.08818	+
+chr1	44167	44168	X	0.924745	+
+chr1	44429	44430	X	1.29814	+
+chr1	44810	44811	X	1.93596	+
+chr1	45112	45113	X	1.30542	+
+chr1	45599	45600	X	1.78117	+
+chr1	45615	45616	X	0.522557	+
+chr1	46144	46145	X	1.96799	+
+chr1	47543	47544	X	0.807906	+
+chr1	49974	49975	X	1.98444	+
+chr1	51340	51341	X	0.387334	+
+chr1	52246	52247	X	0.405837	+
+chr1	52363	52364	X	1.14299	+
+chr1	52675	52676	X	0.40214	+
+chr1	52679	52680	X	1.14962	+
+chr1	52908	52909	X	1.16739	+
+chr1	53752	53753	X	0.564092	+
+chr1	53857	53858	X	1.73067	+
+chr1	54825	54826	X	0.0395156	+
+chr1	54878	54879	X	0.580895	+
+chr1	56750	56751	X	0.327205	+
+chr1	57096	57097	X	1.92645	+
+chr1	58710	58711	X	0.25293	+
+chr1	59270	59271	X	1.79532	+
+chr1	59400	59401	X	0.897785	+
+chr1	59494	59495	X	0.253605	+
+chr1	60979	60980	X	0.735648	+
+chr1	62807	62808	X	1.16891	+
+chr1	62854	62855	X	0.251496	+
+chr1	63277	63278	X	1.64902	+
+chr1	63313	63314	X	1.41063	+
+chr1	64538	64539	X	0.88392	+
+chr1	65534	65535	X	1.92145	+
+chr1	66007	66008	X	0.175415	+
+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	+
+chr1	69752	69753	X	0.7551	+
+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	77322	77323	X	0.895438	+
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+chr1	92273	92274	X	1.11234	+
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+chr1	147700	147701	X	1.19033	+
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+chr1	162570	162571	X	0.544224	+
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+chr1	164842	164843	X	1.42094	+
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+chr1	245899	245900	X	1.74725	+
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+chr1	248781	248782	X	0.843031	+
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+chr1	255660	255661	X	1.84989	+
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+chr1	259086	259087	X	1.53476	+
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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	266859	266860	X	0.081705	+
+chr1	268078	268079	X	1.67059	+
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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	281420	281421	X	0.182561	+
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+chr1	285468	285469	X	0.653354	+
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+chr1	286090	286091	X	1.71122	+
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+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	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	311745	311746	X	0.567786	+
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+chr1	315080	315081	X	1.30334	+
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+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	320166	320167	X	0.996886	+
+chr1	320547	320548	X	1.11164	+
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+chr1	323375	323376	X	0.651284	+
+chr1	323987	323988	X	0.0208138	+
+chr1	324397	324398	X	1.08101	+
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+chr1	325786	325787	X	0.262859	+
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+chr1	326162	326163	X	1.25115	+
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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	+
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+chr1	333712	333713	X	0.221361	+
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+chr1	334625	334626	X	0.171629	+
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+chr1	335358	335359	X	1.25988	+
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+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	+
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+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	353760	353761	X	0.890381	+
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+chr1	357729	357730	X	1.32247	+
+chr1	358592	358593	X	0.368005	+
+chr1	358664	358665	X	1.26971	+
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+chr1	361123	361124	X	0.182067	+
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+chr1	362328	362329	X	0.510634	+
+chr1	362391	362392	X	1.44576	+
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+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	+
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+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	+
+chr1	381545	381546	X	0.819183	+
+chr1	381863	381864	X	1.60841	+
+chr1	382252	382253	X	0.305066	+
+chr1	383647	383648	X	1.74539	+
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+chr1	384337	384338	X	0.253923	+
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+chr1	387934	387935	X	1.02934	+
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+chr1	459966	459967	X	1.37526	+
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+chr1	626531	626532	X	1.46845	+
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+chr1	629215	629216	X	1.56157	+
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+chr1	634633	634634	X	1.93812	+
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+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	+
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+chr1	656709	656710	X	1.55393	+
+chr1	657415	657416	X	1.87391	+
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+chr1	658868	658869	X	0.18641	+
+chr1	659157	659158	X	1.93787	+
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+chr1	661516	661517	X	1.25537	+
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+chr1	663047	663048	X	1.07298	+
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+chr1	668565	668566	X	0.357977	+
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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	683021	683022	X	0.00772518	+
+chr1	683152	683153	X	1.12858	+
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+chr1	684079	684080	X	1.02384	+
+chr1	684087	684088	X	1.20478	+
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+chr1	687635	687636	X	0.596296	+
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+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	694983	694984	X	1.56841	+
+chr1	697390	697391	X	0.0588876	+
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+chr1	698313	698314	X	1.29235	+
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+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	+
+chr1	702539	702540	X	1.25951	+
+chr1	702637	702638	X	0.837661	+
+chr1	702785	702786	X	1.52047	+
+chr1	704120	704121	X	1.41907	+
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+chr1	708472	708473	X	1.59367	+
+chr1	708730	708731	X	0.0710936	+
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+chr1	710164	710165	X	0.29556	+
+chr1	712385	712386	X	1.15161	+
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+chr1	953903	953904	X	0.996929	+
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+chr1	959557	959558	X	0.20533	+
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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	+
+chr2	78	79	X	1.45406	+
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+chr2	3147	3148	X	1.14718	+
+chr2	3328	3329	X	1.85954	+
+chr2	4596	4597	X	0.508919	+
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+chr2	6715	6716	X	1.11762	+
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+chr2	12780	12781	X	1.7149	+
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+chr2	21563	21564	X	0.913196	+
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+chr2	22286	22287	X	1.56168	+
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