changeset 11:ee370ade24cd draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:21:53 +0000
parents 8286e361f89c
children
files hicAggregateContacts.xml macros.xml test-data/DpnII_10k.bed test-data/cHi-C/background.txt test-data/cHi-C/chicQualityControl/histogram.png test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report test-data/cHi-C/chicQualityControl/sparsity.png test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt test-data/find_TADs/multiFDR_score.bedgraph test-data/hicDifferentialTAD/accepted.txt test-data/hicDifferentialTAD/multiNone_domains.bed test-data/hicDifferentialTAD/rejected.txt test-data/hicHyperoptDetectLoops/hyperopt_results.txt test-data/hicHyperoptDetectLoops/loops.bedgraph test-data/hicMergeDomains/100kbtad_domains.bed test-data/hicMergeDomains/10kbtad_domains.bed test-data/hicMergeDomains/50kbtad_domains.bed test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf test-data/hicMergeDomains/ctcf_sorted.bed test-data/hicMergeDomains/merged_list.bed test-data/hicMergeDomains/relationship.txt test-data/hicMergeDomains/two_files_relation_ctcf.txt test-data/hicPlotMatrix/plot1.png test-data/hicPlotMatrix/plot2.pdf test-data/hicPlotMatrix/plot3_pca.svg test-data/hicPlotSVL/p_values.txt test-data/hicPlotSVL/plot.png test-data/hicPlotSVL/ratios.txt test-data/hicQuickQC/QC.log test-data/hicValidateLocations/overlap_smc3_statistics test-data/multiNone_domains.bed test-data/raw_qc_report
diffstat 44 files changed, 19502 insertions(+), 28132 deletions(-) [+]
line wrap: on
line diff
--- a/hicAggregateContacts.xml	Fri Dec 11 21:16:12 2020 +0000
+++ b/hicAggregateContacts.xml	Tue Mar 16 15:21:53 2021 +0000
@@ -1,5 +1,4 @@
-
-<tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>allow plotting of aggregated Hi-C contacts between regions specified in a file</description>
     <macros>
         <token name="@BINARY@">hicAggregateContacts</token>
@@ -10,34 +9,43 @@
     ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
     @BINARY@
     --matrix 'matrix.$matrix_h5_cooler.ext'
-    --BED $BED
+    --BED '$BED'
     #if $BED2:
-        --BED2 $BED2
+        --BED2 '$BED2'
     #end if
 
     --range '$range_min:$range_max'
-
     --numberOfBins '$numberOfBins'
 
     --transform $transform
-    --avgType $avgType
-
+    --operationType $operationType
+    --mode $mode
+    $row_wise
+    $perChr
+    --largeRegionsOperation $largeRegionsOperation
     #if $outputs and 'PrefixMatrix' in $outputs:
         --outFilePrefixMatrix 'matrix_values'
     #end if
 
-    #if $outputs and 'ClusterContactPositions' in $outputs:
-        --outFilePrefixClusterContactPositions 'contact_positions'
+    #if $outputs and 'outFileContactPairs' in $outputs:
+        --outFileContactPairs 'contact_positions'
     #end if
 
     #if $outputs and 'HeatmapFile' in $outputs:
         --diagnosticHeatmapFile 'heatmap'
     #end if
 
+    #if $outputs and 'outFileObsExp' in $outputs:
+        --outFileObsExp 'ObsExp.$matrix_h5_cooler.ext'
+    #end if
+
     #if $clustering:
         $clustering
     #end if
-    $clusterOnDiagonal
+
+    #if $howToCluster:
+        --howToCluster $howToCluster
+    #end if
 
     #if $chromosomes:
         --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
@@ -60,17 +68,33 @@
     #end if
 
     --outFileName plot.$image_file_format
-    && mv plot.$image_file_format plot
+    &&
+    mv plot.$image_file_format plot
+    #if $outputs and 'outFileObsExp' in $outputs:
+        && mv 'ObsExp.$matrix_h5_cooler.ext' matrix
+    #end if
 
 ]]>
     </command>
     <inputs>
         <expand macro='matrix_h5_cooler_macro' />
-        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted"/>
-        <param argument="--BED2" type="data" format="bed" optional="true"
-            label="Interactions between regions in first and second BED file are plotted"/>
+        <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted" />
+        <param argument="--BED2" type="data" format="bed" optional="true" label="Interactions between regions in first and second BED file are plotted" />
 
         <expand macro='range' />
+        <param argument="--mode" type="select" label="Regions to consider.">
+            <option value="inter-chr">inter-chr</option>
+            <option value="intra-chr">intra-chr</option>
+            <option value="all" selected="true">all</option>
+        </param>
+
+        <param argument="--row_wise" type="boolean" truevalue="--row_wise" falsevalue="" label="Row wise" help="If given,the insteractions between each row of the BED file and its 
+                corresponding row of the BED2 file are computed. If intra-chromosomal 
+                contacts are computed, the rows with different chromosomes are ignored. 
+                If inter-chromosomal, the rows with same chromosomes are ignored. 
+                It keeps all the rows if `all`." />
+
+        <param argument="--perChr" type="boolean" truevalue="--perChr" falsevalue="" label="Per chromosome" help="If set, it generates a plot per chromosome. It is only affected if intra-chromosomal contacts are of interest." />
 
         <repeat name="chromosomes" title="List of chromosomes to plot" min="0">
             <param name="chromosome" type="text" label="chromosome (one per field)">
@@ -78,12 +102,9 @@
             </param>
         </repeat>
 
-        <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix"
-            help="The bed regions will be centered between -half number of bins
-            and +half number of bins indicated." />
+        <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix" help="The bed regions will be centered between -half number of bins and +half number of bins indicated." />
 
-        <param argument="--transform" type="select" label="Type of transformation for the matrix"
-            help="If total counts are selected, then the sub-matrix values
+        <param argument="--transform" type="select" label="Type of transformation for the matrix" help="If total counts are selected, then the sub-matrix values
             are divided by the total counts for normalization. If
             z-score or obs/exp are selected, then H-C matrix is
             converted into a z-score or observed / expected matrix.">
@@ -93,50 +114,61 @@
             <option value="obs/exp">obs/exp</option>
         </param>
 
-        <param argument="--avgType" type="select" label="Type of average to compute final matrix">
+        <param argument="--operationType" type="select" label="Type of operation to compute final matrix">
             <option value="median" selected="true">median</option>
             <option value="mean">mean</option>
+            <option value="sum">sum</option>
         </param>
 
-        <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome"
-            help="When this option is set, then the matrix is split into
+        <param argument="--largeRegionsOperation" type="select" label="Large regions operation" help="If a given coordinate in the bed file is larger than 
+                           a bin of the input matrix, by default only the first bin 
+                           is taken into account. However there are more posibilities 
+                           to handel such a case. Users can ask for the last bin or 
+                           for center of the region. As an example if a region falls into bins [4,5,6] 
+                           and `--numberOfBins = 2` then if first, bins [3,4,5] are kept. 
+                           If last: [5,6,7] and if center: [4,5,6].">
+            <option value="first" selected="true">first</option>
+            <option value="last">last</option>
+            <option value="center">center</option>
+        </param>
+
+        <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome" help="When this option is set, then the matrix is split into
                   clusters using the hierarchical clustering algorithm,
                   using 'ward linkage'. hclust could be very slow if
                   you have >1000 submatrices per chromosome. In those
                   cases, you might prefer kmeans.">
             <option value="--kmeans">kmeans</option>
             <option value="--hclust">hclust (#clusters per chromosome)</option>
+            <option value="--spectral">spectral</option>
         </param>
 
-        <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue=""
-            label="Perform clustering on the submatrix diagonal"
-            help="Clustering is by default carried out on the whole
-                  submatrices. If this parameter is given, the
-                  clustering is only carried out based on the submatrix
-                  diagonal (representing values at the same distance to each other)." />
-
+        <param argument="--howToCluster" type="select" optional="true" label="How to cluster" help="Options are 'full', 'center' and 'diagonal'. The full clustering '
+                'takes all values of each submatrix for clustering. center, takes only a square of '
+                'length 3x3 from each submatrix and uses only  this values for clustering. With the '
+                'diagonal option the clustering is only carried out based on the submatrix diagonal '
+                '(representing values at the same distance to each other)">
+            <option value="full">full</option>
+            <option value="center">center</option>
+            <option value="diagonal">diagonal</option>
+        </param>
         <param argument="--plotType" type="select" optional="true" label="Plot type">
             <option value="2d">2D</option>
             <option value="3d">3D</option>
         </param>
         <expand macro="colormap" />
-        <param argument="--vMin" type="float" optional="true" label="vMin"
-            help= "Minimum value of the plotted score." />
-
-        <param argument="--vMax" type="float" optional="true" label="vMax"
-            help= "Maximum value of the plotted score." />
-
+        <param argument="--vMin" type="float" optional="true" label="vMin" help= "Minimum value of the plotted score." />
+        <param argument="--vMax" type="float" optional="true" label="vMax" help= "Maximum value of the plotted score." />
         <param name="image_file_format" type="select" label="Image output format">
             <option value="png" selected="True">png</option>
             <option value="svg">svg</option>
             <option value="pdf">pdf</option>
-
         </param>
 
         <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files">
             <option value="PrefixMatrix">Save values underlying the final matrix</option>
-            <option value="ClusterContactPositions">Save the position of the contacts</option>
+            <option value="outFileContactPairs">Save the position of the contacts</option>
             <option value="HeatmapFile">Heatmap file per chromosome</option>
+            <option value="outFileObsExp">Save obs/exp matrix</option>
         </param>
 
     </inputs>
@@ -145,7 +177,6 @@
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
-
             </change_format>
         </data>
         <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
@@ -157,19 +188,27 @@
         <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values">
             <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
+        <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
+            <filter>'outFileObsExp' in outputs</filter>
+            <change_format>
+                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/>
-            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/>
+            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool" />
+            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed" />
             <param name="numberOfBins" value="30" />
             <param name="range_max" value="900000" />
             <param name="range_min" value="50000" />
+            <param name="howToCluster" value="center" />
             <param name="image_file_format" value="png" />
-            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
+            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
+
 Aggregation of Hi-C contacts
 ============================
 
@@ -215,6 +254,6 @@
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 .. _Colormaps: https://matplotlib.org/examples/color/colormaps_reference.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>
--- a/macros.xml	Fri Dec 11 21:16:12 2020 +0000
+++ b/macros.xml	Tue Mar 16 15:21:53 2021 +0000
@@ -1,6 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">3.4.3</token>
+    <token name="@TOOL_VERSION@">3.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -9,7 +10,7 @@
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>
             <yield />
         </requirements>
         <version_command>@BINARY@ --version</version_command>
@@ -28,7 +29,7 @@
 
     <xml name="chromosome_list">
         <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
-            <param argument="--chromosomes" type="text" value="" >
+            <param argument="--chromosomes" type="text" value="">
                 <validator type="empty_field" />
             </param>
         </repeat>
@@ -40,17 +41,45 @@
             <yield />
         </citations>
     </xml>
+    <xml name="dpi">
+        <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
+    </xml>
+
+    <xml name="restrictionCutFile">
+        <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
+                (i.e. the region between one restriction site and the next)." />
+    </xml>
+
+    <xml name="restrictionSequence">
+        <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
+            &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
+            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
+        </param>
+    </xml>
+    <xml name="danglingSequence">
+        <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
+                    Each restriction enzyme recognizes a different DNA sequence and,
+                    after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
+                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
+                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
+                    This information is easily found on the description of the restriction enzyme.
+                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
+                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
+            <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>
+        </param>
+    </xml>
 
     <xml name="zMax">
-        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
+        <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />
+        <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
     </xml>
     <xml name="use_range">
-        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
-            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
+        <conditional name="use_range">            <!-- argparse specifies one argument of type min_range:max_range -->
+            <param name="select_use_range" argument="--range" type="select" label="Range restriction (in bp)" help="If given, only counts within the specified range are considered.">
                 <option value="no_use_range">No restriction</option>
                 <option value="yes_use_range">Only consider counts within a range</option>
             </param>
-            <when value="no_use_range"/>
+            <when value="no_use_range" />
             <when value="yes_use_range">
                 <expand macro='range' />
             </when>
@@ -58,8 +87,8 @@
     </xml>
 
     <xml name="range">
-        <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
-        <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
+        <param name='range_min' type="integer" value="" min="0" label="Minimum range to consider interactions" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions." />
+        <param name='range_max' type="integer" value="" min="0" label="Maximum range to consider interactions" />
     </xml>
 
     <xml name="colormap">
@@ -209,12 +238,8 @@
 
     <xml name="multiple_input_matrices">
         <repeat name="input_files" title="Hi-C Matrix files" min="2">
-            <param name="matrix" type="data" format="h5,cool"
-                label="Hi-C Matrix file"
-                help=""/>
-            <param name="mlabel" type="text" size="30" optional="true" value=""
-                label="Label"
-                help="Label to use in the output. If not given the dataset name will be used instead."/>
+            <param name="matrix" type="data" format="h5,cool" label="Hi-C Matrix file" help="" />
+            <param name="mlabel" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
         </repeat>
     </xml>
 
@@ -240,17 +265,14 @@
     <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
 
     <xml name="region">
-        <param name="region" type="text" label="Region of the genome to limit the operation"
-            help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
+        <param argument="--region" type="text" label="Region of the genome to limit the operation" help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500">
+            <validator type="expression" message="Only alphanumeric characters, the colon or a dash are allowed.">not value or value.replace(':', '').replace('-', '').isalnum()</validator>
+        </param>
     </xml>
 
-
-
     <xml name="kmeans_clustering">
         <conditional name="used_multiple_regions">
-            <param name="used_multiple_regions_options" type="select"
-                label="Did you compute the matrix with more than one groups of regions?"
-                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
+            <param name="used_multiple_regions_options" type="select" label="Did you compute the matrix with more than one groups of regions?" help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                 <option value="yes">Yes, I used multiple groups of regions</option>
                 <option value="no">No, I used only one group</option>
             </param>
@@ -261,8 +283,7 @@
                         <option value="kmeans">Kmeans clustering</option>
                     </param>
                     <when value="kmeans">
-                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
-                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
+                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)." />
                     </when>
                     <when value="none" />
                 </conditional>
@@ -282,80 +303,51 @@
     </token>
 
     <xml name="samFlag">
-        <param name="samFlag" type="integer" optional="true" value=""
-            label="Filter reads based on the SAM flag"
-            help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
+        <param name="samFlag" type="integer" optional="true" value="" label="Filter reads based on the SAM flag" help="For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)" />
     </xml>
     <xml name="plotNumbers">
-        <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
-            label="Plot the correlation value"
-            help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
+        <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)" />
     </xml>
     <xml name="doNotExtendPairedEnds">
-        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
-            label="Do not extend paired ends"
-            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
+        <param argument="--doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)" />
     </xml>
-
     <xml name="ignoreDuplicates">
-        <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
-            label="Ignore duplicates"
-            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
+        <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" label="Ignore duplicates" help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
     </xml>
-
     <xml name="minMappingQuality">
-        <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
-            label="Minimum mapping quality"
-            help= "If set, only reads that have a mapping quality score higher than the given value are considered.
+        <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" label="Minimum mapping quality" help= "If set, only reads that have a mapping quality score higher than the given value are considered.
                 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
-                A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
+                A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere." />
     </xml>
 
     <xml name="skipZeros">
-        <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
-            label ="Skip zeros"
-            help  ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
+        <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" help="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
     </xml>
 
     <xml name="fragmentLength">
-        <param name="fragmentLength" type="integer" value="300" min="1"
-            label="Fragment length used for the sequencing"
-            help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
+        <param argument="--fragmentLength" type="integer" value="300" min="1" label="Fragment length used for the sequencing" help="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)" />
     </xml>
 
     <xml name="scaleFactor">
-        <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
-        <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
+        <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)" />
+        <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
     </xml>
-
     <xml name="xMax">
-        <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
-            label="Max value for the x-axis in counts per bin" />
+        <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
     </xml>
-
     <xml name="filterThreshold">
-        <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
-            label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
-
-        <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
-            label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
+        <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />
+        <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect." />
     </xml>
-
-
     <xml name="pseudocount">
-        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+        <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero." />
     </xml>
     <xml name='matrix_h5_cooler_macro'>
-        <param name='matrix_h5_cooler' type="data" format="h5,cool"
-            label="Matrix to compute on"/>
+        <param name='matrix_h5_cooler' type="data" format="h5,cool" label="Matrix to compute on" />
     </xml>
     <xml name='matrix_h5_cooler_multiple_macro'>
-        <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
-            label="Matricies to compute on" multiple="true"/>
+        <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" multiple="true" label="Matricies to compute on" />
     </xml>
-
-    
-
     <xml name='convertFormat_single_macro'>
         <conditional name="inputFormat_conditional">
             <param name="inputFormat_selector" type="select" label="Choose input file type">
@@ -367,27 +359,26 @@
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_macro' />
-                <param name='correctionName' type='text' label='Correction factors column name'/>
-                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
-                <param name='chromosome' type='text' label='Load only one chromosome'/>
-                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
-
+                <param name='correctionName' type='text' label='Correction factors column name' />
+                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
+                <param name='chromosome' type='text' label='Load only one chromosome' />
+                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
             </when>
             <when value="optionH5">
                 <expand macro='matrix_h5_cooler_macro' />
             </when>
             <when value="optionHic">
-                <param name='matrixHic' type='data' format='hic' label='.hic matrix'/>
-                <param name='resolutions' type='text' label='List of resolutions'/>
-            </when> 
-
+                <param name='matrixHic' type='data' format='hic' label='.hic matrix' />
+                <param name='resolutions' type='text' label='List of resolutions' help="Resolutions can be specified seperated with a space, e.g. '10000 20000 50000'">
+                    <validator type="expression" message="Only numeric characters and the a space as seperator are allowed.">value.replace(' ', '').isnumeric()</validator>
+                </param>
+            </when>
             <when value="optionHomer">
-                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
+                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' />
             </when>
-
             <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
-                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
+                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' />
+                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' />
             </when>
         </conditional>
     </xml>
@@ -402,45 +393,39 @@
             </param>
             <when value="optionCool">
                 <expand macro='matrix_h5_cooler_multiple_macro' />
-                <param name='correctionName' type='text' label='Correction factors column name'/>
-                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
-                <param name='chromosome' type='text' label='Load only one chromosome'/>
-                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
-
+                <param name='correctionName' type='text' label='Correction factors column name' />
+                <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication' />
+                <param name='chromosome' type='text' label='Load only one chromosome' />
+                <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data' />
             </when>
             <when value="optionH5">
                 <expand macro='matrix_h5_cooler_multiple_macro' />
             </when>
-           
             <when value="optionHomer">
-                <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
+                <param name='matrixHomer' type='data' format='txt' multiple="true" label='Homer interaction matrix' />
             </when>
-
             <when value="optionHicpro">
-                <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
-                <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
+                <param name='matrixHicpro' type='data' format='txt' multiple="true" label='.hic matrix' />
+                <param name='bedHicpro' type='data' format='bed' multiple="true" label='HicPro bed file' />
             </when>
         </conditional>
     </xml>
     <xml name='convertFormat_single_output_macro'>
         <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
-
         <conditional name="outputFormat_conditional">
             <param name="outputFormat_selector" type="select" label="Choose output file type">
                 <option value="cool" selected="True">cool</option>
                 <option value="h5">h5</option>
                 <option value="homer">Homer</option>
                 <option value="ginteractions">ginteractions</option>
-
             </param>
             <when value="cool">
-                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue=""   label='Store applied correction factors in column count'/>
-                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue=""  label='Enforce integer for count column'/>
+                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
+                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
             </when>
-            <when value='h5'/>
-            <when value='homer'/>
-            <when value='ginteractions'/>
-
+            <when value='h5' />
+            <when value='homer' />
+            <when value='ginteractions' />
         </conditional>
     </xml>
     <token name="@REFERENCES@">
@@ -459,33 +444,26 @@
 
     </token>
 
-
     <xml name="multiple_input_bams">
         <repeat name="input_files" title="BAM files" min="2">
-            <param name="bamfile" type="data" format="bam"
-                label="Bam file"
-                help="The BAM file must be sorted."/>
-            <param name="label" type="text" size="30" optional="true" value=""
-                label="Label"
-                help="Label to use in the output. If not given the dataset name will be used instead."/>
+            <param name="bamfile" type="data" format="bam" label="BAM file" />
+            <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead." />
         </repeat>
     </xml>
 
     <xml name="multiple_input_bigwigs">
         <repeat name="input_files" title="BigWig files" min="2">
-            <param name="bigwigfile" type="data" format="bigwig"
-                label="Bigwig file"
-                help="The Bigwig file must be sorted."/>
-            <param name="label" type="text" size="30" optional="true" value=""
-                label="Label"
-                help="Label to use in the output. If not given the dataset name will be used instead."/>
+            <param name="bigwigfile" type="data" format="bigwig" label="Bigwig file" />
+            <param name="label" type="text" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead.">
+                <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
+            </param>
         </repeat>
     </xml>
 
     <xml name="plotTitle">
-        <param name="plotTitle" type="text" value="" size="30" optional="True"
-            label="Title of the plot"
-            help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
+        <param name="plotTitle" type="text" value="" optional="True" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. (--plotTitle)">
+            <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
+        </param>
     </xml>
 
     <token name="@multiple_input_bams@">
@@ -561,8 +539,7 @@
 
     <xml name="effectiveGenomeSize">
         <conditional name="effectiveGenomeSize">
-            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
-                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
+            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
                     Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
                     See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
                 <option value="93260000">ce10 (93260000)</option>
@@ -572,7 +549,7 @@
                 <option value="specific">user specified</option>
             </param>
             <when value="specific">
-                <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
+                <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000" />
             </when>
             <when value="2150570000" />
             <when value="2451960000" />
@@ -592,26 +569,24 @@
     </xml>
 
     <xml name="missingDataAsZero">
-                <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
-                    label ="Treat missing data as zero"
-                    help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+        <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Treat missing data as zero" help="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
     </xml>
 
     <xml name="input_save_matrix_values">
-        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" />
     </xml>
 
     <xml name="input_graphic_output_settings">
-        <conditional name="output" >
-            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
+        <conditional name="output">
+            <param name="showOutputSettings" type="select" label="Show advanced output settings">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
             </param>
             <when value="no" />
             <when value="yes">
                 <yield />
-                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
-                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
+                <param name="saveData" type="boolean" label="Save the data underlying the average profile" />
+                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap." />
             </when>
         </conditional>
     </xml>
@@ -668,32 +643,33 @@
     </xml>
 
     <xml name="track_input_h5_macro">
-        <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
+        <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />
     </xml>
     <xml name="track_input_bed_macro">
-        <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
+        <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />
     </xml>
     <xml name="track_input_bedgraph_macro">
-        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
+        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />
     </xml>
     <xml name="track_input_bigwig_macro">
-        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
+        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />
     </xml>
     <xml name="track_input_bedgraph_matrix_macro">
-        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
+        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />
     </xml>
     <xml name="track_input_tabular_macro">
-        <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
+        <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />
     </xml>
     <xml name="plot_title">
-        <param name="title" type="text" optional="true" label="Plot title"/>
+        <param name="title" type="text" optional="true" label="Plot title">
+            <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>
+        </param>
     </xml>
 
     <xml name="spacer_macro">
-        <param name="spacer_width" type="float" value="" optional="True"
-              label="Include spacer at the end of the track." help="Width of the spacer." />
+        <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />
     </xml>
     <xml name="fontsize_macro">
-        <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+        <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />
     </xml>
 </macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DpnII_10k.bed	Tue Mar 16 15:21:53 2021 +0000
@@ -0,0 +1,5000 @@
+chr2L	79	83	.	0	+
+chr2L	228	232	.	0	+
+chr2L	369	373	.	0	+
+chr2L	537	541	.	0	+
+chr2L	686	690	.	0	+
+chr2L	827	831	.	0	+
+chr2L	995	999	.	0	+
+chr2L	1144	1148	.	0	+
+chr2L	1285	1289	.	0	+
+chr2L	1453	1457	.	0	+
+chr2L	1602	1606	.	0	+
+chr2L	1743	1747	.	0	+
+chr2L	1911	1915	.	0	+
+chr2L	2060	2064	.	0	+
+chr2L	2201	2205	.	0	+
+chr2L	2369	2373	.	0	+
+chr2L	2518	2522	.	0	+
+chr2L	2659	2663	.	0	+
+chr2L	2827	2831	.	0	+
+chr2L	2976	2980	.	0	+
+chr2L	3117	3121	.	0	+
+chr2L	3285	3289	.	0	+
+chr2L	3434	3438	.	0	+
+chr2L	3575	3579	.	0	+
+chr2L	3743	3747	.	0	+
+chr2L	3892	3896	.	0	+
+chr2L	4033	4037	.	0	+
+chr2L	4201	4205	.	0	+
+chr2L	4350	4354	.	0	+
+chr2L	4491	4495	.	0	+
+chr2L	4659	4663	.	0	+
+chr2L	4808	4812	.	0	+
+chr2L	4949	4953	.	0	+
+chr2L	5117	5121	.	0	+
+chr2L	5151	5155	.	0	+
+chr2L	5300	5304	.	0	+
+chr2L	6022	6026	.	0	+
+chr2L	6878	6882	.	0	+
+chr2L	6920	6924	.	0	+
+chr2L	7691	7695	.	0	+
+chr2L	7714	7718	.	0	+
+chr2L	8550	8554	.	0	+
+chr2L	8794	8798	.	0	+
+chr2L	9692	9696	.	0	+
+chr2L	9745	9749	.	0	+
+chr2L	9800	9804	.	0	+
+chr2L	12439	12443	.	0	+
+chr2L	12691	12695	.	0	+
+chr2L	12712	12716	.	0	+
+chr2L	13064	13068	.	0	+
+chr2L	13291	13295	.	0	+
+chr2L	13321	13325	.	0	+
+chr2L	13563	13567	.	0	+
+chr2L	13719	13723	.	0	+
+chr2L	13807	13811	.	0	+
+chr2L	14019	14023	.	0	+
+chr2L	14035	14039	.	0	+
+chr2L	14065	14069	.	0	+
+chr2L	14230	14234	.	0	+
+chr2L	14665	14669	.	0	+
+chr2L	14818	14822	.	0	+
+chr2L	14871	14875	.	0	+
+chr2L	14972	14976	.	0	+
+chr2L	15073	15077	.	0	+
+chr2L	15371	15375	.	0	+
+chr2L	15662	15666	.	0	+
+chr2L	15837	15841	.	0	+
+chr2L	16091	16095	.	0	+
+chr2L	16173	16177	.	0	+
+chr2L	16954	16958	.	0	+
+chr2L	17447	17451	.	0	+
+chr2L	17583	17587	.	0	+
+chr2L	18026	18030	.	0	+
+chr2L	18551	18555	.	0	+
+chr2L	18815	18819	.	0	+
+chr2L	19786	19790	.	0	+
+chr2L	20256	20260	.	0	+
+chr2L	20388	20392	.	0	+
+chr2L	20831	20835	.	0	+
+chr2L	21356	21360	.	0	+
+chr2L	21641	21645	.	0	+
+chr2L	22094	22098	.	0	+
+chr2L	22350	22354	.	0	+
+chr2L	22504	22508	.	0	+
+chr2L	22669	22673	.	0	+
+chr2L	22730	22734	.	0	+
+chr2L	22734	22738	.	0	+
+chr2L	23026	23030	.	0	+
+chr2L	24357	24361	.	0	+
+chr2L	25083	25087	.	0	+
+chr2L	26560	26564	.	0	+
+chr2L	26684	26688	.	0	+
+chr2L	27423	27427	.	0	+
+chr2L	27495	27499	.	0	+
+chr2L	28150	28154	.	0	+
+chr2L	28208	28212	.	0	+
+chr2L	28346	28350	.	0	+
+chr2L	28561	28565	.	0	+
+chr2L	28705	28709	.	0	+
+chr2L	29021	29025	.	0	+
+chr2L	29720	29724	.	0	+
+chr2L	29912	29916	.	0	+
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+chr2L	1668664	1668668	.	0	+
+chr2L	1668716	1668720	.	0	+
+chr2L	1668974	1668978	.	0	+
+chr2L	1669203	1669207	.	0	+
+chr2L	1669931	1669935	.	0	+
+chr2L	1670340	1670344	.	0	+
+chr2L	1671068	1671072	.	0	+
+chr2L	1671331	1671335	.	0	+
+chr2L	1671932	1671936	.	0	+
+chr2L	1672514	1672518	.	0	+
+chr2L	1672999	1673003	.	0	+
+chr2L	1674014	1674018	.	0	+
+chr2L	1675894	1675898	.	0	+
+chr2L	1676791	1676795	.	0	+
+chr2L	1677297	1677301	.	0	+
+chr2L	1677970	1677974	.	0	+
+chr2L	1678760	1678764	.	0	+
+chr2L	1678876	1678880	.	0	+
+chr2L	1679130	1679134	.	0	+
+chr2L	1679284	1679288	.	0	+
+chr2L	1679455	1679459	.	0	+
+chr2L	1680045	1680049	.	0	+
+chr2L	1680078	1680082	.	0	+
+chr2L	1680577	1680581	.	0	+
+chr2L	1680787	1680791	.	0	+
+chr2L	1680979	1680983	.	0	+
+chr2L	1681436	1681440	.	0	+
+chr2L	1681451	1681455	.	0	+
+chr2L	1681786	1681790	.	0	+
+chr2L	1682135	1682139	.	0	+
+chr2L	1682353	1682357	.	0	+
+chr2L	1682763	1682767	.	0	+
+chr2L	1683235	1683239	.	0	+
+chr2L	1683748	1683752	.	0	+
+chr2L	1683943	1683947	.	0	+
+chr2L	1684102	1684106	.	0	+
+chr2L	1684258	1684262	.	0	+
+chr2L	1684301	1684305	.	0	+
+chr2L	1684528	1684532	.	0	+
+chr2L	1684759	1684763	.	0	+
+chr2L	1685026	1685030	.	0	+
+chr2L	1685143	1685147	.	0	+
+chr2L	1685824	1685828	.	0	+
+chr2L	1686139	1686143	.	0	+
+chr2L	1686293	1686297	.	0	+
+chr2L	1687117	1687121	.	0	+
+chr2L	1687221	1687225	.	0	+
+chr2L	1688209	1688213	.	0	+
+chr2L	1688246	1688250	.	0	+
+chr2L	1688617	1688621	.	0	+
+chr2L	1688979	1688983	.	0	+
+chr2L	1689141	1689145	.	0	+
+chr2L	1690544	1690548	.	0	+
+chr2L	1690602	1690606	.	0	+
+chr2L	1690640	1690644	.	0	+
+chr2L	1690721	1690725	.	0	+
+chr2L	1690860	1690864	.	0	+
+chr2L	1692335	1692339	.	0	+
+chr2L	1692465	1692469	.	0	+
+chr2L	1694279	1694283	.	0	+
+chr2L	1694901	1694905	.	0	+
+chr2L	1695054	1695058	.	0	+
+chr2L	1695660	1695664	.	0	+
+chr2L	1695900	1695904	.	0	+
+chr2L	1696351	1696355	.	0	+
+chr2L	1696439	1696443	.	0	+
+chr2L	1696593	1696597	.	0	+
+chr2L	1696642	1696646	.	0	+
+chr2L	1696670	1696674	.	0	+
+chr2L	1696704	1696708	.	0	+
+chr2L	1696758	1696762	.	0	+
+chr2L	1697588	1697592	.	0	+
+chr2L	1697662	1697666	.	0	+
+chr2L	1697902	1697906	.	0	+
+chr2L	1698087	1698091	.	0	+
+chr2L	1698796	1698800	.	0	+
+chr2L	1699066	1699070	.	0	+
+chr2L	1699282	1699286	.	0	+
+chr2L	1700155	1700159	.	0	+
+chr2L	1700334	1700338	.	0	+
+chr2L	1700581	1700585	.	0	+
+chr2L	1700768	1700772	.	0	+
+chr2L	1701327	1701331	.	0	+
+chr2L	1701956	1701960	.	0	+
+chr2L	1702506	1702510	.	0	+
+chr2L	1703467	1703471	.	0	+
+chr2L	1703479	1703483	.	0	+
+chr2L	1703510	1703514	.	0	+
+chr2L	1703526	1703530	.	0	+
+chr2L	1703533	1703537	.	0	+
+chr2L	1704373	1704377	.	0	+
+chr2L	1705029	1705033	.	0	+
+chr2L	1705426	1705430	.	0	+
+chr2L	1705455	1705459	.	0	+
+chr2L	1705474	1705478	.	0	+
+chr2L	1705495	1705499	.	0	+
+chr2L	1705539	1705543	.	0	+
+chr2L	1705610	1705614	.	0	+
+chr2L	1705708	1705712	.	0	+
+chr2L	1705762	1705766	.	0	+
+chr2L	1705768	1705772	.	0	+
+chr2L	1705794	1705798	.	0	+
+chr2L	1705824	1705828	.	0	+
+chr2L	1705967	1705971	.	0	+
+chr2L	1706064	1706068	.	0	+
+chr2L	1706085	1706089	.	0	+
+chr2L	1706146	1706150	.	0	+
+chr2L	1707324	1707328	.	0	+
+chr2L	1707459	1707463	.	0	+
+chr2L	1707619	1707623	.	0	+
+chr2L	1707986	1707990	.	0	+
+chr2L	1708353	1708357	.	0	+
+chr2L	1708570	1708574	.	0	+
+chr2L	1709002	1709006	.	0	+
+chr2L	1709025	1709029	.	0	+
+chr2L	1709092	1709096	.	0	+
+chr2L	1709667	1709671	.	0	+
+chr2L	1709674	1709678	.	0	+
+chr2L	1709742	1709746	.	0	+
+chr2L	1710236	1710240	.	0	+
+chr2L	1710304	1710308	.	0	+
+chr2L	1710721	1710725	.	0	+
+chr2L	1710792	1710796	.	0	+
+chr2L	1710894	1710898	.	0	+
+chr2L	1711471	1711475	.	0	+
+chr2L	1712446	1712450	.	0	+
+chr2L	1712512	1712516	.	0	+
+chr2L	1712732	1712736	.	0	+
+chr2L	1712738	1712742	.	0	+
+chr2L	1712950	1712954	.	0	+
+chr2L	1713197	1713201	.	0	+
+chr2L	1713209	1713213	.	0	+
+chr2L	1713644	1713648	.	0	+
+chr2L	1713730	1713734	.	0	+
+chr2L	1713792	1713796	.	0	+
+chr2L	1713854	1713858	.	0	+
+chr2L	1713909	1713913	.	0	+
+chr2L	1714032	1714036	.	0	+
+chr2L	1714073	1714077	.	0	+
+chr2L	1714177	1714181	.	0	+
+chr2L	1714203	1714207	.	0	+
+chr2L	1714275	1714279	.	0	+
+chr2L	1714336	1714340	.	0	+
+chr2L	1714356	1714360	.	0	+
+chr2L	1714369	1714373	.	0	+
+chr2L	1715235	1715239	.	0	+
+chr2L	1715295	1715299	.	0	+
+chr2L	1715499	1715503	.	0	+
+chr2L	1715613	1715617	.	0	+
+chr2L	1715622	1715626	.	0	+
+chr2L	1715908	1715912	.	0	+
+chr2L	1715926	1715930	.	0	+
+chr2L	1715993	1715997	.	0	+
+chr2L	1716517	1716521	.	0	+
+chr2L	1716840	1716844	.	0	+
+chr2L	1717002	1717006	.	0	+
+chr2L	1717183	1717187	.	0	+
+chr2L	1717774	1717778	.	0	+
+chr2L	1718156	1718160	.	0	+
+chr2L	1718488	1718492	.	0	+
+chr2L	1718705	1718709	.	0	+
+chr2L	1718900	1718904	.	0	+
+chr2L	1719812	1719816	.	0	+
+chr2L	1719966	1719970	.	0	+
+chr2L	1720287	1720291	.	0	+
+chr2L	1720446	1720450	.	0	+
+chr2L	1720843	1720847	.	0	+
+chr2L	1720860	1720864	.	0	+
+chr2L	1720889	1720893	.	0	+
+chr2L	1721487	1721491	.	0	+
+chr2L	1721499	1721503	.	0	+
+chr2L	1721582	1721586	.	0	+
+chr2L	1722014	1722018	.	0	+
+chr2L	1722269	1722273	.	0	+
+chr2L	1722375	1722379	.	0	+
+chr2L	1722948	1722952	.	0	+
+chr2L	1723205	1723209	.	0	+
+chr2L	1723239	1723243	.	0	+
+chr2L	1723250	1723254	.	0	+
+chr2L	1723638	1723642	.	0	+
+chr2L	1723889	1723893	.	0	+
+chr2L	1724299	1724303	.	0	+
+chr2L	1724342	1724346	.	0	+
+chr2L	1724588	1724592	.	0	+
+chr2L	1724645	1724649	.	0	+
+chr2L	1724750	1724754	.	0	+
+chr2L	1724850	1724854	.	0	+
+chr2L	1724985	1724989	.	0	+
+chr2L	1725106	1725110	.	0	+
+chr2L	1725256	1725260	.	0	+
+chr2L	1725284	1725288	.	0	+
+chr2L	1725290	1725294	.	0	+
+chr2L	1725388	1725392	.	0	+
+chr2L	1725409	1725413	.	0	+
+chr2L	1725460	1725464	.	0	+
+chr2L	1725598	1725602	.	0	+
+chr2L	1725681	1725685	.	0	+
+chr2L	1725694	1725698	.	0	+
+chr2L	1725756	1725760	.	0	+
+chr2L	1725867	1725871	.	0	+
+chr2L	1725916	1725920	.	0	+
+chr2L	1725922	1725926	.	0	+
+chr2L	1725961	1725965	.	0	+
+chr2L	1726054	1726058	.	0	+
+chr2L	1726132	1726136	.	0	+
+chr2L	1726183	1726187	.	0	+
+chr2L	1726213	1726217	.	0	+
+chr2L	1726233	1726237	.	0	+
+chr2L	1726357	1726361	.	0	+
+chr2L	1726408	1726412	.	0	+
+chr2L	1726624	1726628	.	0	+
+chr2L	1727555	1727559	.	0	+
+chr2L	1727659	1727663	.	0	+
+chr2L	1728200	1728204	.	0	+
+chr2L	1728459	1728463	.	0	+
+chr2L	1728542	1728546	.	0	+
+chr2L	1729035	1729039	.	0	+
+chr2L	1729071	1729075	.	0	+
+chr2L	1729158	1729162	.	0	+
+chr2L	1729163	1729167	.	0	+
+chr2L	1729173	1729177	.	0	+
+chr2L	1729373	1729377	.	0	+
+chr2L	1729865	1729869	.	0	+
+chr2L	1729869	1729873	.	0	+
+chr2L	1730048	1730052	.	0	+
+chr2L	1730316	1730320	.	0	+
+chr2L	1730398	1730402	.	0	+
+chr2L	1730429	1730433	.	0	+
+chr2L	1730784	1730788	.	0	+
+chr2L	1730817	1730821	.	0	+
+chr2L	1731386	1731390	.	0	+
+chr2L	1731438	1731442	.	0	+
+chr2L	1731779	1731783	.	0	+
+chr2L	1733293	1733297	.	0	+
+chr2L	1733375	1733379	.	0	+
+chr2L	1733399	1733403	.	0	+
+chr2L	1733406	1733410	.	0	+
+chr2L	1733433	1733437	.	0	+
+chr2L	1734073	1734077	.	0	+
+chr2L	1734237	1734241	.	0	+
+chr2L	1734683	1734687	.	0	+
+chr2L	1734782	1734786	.	0	+
+chr2L	1734909	1734913	.	0	+
+chr2L	1735511	1735515	.	0	+
+chr2L	1736167	1736171	.	0	+
+chr2L	1736179	1736183	.	0	+
+chr2L	1736184	1736188	.	0	+
+chr2L	1736244	1736248	.	0	+
+chr2L	1736432	1736436	.	0	+
+chr2L	1736563	1736567	.	0	+
+chr2L	1736752	1736756	.	0	+
+chr2L	1736964	1736968	.	0	+
+chr2L	1737472	1737476	.	0	+
+chr2L	1737532	1737536	.	0	+
+chr2L	1738566	1738570	.	0	+
+chr2L	1739061	1739065	.	0	+
+chr2L	1739125	1739129	.	0	+
+chr2L	1739290	1739294	.	0	+
+chr2L	1739358	1739362	.	0	+
+chr2L	1739612	1739616	.	0	+
+chr2L	1740131	1740135	.	0	+
+chr2L	1740154	1740158	.	0	+
+chr2L	1740993	1740997	.	0	+
+chr2L	1741412	1741416	.	0	+
+chr2L	1742003	1742007	.	0	+
+chr2L	1742094	1742098	.	0	+
+chr2L	1742152	1742156	.	0	+
+chr2L	1742517	1742521	.	0	+
+chr2L	1743441	1743445	.	0	+
+chr2L	1743534	1743538	.	0	+
+chr2L	1743632	1743636	.	0	+
+chr2L	1743837	1743841	.	0	+
+chr2L	1744635	1744639	.	0	+
+chr2L	1744841	1744845	.	0	+
+chr2L	1745303	1745307	.	0	+
+chr2L	1745375	1745379	.	0	+
+chr2L	1745380	1745384	.	0	+
+chr2L	1745471	1745475	.	0	+
+chr2L	1745836	1745840	.	0	+
+chr2L	1745870	1745874	.	0	+
+chr2L	1745876	1745880	.	0	+
+chr2L	1745958	1745962	.	0	+
+chr2L	1746543	1746547	.	0	+
+chr2L	1746993	1746997	.	0	+
+chr2L	1747008	1747012	.	0	+
+chr2L	1747249	1747253	.	0	+
+chr2L	1748243	1748247	.	0	+
+chr2L	1748368	1748372	.	0	+
+chr2L	1748387	1748391	.	0	+
+chr2L	1748397	1748401	.	0	+
+chr2L	1748464	1748468	.	0	+
\ No newline at end of file
--- a/test-data/cHi-C/background.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/background.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,1002 +1,1002 @@
 Relative position	size nbinom	prob nbinom	max value	mean value
--500000	58.254577634279	0.998604709282	1.333333333333	0.000105073709
--499000	10.000013353187	0.991925224088	1.500000000000	0.000105073709
--498000	72.266262784304	0.998828265884	1.200000000000	0.000111077921
--497000	51.093422441771	0.998183086351	1.000000000000	0.000120084239
--496000	86.575220693033	0.998899865570	0.800000000000	0.000123086345
--495000	72.441590407550	0.998655447638	0.800000000000	0.000126088451
--494000	75.085350270547	0.998668414055	1.000000000000	0.000129090557
--493000	71.967411178924	0.998612779641	1.000000000000	0.000129090557
--492000	77.026231982211	0.998763649786	1.200000000000	0.000123086345
--491000	96.154018360868	0.999129584825	1.000000000000	0.000108075815
--490000	70.641792331241	0.998918479365	1.400000000000	0.000099069497
--489000	72.297114570842	0.998971709245	0.800000000000	0.000096067391
--488000	55.276417890737	0.998907322028	0.800000000000	0.000078054755
--487000	75.866231077639	0.999020037562	0.600000000000	0.000096067391
--486000	77.908114872120	0.999075493568	0.600000000000	0.000093065285
--485000	70.196050128375	0.998940963837	0.600000000000	0.000096067391
--484000	48.306835304302	0.998789125810	0.600000000000	0.000078054755
--483000	65.826727385050	0.999115985283	0.600000000000	0.000075052649
--482000	10.000003651221	0.996523342626	0.400000000000	0.000045031590
--481000	48.188933357556	0.999179280048	0.400000000000	0.000051035802
--480000	10.000001173914	0.997216871755	0.400000000000	0.000036025272
--479000	10.000002160096	0.996985563716	0.400000000000	0.000039027378
--478000	61.980720096540	0.999287603012	0.800000000000	0.000057040014
--477000	47.193502172887	0.999138448161	0.600000000000	0.000054037908
--476000	75.435666576826	0.999477638616	0.600000000000	0.000051035802
--475000	83.258498044933	0.999385868055	0.600000000000	0.000066046332
--474000	64.452927063111	0.999206823435	0.600000000000	0.000066046332
--473000	68.592799621533	0.999390093904	0.600000000000	0.000054037908
--472000	48.567204011739	0.999139405277	0.600000000000	0.000054037908
--471000	10.000004448331	0.996292395667	0.600000000000	0.000048033696
--470000	10.000000920405	0.995831238986	1.400000000000	0.000054037908
--469000	10.000003872489	0.994909340544	1.400000000000	0.000066046332
--468000	63.250123985231	0.999022818205	1.400000000000	0.000081056861
--467000	51.399551404579	0.998558644000	1.400000000000	0.000096067391
--466000	64.883458129266	0.998762977849	1.000000000000	0.000105073709
--465000	86.383451689662	0.999139519880	0.800000000000	0.000096067391
--464000	64.657320565128	0.998830168725	1.000000000000	0.000099069497
--463000	69.011442263596	0.998889631783	1.000000000000	0.000099069497
--462000	120.365580780362	0.999304923056	1.000000000000	0.000108075815
--461000	83.873478804403	0.999085832019	1.000000000000	0.000099069497
--460000	76.791436688795	0.998822607239	0.800000000000	0.000117082133
--459000	71.300309154477	0.998707418591	1.000000000000	0.000120084239
--458000	70.551044686671	0.998794143443	0.600000000000	0.000111077921
--457000	88.657625851365	0.999084917164	0.800000000000	0.000105073709
--456000	66.985331452249	0.998825498193	0.800000000000	0.000102071603
--455000	212.376735013798	0.999710065148	0.600000000000	0.000078054755
--454000	62.703317289439	0.999261443476	0.600000000000	0.000060042120
--453000	45.696967611307	0.998932417121	0.600000000000	0.000063044226
--452000	82.313181248075	0.999548168551	0.600000000000	0.000048033696
--451000	61.955802866608	0.999249835457	0.600000000000	0.000060042120
--450000	71.163546816639	0.999118429295	1.000000000000	0.000081056861
--449000	57.404577886000	0.998868956077	1.000000000000	0.000084058967
--448000	78.889496868591	0.999175114488	1.000000000000	0.000084058967
--447000	59.455705064746	0.998872066360	1.000000000000	0.000087061073
--446000	69.521205032032	0.998763823049	1.000000000000	0.000111077921
--445000	99.901425243691	0.999325366218	0.800000000000	0.000087061073
--444000	57.825377611967	0.998714905749	1.400000000000	0.000096067391
--443000	74.780716852780	0.999190452885	1.400000000000	0.000078054755
--442000	70.795891257506	0.998917147837	1.400000000000	0.000099069497
--441000	51.279215449017	0.998912746029	0.600000000000	0.000072050543
--440000	76.363418055254	0.999244164363	0.600000000000	0.000075052649
--439000	74.401139539007	0.999187307338	0.800000000000	0.000078054755
--438000	52.200730226460	0.998448424743	1.000000000000	0.000105073709
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+430000	118.469353414953	0.995841025758	1.400000000000	0.000424489831
+431000	196.824202082581	0.997286791436	1.800000000000	0.000456923677
+432000	120.135982824242	0.995542270605	1.400000000000	0.000459174533
+433000	134.618808757883	0.996275763050	1.400000000000	0.000429550369
+434000	128.279493141976	0.996591698681	1.200000000000	0.000374479809
+435000	189.199463585662	0.997959863242	0.800000000000	0.000331953099
+436000	102.098921943664	0.996092950814	1.000000000000	0.000351192829
+437000	140.544827573829	0.996998697469	1.000000000000	0.000360948186
+438000	186.818550488660	0.997760329166	1.000000000000	0.000357958641
+439000	107.036799514735	0.995863971016	1.000000000000	0.000379374970
+440000	128.546164980955	0.996946247067	1.200000000000	0.000336102513
+441000	187.948043854145	0.997909380957	0.800000000000	0.000336102513
+442000	166.275455185898	0.997360767582	1.400000000000	0.000375581220
+443000	150.591835330413	0.997030691147	1.400000000000	0.000382823833
+444000	144.859828494596	0.996903162520	1.400000000000	0.000384117157
+445000	181.127453398191	0.997559041921	1.400000000000	0.000384117157
+446000	160.136119588827	0.997366406029	1.600000000000	0.000359893553
+447000	153.653411583530	0.997172630419	1.200000000000	0.000375581220
+448000	141.661704353510	0.997163979271	1.400000000000	0.000345930071
+449000	124.591789049055	0.996755483579	1.400000000000	0.000346179660
+450000	140.232016383950	0.997067070092	1.200000000000	0.000352107394
+451000	136.018310879152	0.997198243244	1.000000000000	0.000330767552
+452000	246.419596102391	0.998452925685	1.000000000000	0.000325917588
+453000	133.267828865974	0.997093260709	1.000000000000	0.000330767552
+454000	111.562325167782	0.996668013833	1.000000000000	0.000325432591
+455000	136.735744503062	0.997168723327	1.000000000000	0.000331395194
+456000	107.078418601392	0.996473504625	1.000000000000	0.000323467080
+457000	129.245163973247	0.997085556223	1.000000000000	0.000322468725
+458000	105.576577704040	0.996545373786	1.000000000000	0.000312171404
+459000	127.868794891999	0.997409239339	0.800000000000	0.000283033695
+460000	106.303153236011	0.997074941993	0.600000000000	0.000266120383
+461000	126.838873099817	0.997248182634	0.800000000000	0.000298757789
+462000	142.511212214533	0.997018798351	0.800000000000	0.000363705134
+463000	110.665900101286	0.996960672273	0.800000000000	0.000288455796
+464000	95.203501929856	0.995744217821	1.800000000000	0.000347324326
+465000	137.363904547769	0.997021971833	1.800000000000	0.000352107394
+466000	118.557203735630	0.996290881001	2.400000000000	0.000376758591
+467000	104.819090517074	0.995525960971	2.800000000000	0.000402408450
+468000	114.597405436879	0.995690757202	2.800000000000	0.000423382467
+469000	129.271097317921	0.997170331551	1.400000000000	0.000314762670
+470000	192.030681022578	0.997984998366	1.400000000000	0.000330423361
+471000	148.206038001898	0.997389657398	1.000000000000	0.000331090883
+472000	97.546089803069	0.995843333605	1.200000000000	0.000347128098
+473000	95.851837787801	0.995983996487	1.200000000000	0.000330056224
+474000	99.818854582017	0.996557343281	1.000000000000	0.000294342649
+475000	148.008769541300	0.997902427625	0.600000000000	0.000265562479
+476000	148.345768593866	0.997933098098	0.600000000000	0.000262644210
+477000	123.596807612976	0.997297923191	0.600000000000	0.000284531228
+478000	204.246569441019	0.998287432528	1.000000000000	0.000298757789
+479000	132.924248355030	0.997278666969	0.800000000000	0.000309427710
+480000	136.416688826340	0.997425348906	0.800000000000	0.000301268359
+481000	118.446922382493	0.997078476496	1.000000000000	0.000296247219
+482000	118.529156084928	0.997003411887	1.200000000000	0.000304092749
+483000	190.680584441799	0.998045921750	1.000000000000	0.000318674975
+484000	192.305361142196	0.998005560472	1.200000000000	0.000328791641
+485000	171.354362305989	0.997464844394	1.200000000000	0.000373052054
+486000	120.791244594597	0.996480163123	1.600000000000	0.000364199971
+487000	230.056159698575	0.998148828248	1.600000000000	0.000364199971
+488000	195.433175858843	0.997957440166	1.400000000000	0.000341437473
+489000	126.632801152788	0.996613466031	1.600000000000	0.000367303948
+490000	169.329748474940	0.997643487089	1.200000000000	0.000341437473
+491000	136.266699963976	0.997144438338	1.000000000000	0.000336264178
+492000	132.474984457930	0.997281892907	1.000000000000	0.000312171404
+493000	143.910368825532	0.997529065543	1.200000000000	0.000304092749
+494000	115.246894063938	0.997187873361	1.200000000000	0.000278027657
+495000	170.264731113853	0.997728931336	1.200000000000	0.000331682117
+496000	150.361715442266	0.997070480810	1.200000000000	0.000380834105
+497000	132.494299731452	0.996465234668	1.400000000000	0.000400817903
+498000	197.912620506313	0.997679641998	1.200000000000	0.000393395349
+499000	142.734281997358	0.996531092376	1.000000000000	0.000426796841
+500000	10.000000000000	nan	0.000000000000	0.000000000000
Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.4.3
+# Created with chicQualityControl version 3.6
 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
 # Used Matrices 0_matrix.cool	1_matrix.cool	
 # Chromosome	Start	End	Sparsity 0_matrix.cool	Sparsity 1_matrix.cool
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.4.3
+# Created with chicQualityControl version 3.6
 # QC report for matrices: 0_matrix.cool 1_matrix.cool 
 #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
 
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
--- a/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,8 +1,8 @@
 # /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool	chr1_14300280_14300280	14.10  Mbp	14.50  Mbp	Eya1	Sum of interactions in fixate range: 673.0
 #Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative interactions	p-value	x-fold	Raw target
-chr1	14274000	14278000	Eya1	673.0	-26000	0.00832095096400000019	0.00703769867936687721	7.81112575817000021061	5.59999999999999964473
-chr1	14296000	14298000	Eya1	673.0	-3000	0.05794947993999999963	0.10421572859864070004	3.78135593591500018817	39.00000000000000000000
-chr1	14314000	14316000	Eya1	673.0	14000	0.01515601783000000008	0.04850785315391703545	3.19033393500999995496	10.19999999999999928946
-chr1	14317000	14319000	Eya1	673.0	17000	0.01456166419000000031	0.03491443188205700654	3.51709033858399999772	9.80000000000000071054
-chr1	14480000	14488000	Eya1	673.0	184000	0.01129271916799999900	0.00000001048074382837	19.28508294646199772160	7.59999999999999875655
+chr1	14274000	14278000	Eya1	673.0	-26000	0.00832095096400000019	0.00706210137955387562	7.81112575817000021061	5.59999999999999964473
+chr1	14296000	14298000	Eya1	673.0	-3000	0.05794947993999999963	0.10178166638720864690	3.78135593591500018817	39.00000000000000000000
+chr1	14314000	14316000	Eya1	673.0	14000	0.01515601783000000008	0.04060984916018672841	3.19033393500999995496	10.19999999999999928946
+chr1	14317000	14319000	Eya1	673.0	17000	0.01456166419000000031	0.02428991556274540109	3.51709033858399999772	9.80000000000000071054
+chr1	14480000	14488000	Eya1	673.0	184000	0.01129271916799999900	0.00000047362266253348	19.28508294646199772160	7.59999999999999875655
 chr1	14491000	14501000	Eya1	673.0	200000	0.03068350668399999828	0.00000000000000011102	56.96782483342801128856	20.64999999999999857891
--- a/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
 # targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
 # Mode: x-fold background with 1.5
 # Used p-value: 0.2
--- a/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
 # targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
 # Mode: x-fold background with 1.5
 # Used p-value: 0.2
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,8 +1,8 @@
 # FL-E13-5_chr1.cool	chr1_14300280_14300280	14.10  Mbp	14.50  Mbp	Eya1	Sum of interactions in fixate range: 673.0
 #Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative interactions	p-value	x-fold	Raw target
-chr1	14274000	14279000	Eya1	673.0	-26000	0.01040118870499999980	0.00284160000885902431	9.15400589712000112286	7.00000000000000000000
-chr1	14295000	14372000	Eya1	673.0	-1000	0.73997028231099992723	0.00004780944416038491	71.55022378473699973256	497.99999999999977262632
-chr1	14391000	14404000	Eya1	673.0	99000	0.01485884100899999803	0.00001657170147506548	12.71460890380599906280	10.00000000000000000000
-chr1	14405000	14431000	Eya1	673.0	126000	0.01485884100399999762	0.00000000019301882315	16.50018487636599928692	10.00000000000000532907
-chr1	14447000	14465000	Eya1	673.0	150000	0.01485884100799999760	0.00000000084501772246	20.98645213257099939597	10.00000000000000177636
+chr1	14274000	14279000	Eya1	673.0	-26000	0.01040118870499999980	0.00132401127244263783	9.15400589712000112286	7.00000000000000000000
+chr1	14295000	14372000	Eya1	673.0	-1000	0.73997028231099992723	0.00000273538672768137	71.55022378473699973256	497.99999999999977262632
+chr1	14391000	14404000	Eya1	673.0	99000	0.01485884100899999803	0.00000099822649402004	12.71460890380599906280	10.00000000000000000000
+chr1	14405000	14431000	Eya1	673.0	126000	0.01485884100399999762	0.00000000706881753132	16.50018487636599928692	10.00000000000000532907
+chr1	14447000	14465000	Eya1	673.0	150000	0.01485884100799999760	0.00000000163091362637	20.98645213257099939597	10.00000000000000177636
 chr1	14476000	14501000	Eya1	673.0	200000	0.04494799405200000653	0.00000000000000011102	81.22289233532099217427	30.24999999999999644729
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,10 +1,10 @@
 # FL-E13-5_chr1.cool	chr1_19093103_19093103	18.89  Mbp	19.29  Mbp	Tfap2d	Sum of interactions in fixate range: 472.0
 #Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative interactions	p-value	x-fold	Raw target
-chr1	19088000	19093000	Tfap2d	472.0	-1000	0.25550847457600001089	0.11635169910476195199	8.11832748109999968733	120.59999999999999431566
-chr1	19094000	19118000	Tfap2d	472.0	1000	0.38686440678100009194	0.03474409585293225522	32.83428528261499934615	182.60000000000005115908
-chr1	19124000	19141000	Tfap2d	472.0	33000	0.04661016949300000184	0.00000002462477854959	22.39995010446000023308	22.00000000000000000000
-chr1	19143000	19150000	Tfap2d	472.0	52000	0.01059322034000000079	0.01821075341789391011	7.00310519245599927274	5.00000000000000000000
-chr1	19153000	19185000	Tfap2d	472.0	65000	0.03177966102100000800	0.00000000020590662508	24.96572554191800108470	14.99999999999999467093
-chr1	19186000	19210000	Tfap2d	472.0	108000	0.03177966101800000498	0.00000007308534966111	29.45424687062300250773	15.00000000000000000000
-chr1	19215000	19251000	Tfap2d	472.0	137000	0.04237288135900001140	0.00000000012967626972	56.40252329690899557590	19.99999999999999644729
-chr1	19252000	19264000	Tfap2d	472.0	163000	0.01694915254200000249	0.00000130986798663191	24.34766306781100198009	8.00000000000000000000
+chr1	19088000	19093000	Tfap2d	472.0	-1000	0.25550847457600001089	0.10302839603584690309	8.11832748109999968733	120.59999999999999431566
+chr1	19094000	19118000	Tfap2d	472.0	1000	0.38686440678100009194	0.02157410618457478169	32.83428528261499934615	182.60000000000005115908
+chr1	19124000	19141000	Tfap2d	472.0	33000	0.04661016949300000184	0.00000000000393274302	22.39995010446000023308	22.00000000000000000000
+chr1	19143000	19150000	Tfap2d	472.0	52000	0.01059322034000000079	0.01905738347386221054	7.00310519245599927274	5.00000000000000000000
+chr1	19153000	19185000	Tfap2d	472.0	65000	0.03177966102100000800	0.00000000000269295697	24.96572554191800108470	14.99999999999999467093
+chr1	19186000	19210000	Tfap2d	472.0	108000	0.03177966101800000498	0.00000001275562755421	29.45424687062300250773	15.00000000000000000000
+chr1	19215000	19251000	Tfap2d	472.0	137000	0.04237288135900001140	0.00000000000112376775	56.40252329690899557590	19.99999999999999644729
+chr1	19252000	19264000	Tfap2d	472.0	163000	0.01694915254200000249	0.00000062934133893133	24.34766306781100198009	8.00000000000000000000
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,5 +1,5 @@
 # MB-E10-5_chr1.cool	chr1_14300280_14300280	14.10  Mbp	14.50  Mbp	Eya1	Sum of interactions in fixate range: 832.0
 #Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative interactions	p-value	x-fold	Raw target
-chr1	14290000	14439000	Eya1	832.0	-1000	0.77524038462200028921	0.00000214655292485322	124.40376311550902244107	645.00000000000000000000
+chr1	14290000	14439000	Eya1	832.0	-1000	0.77524038462200028921	0.00000003592597119795	124.40376311550902244107	645.00000000000000000000
 chr1	14444000	14467000	Eya1	832.0	149000	0.03004807692100000191	0.00000000000000011102	43.43355247431500032462	25.00000000000000000000
 chr1	14484000	14501000	Eya1	832.0	200000	0.02902644230799999656	0.00000000000000011102	53.10190206687700253951	24.15000000000000213163
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,6 +1,6 @@
 # MB-E10-5_chr1.cool	chr1_19093103_19093103	18.89  Mbp	19.29  Mbp	Tfap2d	Sum of interactions in fixate range: 800.0
 #Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative interactions	p-value	x-fold	Raw target
-chr1	19077000	19083000	Tfap2d	800.0	-15000	0.01875000000000000278	0.00087756598335464453	9.05078678760400023862	15.00000000000000000000
-chr1	19084000	19118000	Tfap2d	800.0	0	0.64874999999999971578	0.00000017949046560162	44.36507725070399033029	518.99999999999988631316
+chr1	19077000	19083000	Tfap2d	800.0	-15000	0.01875000000000000278	0.00009145581248537482	9.05078678760400023862	15.00000000000000000000
+chr1	19084000	19118000	Tfap2d	800.0	0	0.64874999999999971578	0.00000005045883955113	44.36507725070399033029	518.99999999999988631316
 chr1	19120000	19249000	Tfap2d	800.0	105000	0.25625000000000008882	0.00000000000000011102	244.06286621622496113559	204.99999999999994315658
-chr1	19258000	19274000	Tfap2d	800.0	169000	0.01000000000000000021	0.00000195299526528636	14.62211731845800244400	8.00000000000000000000
+chr1	19258000	19274000	Tfap2d	800.0	169000	0.01000000000000000021	0.00000152506365280747	14.62211731845800244400	8.00000000000000000000
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
 # targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
 # Mode: loose p-value with 0.5
 # Used p-value: 0.2
@@ -6,4 +6,4 @@
 chr1	14274000	14279000
 chr1	14290000	14439000
 chr1	14444000	14467000
-chr1	14476000	14501000
+chr1	14484000	14501000
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
 # targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
 # Mode: loose p-value with 0.5
 # Used p-value: 0.2
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
 # targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
 # Mode: loose p-value with 0.5
 # Used p-value: 0.2
--- a/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3
+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6
 # FL-E13-5_chr1.cool	chr1_14300280_14300280	14.10  Mbp	14.50  Mbp	Eya1	Sum of interactions in fixate range: 673.0
 # Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative Interactions	p-value	x-fold	Raw
 #
@@ -42,11 +42,11 @@
 chr1	14137000	14138000	Eya1	673.0	-163000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14138000	14139000	Eya1	673.0	-162000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14139000	14140000	Eya1	673.0	-161000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14140000	14141000	Eya1	673.0	-160000	0.000891530461	0.012107544045	4.242405017910	0.600000000000
-chr1	14141000	14142000	Eya1	673.0	-159000	0.000891530461	0.012107544045	4.789812097144	0.600000000000
-chr1	14142000	14143000	Eya1	673.0	-158000	0.000891530461	0.012107544045	4.303889149198	0.600000000000
-chr1	14143000	14144000	Eya1	673.0	-157000	0.000891530461	0.012107544045	4.367181637306	0.600000000000
-chr1	14144000	14145000	Eya1	673.0	-156000	0.000891530461	0.012107544045	5.120143967809	0.600000000000
+chr1	14140000	14141000	Eya1	673.0	-160000	0.000891530461	0.232516348110	2.088887205761	0.600000000000
+chr1	14141000	14142000	Eya1	673.0	-159000	0.000891530461	0.232516348110	2.274191716551	0.600000000000
+chr1	14142000	14143000	Eya1	673.0	-158000	0.000891530461	0.232516348110	2.043476610792	0.600000000000
+chr1	14143000	14144000	Eya1	673.0	-157000	0.000891530461	0.232516348110	2.303919713268	0.600000000000
+chr1	14144000	14145000	Eya1	673.0	-156000	0.000891530461	0.232516348110	2.431032520312	0.600000000000
 chr1	14145000	14146000	Eya1	673.0	-155000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14146000	14147000	Eya1	673.0	-154000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14147000	14148000	Eya1	673.0	-153000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -77,53 +77,53 @@
 chr1	14172000	14173000	Eya1	673.0	-128000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14173000	14174000	Eya1	673.0	-127000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14174000	14175000	Eya1	673.0	-126000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14175000	14176000	Eya1	673.0	-125000	0.000297176820	0.042850447268	0.916568982282	0.200000000000
-chr1	14176000	14177000	Eya1	673.0	-124000	0.000297176820	0.042850447268	0.908160092485	0.200000000000
-chr1	14177000	14178000	Eya1	673.0	-123000	0.000297176820	0.042850447268	0.798302018335	0.200000000000
-chr1	14178000	14179000	Eya1	673.0	-122000	0.000297176820	0.042850447268	0.925135047590	0.200000000000
-chr1	14179000	14180000	Eya1	673.0	-121000	0.000297176820	0.042850447268	0.883834378206	0.200000000000
+chr1	14175000	14176000	Eya1	673.0	-125000	0.000297176820	0.378306706409	0.499656661362	0.200000000000
+chr1	14176000	14177000	Eya1	673.0	-124000	0.000297176820	0.378306706409	0.415222227347	0.200000000000
+chr1	14177000	14178000	Eya1	673.0	-123000	0.000297176820	0.378306706409	0.393070172785	0.200000000000
+chr1	14178000	14179000	Eya1	673.0	-122000	0.000297176820	0.378306706409	0.455520574435	0.200000000000
+chr1	14179000	14180000	Eya1	673.0	-121000	0.000297176820	0.378306706409	0.450727149836	0.200000000000
 chr1	14180000	14181000	Eya1	673.0	-120000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14181000	14182000	Eya1	673.0	-119000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14182000	14183000	Eya1	673.0	-118000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14183000	14184000	Eya1	673.0	-117000	0.000297176820	0.042850447268	0.860777829009	0.200000000000
-chr1	14184000	14185000	Eya1	673.0	-116000	0.000297176820	0.042850447268	0.791915602137	0.200000000000
-chr1	14185000	14186000	Eya1	673.0	-115000	0.000297176820	0.042850447268	0.761457309513	0.200000000000
-chr1	14186000	14187000	Eya1	673.0	-114000	0.000297176820	0.042850447268	0.811388936776	0.200000000000
-chr1	14187000	14188000	Eya1	673.0	-113000	0.000297176820	0.042850447268	0.891796850153	0.200000000000
+chr1	14183000	14184000	Eya1	673.0	-117000	0.000297176820	0.378306706409	0.529790233372	0.200000000000
+chr1	14184000	14185000	Eya1	673.0	-116000	0.000297176820	0.378306706409	0.473481099396	0.200000000000
+chr1	14185000	14186000	Eya1	673.0	-115000	0.000297176820	0.378306706409	0.468660590867	0.200000000000
+chr1	14186000	14187000	Eya1	673.0	-114000	0.000297176820	0.378306706409	0.456587367046	0.200000000000
+chr1	14187000	14188000	Eya1	673.0	-113000	0.000297176820	0.378306706409	0.454787754802	0.200000000000
 chr1	14188000	14189000	Eya1	673.0	-112000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14189000	14190000	Eya1	673.0	-111000	0.000297176820	0.042850447268	1.064402690160	0.200000000000
-chr1	14190000	14191000	Eya1	673.0	-110000	0.000297176820	0.042850447268	1.207188418049	0.200000000000
-chr1	14191000	14192000	Eya1	673.0	-109000	0.000297176820	0.042850447268	1.010096430089	0.200000000000
-chr1	14192000	14193000	Eya1	673.0	-108000	0.000297176820	0.042850447268	0.951821635672	0.200000000000
-chr1	14193000	14194000	Eya1	673.0	-107000	0.000297176820	0.042850447268	0.824912085835	0.200000000000
+chr1	14189000	14190000	Eya1	673.0	-111000	0.000297176820	0.378306706409	0.505375936152	0.200000000000
+chr1	14190000	14191000	Eya1	673.0	-110000	0.000297176820	0.378306706409	0.615627326013	0.200000000000
+chr1	14191000	14192000	Eya1	673.0	-109000	0.000297176820	0.378306706409	0.515116742893	0.200000000000
+chr1	14192000	14193000	Eya1	673.0	-108000	0.000297176820	0.378306706409	0.518874225194	0.200000000000
+chr1	14193000	14194000	Eya1	673.0	-107000	0.000297176820	0.378306706409	0.493209478897	0.200000000000
 chr1	14194000	14195000	Eya1	673.0	-106000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14195000	14196000	Eya1	673.0	-105000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14196000	14197000	Eya1	673.0	-104000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14197000	14198000	Eya1	673.0	-103000	0.001188707281	0.006261619191	5.424079472832	0.800000000000
-chr1	14198000	14199000	Eya1	673.0	-102000	0.001188707281	0.006261619191	5.499413910652	0.800000000000
-chr1	14199000	14200000	Eya1	673.0	-101000	0.001188707281	0.006261619191	5.822908849742	0.800000000000
-chr1	14200000	14201000	Eya1	673.0	-100000	0.001188707281	0.006261619191	4.888367915554	0.800000000000
-chr1	14201000	14202000	Eya1	673.0	-99000	0.001188707281	0.006261619191	4.499520464782	0.800000000000
+chr1	14197000	14198000	Eya1	673.0	-103000	0.001188707281	0.177992691518	2.956872299965	0.800000000000
+chr1	14198000	14199000	Eya1	673.0	-102000	0.001188707281	0.177992691518	3.288063194467	0.800000000000
+chr1	14199000	14200000	Eya1	673.0	-101000	0.001188707281	0.177992691518	2.867100083177	0.800000000000
+chr1	14200000	14201000	Eya1	673.0	-100000	0.001188707281	0.177992691518	2.922722837730	0.800000000000
+chr1	14201000	14202000	Eya1	673.0	-99000	0.001188707281	0.177992691518	3.006731581888	0.800000000000
 chr1	14202000	14203000	Eya1	673.0	-98000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14203000	14204000	Eya1	673.0	-97000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14204000	14205000	Eya1	673.0	-96000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14205000	14206000	Eya1	673.0	-95000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14206000	14207000	Eya1	673.0	-94000	0.000594353640	0.023000625561	1.546710160135	0.400000000000
-chr1	14207000	14208000	Eya1	673.0	-93000	0.000594353640	0.023000625561	1.488563161197	0.400000000000
-chr1	14208000	14209000	Eya1	673.0	-92000	0.000594353640	0.023000625561	1.093806079608	0.400000000000
-chr1	14209000	14210000	Eya1	673.0	-91000	0.000594353640	0.023000625561	1.031140105862	0.400000000000
-chr1	14210000	14211000	Eya1	673.0	-90000	0.000594353640	0.023000625561	1.020509795419	0.400000000000
+chr1	14206000	14207000	Eya1	673.0	-94000	0.000594353640	0.299067125362	0.951966824636	0.400000000000
+chr1	14207000	14208000	Eya1	673.0	-93000	0.000594353640	0.299067125362	0.942355129306	0.400000000000
+chr1	14208000	14209000	Eya1	673.0	-92000	0.000594353640	0.299067125362	0.653979419394	0.400000000000
+chr1	14209000	14210000	Eya1	673.0	-91000	0.000594353640	0.299067125362	0.616511848749	0.400000000000
+chr1	14210000	14211000	Eya1	673.0	-90000	0.000594353640	0.299067125362	0.610156056253	0.400000000000
 chr1	14211000	14212000	Eya1	673.0	-89000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14212000	14213000	Eya1	673.0	-88000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14213000	14214000	Eya1	673.0	-87000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14214000	14215000	Eya1	673.0	-86000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14215000	14216000	Eya1	673.0	-85000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14216000	14217000	Eya1	673.0	-84000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14217000	14218000	Eya1	673.0	-83000	0.000594353640	0.023000625561	1.466510373460	0.400000000000
-chr1	14218000	14219000	Eya1	673.0	-82000	0.000594353640	0.023000625561	1.546710160135	0.400000000000
-chr1	14219000	14220000	Eya1	673.0	-81000	0.000594353640	0.023000625561	1.816320184969	0.400000000000
-chr1	14220000	14221000	Eya1	673.0	-80000	0.000594353640	0.023000625561	2.106158514412	0.400000000000
-chr1	14221000	14222000	Eya1	673.0	-79000	0.000594353640	0.023000625561	1.885513335312	0.400000000000
+chr1	14217000	14218000	Eya1	673.0	-83000	0.000594353640	0.299067125362	0.722084465625	0.400000000000
+chr1	14218000	14219000	Eya1	673.0	-82000	0.000594353640	0.299067125362	0.734374408148	0.400000000000
+chr1	14219000	14220000	Eya1	673.0	-81000	0.000594353640	0.299067125362	0.766564111695	0.400000000000
+chr1	14220000	14221000	Eya1	673.0	-80000	0.000594353640	0.299067125362	0.777777150044	0.400000000000
+chr1	14221000	14222000	Eya1	673.0	-79000	0.000594353640	0.299067125362	0.895237372699	0.400000000000
 chr1	14222000	14223000	Eya1	673.0	-78000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14223000	14224000	Eya1	673.0	-77000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14224000	14225000	Eya1	673.0	-76000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -160,11 +160,11 @@
 chr1	14255000	14256000	Eya1	673.0	-45000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14256000	14257000	Eya1	673.0	-44000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14257000	14258000	Eya1	673.0	-43000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14258000	14259000	Eya1	673.0	-42000	0.000297176820	0.042850447268	0.363931802218	0.200000000000
-chr1	14259000	14260000	Eya1	673.0	-41000	0.000297176820	0.042850447268	0.358657428234	0.200000000000
-chr1	14260000	14261000	Eya1	673.0	-40000	0.000297176820	0.042850447268	0.367990521232	0.200000000000
-chr1	14261000	14262000	Eya1	673.0	-39000	0.000297176820	0.042850447268	0.400767005169	0.200000000000
-chr1	14262000	14263000	Eya1	673.0	-38000	0.000297176820	0.042850447268	0.438006416838	0.200000000000
+chr1	14258000	14259000	Eya1	673.0	-42000	0.000297176820	0.378306706409	0.255991079032	0.200000000000
+chr1	14259000	14260000	Eya1	673.0	-41000	0.000297176820	0.378306706409	0.264895116450	0.200000000000
+chr1	14260000	14261000	Eya1	673.0	-40000	0.000297176820	0.378306706409	0.284730597734	0.200000000000
+chr1	14261000	14262000	Eya1	673.0	-39000	0.000297176820	0.378306706409	0.288948634799	0.200000000000
+chr1	14262000	14263000	Eya1	673.0	-38000	0.000297176820	0.378306706409	0.323500230665	0.200000000000
 chr1	14263000	14264000	Eya1	673.0	-37000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14264000	14265000	Eya1	673.0	-36000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14265000	14266000	Eya1	673.0	-35000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -176,11 +176,11 @@
 chr1	14271000	14272000	Eya1	673.0	-29000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14272000	14273000	Eya1	673.0	-28000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14273000	14274000	Eya1	673.0	-27000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14274000	14275000	Eya1	673.0	-26000	0.002080237741	0.000789856579	2.348902209517	1.400000000000
-chr1	14275000	14276000	Eya1	673.0	-25000	0.002080237741	0.000789856579	1.946421773926	1.400000000000
-chr1	14276000	14277000	Eya1	673.0	-24000	0.002080237741	0.000789856579	1.940969612053	1.400000000000
-chr1	14277000	14278000	Eya1	673.0	-23000	0.002080237741	0.000789856579	1.574832162674	1.400000000000
-chr1	14278000	14279000	Eya1	673.0	-22000	0.002080237741	0.000789856579	1.342880138950	1.400000000000
+chr1	14274000	14275000	Eya1	673.0	-26000	0.002080237741	0.073459752807	1.445698771287	1.400000000000
+chr1	14275000	14276000	Eya1	673.0	-25000	0.002080237741	0.073459752807	1.334892806270	1.400000000000
+chr1	14276000	14277000	Eya1	673.0	-24000	0.002080237741	0.073459752807	1.433550042577	1.400000000000
+chr1	14277000	14278000	Eya1	673.0	-23000	0.002080237741	0.073459752807	1.273904696232	1.400000000000
+chr1	14278000	14279000	Eya1	673.0	-22000	0.002080237741	0.073459752807	1.062660641952	1.400000000000
 chr1	14279000	14280000	Eya1	673.0	-21000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14280000	14281000	Eya1	673.0	-20000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14281000	14282000	Eya1	673.0	-19000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -197,91 +197,91 @@
 chr1	14292000	14293000	Eya1	673.0	-8000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14293000	14294000	Eya1	673.0	-7000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14294000	14295000	Eya1	673.0	-6000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14295000	14296000	Eya1	673.0	-5000	0.008023774146	0.000000000085	1.372030367534	5.400000000000
-chr1	14296000	14297000	Eya1	673.0	-4000	0.020208023774	0.000000000000	2.029940474990	13.600000000000
-chr1	14297000	14298000	Eya1	673.0	-3000	0.037741456166	0.000000000000	1.751415460925	25.400000000000
-chr1	14298000	14299000	Eya1	673.0	-2000	0.090638930163	0.000000000000	1.354924485843	61.000000000000
-chr1	14299000	14300000	Eya1	673.0	-1000	0.097771173848	0.000000000000	1.278913376138	65.800000000000
-chr1	14300000	14301000	Eya1	673.0	0	0.094205052006	0.392071887492	1.184182637854	63.400000000000
-chr1	14301000	14302000	Eya1	673.0	1000	0.083209509658	0.000000000000	1.063381778729	56.000000000000
-chr1	14302000	14303000	Eya1	673.0	2000	0.071025260030	0.000000000000	1.038198990836	47.800000000000
-chr1	14303000	14304000	Eya1	673.0	3000	0.021396731055	0.000000000000	0.863071011870	14.400000000000
-chr1	14304000	14305000	Eya1	673.0	4000	0.017533432392	0.000000000000	1.120778653450	11.800000000000
-chr1	14305000	14306000	Eya1	673.0	5000	0.013670133730	0.000000000000	1.128784013412	9.200000000000
-chr1	14306000	14307000	Eya1	673.0	6000	0.013967310550	0.000000000000	1.335008367430	9.400000000000
-chr1	14307000	14308000	Eya1	673.0	7000	0.009212481426	0.000000000000	0.964688134828	6.200000000000
-chr1	14308000	14309000	Eya1	673.0	8000	0.008023774146	0.000000000000	0.920990749860	5.400000000000
-chr1	14309000	14310000	Eya1	673.0	9000	0.007132243685	0.000000000000	0.891127833920	4.800000000000
-chr1	14310000	14311000	Eya1	673.0	10000	0.007726597325	0.000000000000	1.066166406754	5.200000000000
-chr1	14311000	14312000	Eya1	673.0	11000	0.008320950966	0.000000000000	1.299439571542	5.600000000000
-chr1	14312000	14313000	Eya1	673.0	12000	0.007726597325	0.000000000000	1.297894960074	5.200000000000
-chr1	14313000	14314000	Eya1	673.0	13000	0.007429420505	0.000000000000	1.383307018327	5.000000000000
-chr1	14314000	14315000	Eya1	673.0	14000	0.007726597325	0.000000000000	1.591667103270	5.200000000000
-chr1	14315000	14316000	Eya1	673.0	15000	0.007429420505	0.000000000000	1.598666831740	5.000000000000
-chr1	14316000	14317000	Eya1	673.0	16000	0.006240713224	0.000000000000	1.370321987153	4.200000000000
-chr1	14317000	14318000	Eya1	673.0	17000	0.007429420505	0.000000000000	1.768932277163	5.000000000000
-chr1	14318000	14319000	Eya1	673.0	18000	0.007132243685	0.000000000000	1.748158061421	4.800000000000
-chr1	14319000	14320000	Eya1	673.0	19000	0.004457652303	0.000000000000	1.120635285536	3.000000000000
-chr1	14320000	14321000	Eya1	673.0	20000	0.004754829123	0.000000000000	1.269095515585	3.200000000000
-chr1	14321000	14322000	Eya1	673.0	21000	0.005052005944	0.000000000000	1.386178462947	3.400000000000
-chr1	14322000	14323000	Eya1	673.0	22000	0.003863298663	0.000000000000	1.104603307083	2.600000000000
-chr1	14323000	14324000	Eya1	673.0	23000	0.002377414562	0.000000000000	0.759267115893	1.600000000000
-chr1	14324000	14325000	Eya1	673.0	24000	0.002377414562	0.000000000000	0.773355079816	1.600000000000
-chr1	14325000	14326000	Eya1	673.0	25000	0.001188707281	0.000000000000	0.407783523060	0.800000000000
-chr1	14326000	14327000	Eya1	673.0	26000	0.000297176820	0.000000000000	0.113911910512	0.200000000000
-chr1	14327000	14328000	Eya1	673.0	27000	0.000594353640	0.000000000000	0.233465684468	0.400000000000
-chr1	14328000	14329000	Eya1	673.0	28000	0.000891530461	0.000000000000	0.336698810284	0.600000000000
-chr1	14329000	14330000	Eya1	673.0	29000	0.000891530461	0.000000000000	0.354377506766	0.600000000000
-chr1	14330000	14331000	Eya1	673.0	30000	0.001485884101	0.000000000000	0.599936062031	1.000000000000
-chr1	14331000	14332000	Eya1	673.0	31000	0.001188707281	0.000000000000	0.478209904505	0.800000000000
-chr1	14332000	14333000	Eya1	673.0	32000	0.000891530461	0.000000000000	0.374015555000	0.600000000000
-chr1	14333000	14334000	Eya1	673.0	33000	0.000594353640	0.000000000000	0.253494110719	0.400000000000
-chr1	14334000	14335000	Eya1	673.0	34000	0.000891530461	0.000000000000	0.396486449496	0.600000000000
-chr1	14335000	14336000	Eya1	673.0	35000	0.000297176820	0.000000000000	0.139815607657	0.200000000000
-chr1	14336000	14337000	Eya1	673.0	36000	0.001485884101	0.000000000000	0.718355952406	1.000000000000
-chr1	14337000	14338000	Eya1	673.0	37000	0.002080237741	0.000000000000	1.031140106373	1.400000000000
-chr1	14338000	14339000	Eya1	673.0	38000	0.002080237741	0.000000000000	1.056289865257	1.400000000000
-chr1	14339000	14340000	Eya1	673.0	39000	0.002080237741	0.000000000000	1.062770171228	1.400000000000
-chr1	14340000	14341000	Eya1	673.0	40000	0.002080237741	0.000000000000	0.999893436738	1.400000000000
-chr1	14341000	14342000	Eya1	673.0	41000	0.000891530461	0.000000000000	0.436076873137	0.600000000000
-chr1	14342000	14343000	Eya1	673.0	42000	0.000594353640	0.000000000000	0.286925942726	0.400000000000
-chr1	14343000	14344000	Eya1	673.0	43000	0.001485884101	0.000000000000	0.748785553889	1.000000000000
-chr1	14344000	14345000	Eya1	673.0	44000	0.001188707281	0.000000000000	0.644882411906	0.800000000000
-chr1	14345000	14346000	Eya1	673.0	45000	0.001485884101	0.000000000000	0.895022154168	1.000000000000
-chr1	14346000	14347000	Eya1	673.0	46000	0.001485884101	0.000000000000	0.896643571126	1.000000000000
-chr1	14347000	14348000	Eya1	673.0	47000	0.001485884101	0.000000000000	0.939178844655	1.000000000000
-chr1	14348000	14349000	Eya1	673.0	48000	0.000594353640	0.000000000000	0.381462235985	0.400000000000
-chr1	14349000	14350000	Eya1	673.0	49000	0.000594353640	0.000000000000	0.367307792987	0.400000000000
-chr1	14350000	14351000	Eya1	673.0	50000	0.000891530461	0.000000000000	0.551985781847	0.600000000000
-chr1	14351000	14352000	Eya1	673.0	51000	0.001485884101	0.000000000000	0.932104051045	1.000000000000
-chr1	14352000	14353000	Eya1	673.0	52000	0.001783060921	0.000000000000	1.093806079608	1.200000000000
-chr1	14353000	14354000	Eya1	673.0	53000	0.001783060921	0.000000000000	1.144386707956	1.200000000000
-chr1	14354000	14355000	Eya1	673.0	54000	0.001783060921	0.000000000000	1.245150317436	1.200000000000
-chr1	14355000	14356000	Eya1	673.0	55000	0.001188707281	0.000000000000	0.842463406362	0.800000000000
-chr1	14356000	14357000	Eya1	673.0	56000	0.001783060921	0.000000000000	1.269095516036	1.200000000000
-chr1	14357000	14358000	Eya1	673.0	57000	0.001783060921	0.000000000000	1.302492765775	1.200000000000
-chr1	14358000	14359000	Eya1	673.0	58000	0.001783060921	0.000000000000	1.299642672175	1.200000000000
-chr1	14359000	14360000	Eya1	673.0	59000	0.001783060921	0.000000000000	1.288365946088	1.200000000000
-chr1	14360000	14361000	Eya1	673.0	60000	0.001783060921	0.000000000000	1.224611755344	1.200000000000
-chr1	14361000	14362000	Eya1	673.0	61000	0.001188707281	0.000000000000	0.837120086618	0.800000000000
-chr1	14362000	14363000	Eya1	673.0	62000	0.000594353640	0.000000000000	0.447916064352	0.400000000000
-chr1	14363000	14364000	Eya1	673.0	63000	0.001188707281	0.000000000000	0.874079030496	0.800000000000
-chr1	14364000	14365000	Eya1	673.0	64000	0.001188707281	0.000000000000	0.877955212478	0.800000000000
-chr1	14365000	14366000	Eya1	673.0	65000	0.001188707281	0.000000000000	0.927301641668	0.800000000000
-chr1	14366000	14367000	Eya1	673.0	66000	0.000594353640	0.000000000000	0.507638206342	0.400000000000
-chr1	14367000	14368000	Eya1	673.0	67000	0.001188707281	0.000000000000	0.970484805913	0.800000000000
-chr1	14368000	14369000	Eya1	673.0	68000	0.000594353640	0.000000000000	0.493712968658	0.400000000000
-chr1	14369000	14370000	Eya1	673.0	69000	0.000594353640	0.000000000000	0.488836791153	0.400000000000
-chr1	14370000	14371000	Eya1	673.0	70000	0.000594353640	0.000000000000	0.479367797551	0.400000000000
-chr1	14371000	14372000	Eya1	673.0	71000	0.000594353640	0.000000000000	0.463650820834	0.400000000000
+chr1	14295000	14296000	Eya1	673.0	-5000	0.008023774146	0.000022975150	1.495892017542	5.400000000000
+chr1	14296000	14297000	Eya1	673.0	-4000	0.020208023774	0.000000000000	2.498769373810	13.600000000000
+chr1	14297000	14298000	Eya1	673.0	-3000	0.037741456166	0.000000000000	2.371508773423	25.400000000000
+chr1	14298000	14299000	Eya1	673.0	-2000	0.090638930163	0.000000000000	1.906118557690	61.000000000000
+chr1	14299000	14300000	Eya1	673.0	-1000	0.097771173848	0.000000000000	1.844165161272	65.800000000000
+chr1	14300000	14301000	Eya1	673.0	0	0.094205052006	0.427204913295	1.707565505267	63.400000000000
+chr1	14301000	14302000	Eya1	673.0	1000	0.083209509658	1.000000000000	1.533373304270	56.000000000000
+chr1	14302000	14303000	Eya1	673.0	2000	0.071025260030	1.000000000000	1.424032943621	47.800000000000
+chr1	14303000	14304000	Eya1	673.0	3000	0.021396731055	1.000000000000	1.183820793948	14.400000000000
+chr1	14304000	14305000	Eya1	673.0	4000	0.017533432392	1.000000000000	1.517593323295	11.800000000000
+chr1	14305000	14306000	Eya1	673.0	5000	0.013670133730	1.000000000000	1.528433002398	9.200000000000
+chr1	14306000	14307000	Eya1	673.0	6000	0.013967310550	1.000000000000	1.760719128357	9.400000000000
+chr1	14307000	14308000	Eya1	673.0	7000	0.009212481426	1.000000000000	1.255346129863	6.200000000000
+chr1	14308000	14309000	Eya1	673.0	8000	0.008023774146	1.000000000000	1.214678551849	5.400000000000
+chr1	14309000	14310000	Eya1	673.0	9000	0.007132243685	1.000000000000	1.175292875601	4.800000000000
+chr1	14310000	14311000	Eya1	673.0	10000	0.007726597325	1.000000000000	1.387399537905	5.200000000000
+chr1	14311000	14312000	Eya1	673.0	11000	0.008320950966	1.000000000000	1.668106518936	5.600000000000
+chr1	14312000	14313000	Eya1	673.0	12000	0.007726597325	1.000000000000	1.666123682021	5.200000000000
+chr1	14313000	14314000	Eya1	673.0	13000	0.007429420505	1.000000000000	1.800093780426	5.000000000000
+chr1	14314000	14315000	Eya1	673.0	14000	0.007726597325	1.000000000000	2.071232210376	5.200000000000
+chr1	14315000	14316000	Eya1	673.0	15000	0.007429420505	1.000000000000	1.996002792638	5.000000000000
+chr1	14316000	14317000	Eya1	673.0	16000	0.006240713224	1.000000000000	1.710904648367	4.200000000000
+chr1	14317000	14318000	Eya1	673.0	17000	0.007429420505	1.000000000000	2.208586363986	5.000000000000
+chr1	14318000	14319000	Eya1	673.0	18000	0.007132243685	1.000000000000	2.274873482297	4.800000000000
+chr1	14319000	14320000	Eya1	673.0	19000	0.004457652303	1.000000000000	1.438573263556	3.000000000000
+chr1	14320000	14321000	Eya1	673.0	20000	0.004754829123	1.000000000000	1.629153481781	3.200000000000
+chr1	14321000	14322000	Eya1	673.0	21000	0.005052005944	1.000000000000	1.779454297737	3.400000000000
+chr1	14322000	14323000	Eya1	673.0	22000	0.003863298663	1.000000000000	1.417992815989	2.600000000000
+chr1	14323000	14324000	Eya1	673.0	23000	0.002377414562	1.000000000000	0.961328722964	1.600000000000
+chr1	14324000	14325000	Eya1	673.0	24000	0.002377414562	1.000000000000	0.979165877127	1.600000000000
+chr1	14325000	14326000	Eya1	673.0	25000	0.001188707281	1.000000000000	0.509134883212	0.800000000000
+chr1	14326000	14327000	Eya1	673.0	26000	0.000297176820	1.000000000000	0.138217507784	0.200000000000
+chr1	14327000	14328000	Eya1	673.0	27000	0.000594353640	1.000000000000	0.291491728623	0.400000000000
+chr1	14328000	14329000	Eya1	673.0	28000	0.000891530461	1.000000000000	0.414461746913	0.600000000000
+chr1	14329000	14330000	Eya1	673.0	29000	0.000891530461	1.000000000000	0.423759933973	0.600000000000
+chr1	14330000	14331000	Eya1	673.0	30000	0.001485884101	1.000000000000	0.738495476207	1.000000000000
+chr1	14331000	14332000	Eya1	673.0	31000	0.001188707281	1.000000000000	0.571837076886	0.800000000000
+chr1	14332000	14333000	Eya1	673.0	32000	0.000891530461	1.000000000000	0.460397053832	0.600000000000
+chr1	14333000	14334000	Eya1	673.0	33000	0.000594353640	1.000000000000	0.316498061209	0.400000000000
+chr1	14334000	14335000	Eya1	673.0	34000	0.000891530461	1.000000000000	0.495030011650	0.600000000000
+chr1	14335000	14336000	Eya1	673.0	35000	0.000297176820	1.000000000000	0.172106996582	0.200000000000
+chr1	14336000	14337000	Eya1	673.0	36000	0.001485884101	1.000000000000	0.909529987218	1.000000000000
+chr1	14337000	14338000	Eya1	673.0	37000	0.002080237741	1.000000000000	1.305554502836	1.400000000000
+chr1	14338000	14339000	Eya1	673.0	38000	0.002080237741	1.000000000000	1.318822332890	1.400000000000
+chr1	14339000	14340000	Eya1	673.0	39000	0.002080237741	1.000000000000	1.270846509667	1.400000000000
+chr1	14340000	14341000	Eya1	673.0	40000	0.002080237741	1.000000000000	1.213242568123	1.400000000000
+chr1	14341000	14342000	Eya1	673.0	41000	0.000891530461	1.000000000000	0.506118045146	0.600000000000
+chr1	14342000	14343000	Eya1	673.0	42000	0.000594353640	1.000000000000	0.338056624863	0.400000000000
+chr1	14343000	14344000	Eya1	673.0	43000	0.001485884101	1.000000000000	0.921722795394	1.000000000000
+chr1	14344000	14345000	Eya1	673.0	44000	0.001188707281	1.000000000000	0.771141856085	0.800000000000
+chr1	14345000	14346000	Eya1	673.0	45000	0.001485884101	1.000000000000	1.070255650220	1.000000000000
+chr1	14346000	14347000	Eya1	673.0	46000	0.001485884101	1.000000000000	1.040659385987	1.000000000000
+chr1	14347000	14348000	Eya1	673.0	47000	0.001485884101	1.000000000000	1.073510976166	1.000000000000
+chr1	14348000	14349000	Eya1	673.0	48000	0.000594353640	1.000000000000	0.429315289247	0.400000000000
+chr1	14349000	14350000	Eya1	673.0	49000	0.000594353640	1.000000000000	0.400466934522	0.400000000000
+chr1	14350000	14351000	Eya1	673.0	50000	0.000891530461	1.000000000000	0.621230395273	0.600000000000
+chr1	14351000	14352000	Eya1	673.0	51000	0.001485884101	1.000000000000	1.016250837306	1.000000000000
+chr1	14352000	14353000	Eya1	673.0	52000	0.001783060921	1.000000000000	1.173316016997	1.200000000000
+chr1	14353000	14354000	Eya1	673.0	53000	0.001783060921	1.000000000000	1.207449250953	1.200000000000
+chr1	14354000	14355000	Eya1	673.0	54000	0.001783060921	1.000000000000	1.335661629809	1.200000000000
+chr1	14355000	14356000	Eya1	673.0	55000	0.001188707281	1.000000000000	0.918517777733	0.800000000000
+chr1	14356000	14357000	Eya1	673.0	56000	0.001783060921	1.000000000000	1.428298942880	1.200000000000
+chr1	14357000	14358000	Eya1	673.0	57000	0.001783060921	1.000000000000	1.488790222035	1.200000000000
+chr1	14358000	14359000	Eya1	673.0	58000	0.001783060921	1.000000000000	1.485532475503	1.200000000000
+chr1	14359000	14360000	Eya1	673.0	59000	0.001783060921	1.000000000000	1.472642823277	1.200000000000
+chr1	14360000	14361000	Eya1	673.0	60000	0.001783060921	1.000000000000	1.442839615496	1.200000000000
+chr1	14361000	14362000	Eya1	673.0	61000	0.001188707281	1.000000000000	0.927412924049	0.800000000000
+chr1	14362000	14363000	Eya1	673.0	62000	0.000594353640	1.000000000000	0.504105509371	0.400000000000
+chr1	14363000	14364000	Eya1	673.0	63000	0.001188707281	1.000000000000	0.983729073341	0.800000000000
+chr1	14364000	14365000	Eya1	673.0	64000	0.001188707281	1.000000000000	0.988091508653	0.800000000000
+chr1	14365000	14366000	Eya1	673.0	65000	0.001188707281	1.000000000000	1.043628267763	0.800000000000
+chr1	14366000	14367000	Eya1	673.0	66000	0.000594353640	1.000000000000	0.571319577061	0.400000000000
+chr1	14367000	14368000	Eya1	673.0	67000	0.001188707281	1.000000000000	1.041030387957	0.800000000000
+chr1	14368000	14369000	Eya1	673.0	68000	0.000594353640	1.000000000000	0.538283485905	0.400000000000
+chr1	14369000	14370000	Eya1	673.0	69000	0.000594353640	1.000000000000	0.515774618572	0.400000000000
+chr1	14370000	14371000	Eya1	673.0	70000	0.000594353640	1.000000000000	0.522643287809	0.400000000000
+chr1	14371000	14372000	Eya1	673.0	71000	0.000594353640	1.000000000000	0.513660787779	0.400000000000
 chr1	14372000	14373000	Eya1	673.0	72000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14373000	14374000	Eya1	673.0	73000	0.000297176820	0.000000000000	0.245023391610	0.200000000000
-chr1	14374000	14375000	Eya1	673.0	74000	0.000297176820	0.000000000000	0.235689167288	0.200000000000
-chr1	14375000	14376000	Eya1	673.0	75000	0.001188707281	0.000000000000	0.918695593883	0.800000000000
-chr1	14376000	14377000	Eya1	673.0	76000	0.001188707281	0.000000000000	0.912345163461	0.800000000000
-chr1	14377000	14378000	Eya1	673.0	77000	0.001188707281	0.000000000000	0.883834376891	0.800000000000
-chr1	14378000	14379000	Eya1	673.0	78000	0.000891530461	0.000000000000	0.729651967113	0.600000000000
-chr1	14379000	14380000	Eya1	673.0	79000	0.000891530461	0.000000000000	0.740569452986	0.600000000000
+chr1	14373000	14374000	Eya1	673.0	73000	0.000297176820	1.000000000000	0.288686969186	0.200000000000
+chr1	14374000	14375000	Eya1	673.0	74000	0.000297176820	1.000000000000	0.277689370491	0.200000000000
+chr1	14375000	14376000	Eya1	673.0	75000	0.001188707281	1.000000000000	1.098564036468	0.800000000000
+chr1	14376000	14377000	Eya1	673.0	76000	0.001188707281	1.000000000000	1.090970275810	0.800000000000
+chr1	14377000	14378000	Eya1	673.0	77000	0.001188707281	1.000000000000	0.979165877127	0.800000000000
+chr1	14378000	14379000	Eya1	673.0	78000	0.000891530461	1.000000000000	0.795522154262	0.600000000000
+chr1	14379000	14380000	Eya1	673.0	79000	0.000891530461	1.000000000000	0.794402240703	0.600000000000
 chr1	14380000	14381000	Eya1	673.0	80000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14381000	14382000	Eya1	673.0	81000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14382000	14383000	Eya1	673.0	82000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -293,53 +293,53 @@
 chr1	14388000	14389000	Eya1	673.0	88000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14389000	14390000	Eya1	673.0	89000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14390000	14391000	Eya1	673.0	90000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14391000	14392000	Eya1	673.0	91000	0.000594353640	0.000000000000	0.466931369120	0.400000000000
-chr1	14392000	14393000	Eya1	673.0	92000	0.000891530461	0.000000000000	0.785630557626	0.600000000000
-chr1	14393000	14394000	Eya1	673.0	93000	0.000891530461	0.000000000000	0.815847117037	0.600000000000
-chr1	14394000	14395000	Eya1	673.0	94000	0.000891530461	0.000000000000	0.748031110000	0.600000000000
-chr1	14395000	14396000	Eya1	673.0	95000	0.001485884101	0.000000000000	1.195524760780	1.000000000000
-chr1	14396000	14397000	Eya1	673.0	96000	0.001783060921	0.000000000000	1.394217609153	1.200000000000
-chr1	14397000	14398000	Eya1	673.0	97000	0.001485884101	0.000000000000	1.204251218952	1.000000000000
-chr1	14398000	14399000	Eya1	673.0	98000	0.001783060921	0.000000000000	1.410776013193	1.200000000000
-chr1	14399000	14400000	Eya1	673.0	99000	0.002080237741	0.000000000000	1.767668754158	1.400000000000
-chr1	14400000	14401000	Eya1	673.0	100000	0.001485884101	0.000000000000	1.410106128595	1.000000000000
-chr1	14401000	14402000	Eya1	673.0	101000	0.000594353640	0.000000000000	0.603594208412	0.400000000000
-chr1	14402000	14403000	Eya1	673.0	102000	0.000594353640	0.000000000000	0.587474482247	0.400000000000
-chr1	14403000	14404000	Eya1	673.0	103000	0.000297176820	0.000000000000	0.324555574533	0.200000000000
+chr1	14391000	14392000	Eya1	673.0	91000	0.000594353640	1.000000000000	0.517295180305	0.400000000000
+chr1	14392000	14393000	Eya1	673.0	92000	0.000891530461	1.000000000000	0.842738885219	0.600000000000
+chr1	14393000	14394000	Eya1	673.0	93000	0.000891530461	1.000000000000	0.803418155772	0.600000000000
+chr1	14394000	14395000	Eya1	673.0	94000	0.000891530461	1.000000000000	0.762943689365	0.600000000000
+chr1	14395000	14396000	Eya1	673.0	95000	0.001485884101	1.000000000000	1.324475582250	1.000000000000
+chr1	14396000	14397000	Eya1	673.0	96000	0.001783060921	1.000000000000	1.569117148711	1.200000000000
+chr1	14397000	14398000	Eya1	673.0	97000	0.001485884101	1.000000000000	1.312966410354	1.000000000000
+chr1	14398000	14399000	Eya1	673.0	98000	0.001783060921	1.000000000000	1.538135470472	1.200000000000
+chr1	14399000	14400000	Eya1	673.0	99000	0.002080237741	1.000000000000	1.865077860860	1.400000000000
+chr1	14400000	14401000	Eya1	673.0	100000	0.001485884101	1.000000000000	1.438217685203	1.000000000000
+chr1	14401000	14402000	Eya1	673.0	101000	0.000594353640	1.000000000000	0.626241590411	0.400000000000
+chr1	14402000	14403000	Eya1	673.0	102000	0.000594353640	1.000000000000	0.619847834964	0.400000000000
+chr1	14403000	14404000	Eya1	673.0	103000	0.000297176820	1.000000000000	0.342440525285	0.200000000000
 chr1	14404000	14405000	Eya1	673.0	104000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14405000	14406000	Eya1	673.0	105000	0.000594353640	0.000000000000	0.592751199195	0.400000000000
-chr1	14406000	14407000	Eya1	673.0	106000	0.000594353640	0.000000000000	0.578885673960	0.400000000000
-chr1	14407000	14408000	Eya1	673.0	107000	0.000594353640	0.000000000000	0.556120506836	0.400000000000
-chr1	14408000	14409000	Eya1	673.0	108000	0.000891530461	0.000000000000	0.813611919440	0.600000000000
-chr1	14409000	14410000	Eya1	673.0	109000	0.000891530461	0.000000000000	0.843660087147	0.600000000000
-chr1	14410000	14411000	Eya1	673.0	110000	0.000297176820	0.000000000000	0.291145441917	0.200000000000
-chr1	14411000	14412000	Eya1	673.0	111000	0.000297176820	0.000000000000	0.275736630113	0.200000000000
-chr1	14412000	14413000	Eya1	673.0	112000	0.000297176820	0.000000000000	0.282827000656	0.200000000000
-chr1	14413000	14414000	Eya1	673.0	113000	0.000297176820	0.000000000000	0.290291642960	0.200000000000
-chr1	14414000	14415000	Eya1	673.0	114000	0.000297176820	0.000000000000	0.286096676989	0.200000000000
-chr1	14415000	14416000	Eya1	673.0	115000	0.000297176820	0.000000000000	0.288598980306	0.200000000000
-chr1	14416000	14417000	Eya1	673.0	116000	0.000594353640	0.000000000000	0.664358726512	0.400000000000
-chr1	14417000	14418000	Eya1	673.0	117000	0.000891530461	0.000000000000	1.017014899996	0.600000000000
-chr1	14418000	14419000	Eya1	673.0	118000	0.000594353640	0.000000000000	0.687426738036	0.400000000000
-chr1	14419000	14420000	Eya1	673.0	119000	0.000594353640	0.000000000000	0.671114917005	0.400000000000
-chr1	14420000	14421000	Eya1	673.0	120000	0.000594353640	0.000000000000	0.662136790955	0.400000000000
-chr1	14421000	14422000	Eya1	673.0	121000	0.000297176820	0.000000000000	0.325623191563	0.200000000000
-chr1	14422000	14423000	Eya1	673.0	122000	0.000594353640	0.000000000000	0.668847636862	0.400000000000
-chr1	14423000	14424000	Eya1	673.0	123000	0.000594353640	0.000000000000	0.682685863943	0.400000000000
-chr1	14424000	14425000	Eya1	673.0	124000	0.000594353640	0.000000000000	0.725197437366	0.400000000000
-chr1	14425000	14426000	Eya1	673.0	125000	0.000594353640	0.000000000000	0.791915602137	0.400000000000
-chr1	14426000	14427000	Eya1	673.0	126000	0.001188707281	0.000000000000	1.477454480806	0.800000000000
-chr1	14427000	14428000	Eya1	673.0	127000	0.000594353640	0.000000000000	0.755644658251	0.400000000000
-chr1	14428000	14429000	Eya1	673.0	128000	0.000594353640	0.000000000000	0.791915602137	0.400000000000
-chr1	14429000	14430000	Eya1	673.0	129000	0.000594353640	0.000000000000	0.764397299148	0.400000000000
-chr1	14430000	14431000	Eya1	673.0	130000	0.000594353640	0.000000000000	0.714725272130	0.400000000000
+chr1	14405000	14406000	Eya1	673.0	105000	0.000594353640	1.000000000000	0.625415330601	0.400000000000
+chr1	14406000	14407000	Eya1	673.0	106000	0.000594353640	1.000000000000	0.600605970188	0.400000000000
+chr1	14407000	14408000	Eya1	673.0	107000	0.000594353640	1.000000000000	0.567207199697	0.400000000000
+chr1	14408000	14409000	Eya1	673.0	108000	0.000891530461	1.000000000000	0.829831903445	0.600000000000
+chr1	14409000	14410000	Eya1	673.0	109000	0.000891530461	1.000000000000	0.830807410785	0.600000000000
+chr1	14410000	14411000	Eya1	673.0	110000	0.000297176820	1.000000000000	0.281590186959	0.200000000000
+chr1	14411000	14412000	Eya1	673.0	111000	0.000297176820	1.000000000000	0.271535941146	0.200000000000
+chr1	14412000	14413000	Eya1	673.0	112000	0.000297176820	1.000000000000	0.298412457866	0.200000000000
+chr1	14413000	14414000	Eya1	673.0	113000	0.000297176820	1.000000000000	0.301183639038	0.200000000000
+chr1	14414000	14415000	Eya1	673.0	114000	0.000297176820	1.000000000000	0.316955428482	0.200000000000
+chr1	14415000	14416000	Eya1	673.0	115000	0.000297176820	1.000000000000	0.314652591470	0.200000000000
+chr1	14416000	14417000	Eya1	673.0	116000	0.000594353640	1.000000000000	0.736017303482	0.400000000000
+chr1	14417000	14418000	Eya1	673.0	117000	0.000891530461	1.000000000000	1.019405571137	0.600000000000
+chr1	14418000	14419000	Eya1	673.0	118000	0.000594353640	1.000000000000	0.713219589643	0.400000000000
+chr1	14419000	14420000	Eya1	673.0	119000	0.000594353640	1.000000000000	0.696295734438	0.400000000000
+chr1	14420000	14421000	Eya1	673.0	120000	0.000594353640	1.000000000000	0.721911965377	0.400000000000
+chr1	14421000	14422000	Eya1	673.0	121000	0.000297176820	1.000000000000	0.320662509567	0.200000000000
+chr1	14422000	14423000	Eya1	673.0	122000	0.000594353640	1.000000000000	0.682181631680	0.400000000000
+chr1	14423000	14424000	Eya1	673.0	123000	0.000594353640	1.000000000000	0.708300833694	0.400000000000
+chr1	14424000	14425000	Eya1	673.0	124000	0.000594353640	1.000000000000	0.714149471154	0.400000000000
+chr1	14425000	14426000	Eya1	673.0	125000	0.000594353640	1.000000000000	0.807703052251	0.400000000000
+chr1	14426000	14427000	Eya1	673.0	126000	0.001188707281	1.000000000000	1.480927495948	0.800000000000
+chr1	14427000	14428000	Eya1	673.0	127000	0.000594353640	1.000000000000	0.717556673170	0.400000000000
+chr1	14428000	14429000	Eya1	673.0	128000	0.000594353640	1.000000000000	0.779851222534	0.400000000000
+chr1	14429000	14430000	Eya1	673.0	129000	0.000594353640	1.000000000000	0.752752146077	0.400000000000
+chr1	14430000	14431000	Eya1	673.0	130000	0.000594353640	1.000000000000	0.653562783700	0.400000000000
 chr1	14431000	14432000	Eya1	673.0	131000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14432000	14433000	Eya1	673.0	132000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14433000	14434000	Eya1	673.0	133000	0.000297176820	0.000000000000	0.358657428234	0.200000000000
-chr1	14434000	14435000	Eya1	673.0	134000	0.000297176820	0.000000000000	0.373545095179	0.200000000000
-chr1	14435000	14436000	Eya1	673.0	135000	0.000297176820	0.000000000000	0.391262649240	0.200000000000
-chr1	14436000	14437000	Eya1	673.0	136000	0.000297176820	0.000000000000	0.358657428234	0.200000000000
-chr1	14437000	14438000	Eya1	673.0	137000	0.000297176820	0.000000000000	0.334423818431	0.200000000000
+chr1	14433000	14434000	Eya1	673.0	133000	0.000297176820	1.000000000000	0.315351329013	0.200000000000
+chr1	14434000	14435000	Eya1	673.0	134000	0.000297176820	1.000000000000	0.321872556478	0.200000000000
+chr1	14435000	14436000	Eya1	673.0	135000	0.000297176820	1.000000000000	0.344019631717	0.200000000000
+chr1	14436000	14437000	Eya1	673.0	136000	0.000297176820	1.000000000000	0.315351329013	0.200000000000
+chr1	14437000	14438000	Eya1	673.0	137000	0.000297176820	1.000000000000	0.299924683066	0.200000000000
 chr1	14438000	14439000	Eya1	673.0	138000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14439000	14440000	Eya1	673.0	139000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14440000	14441000	Eya1	673.0	140000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -349,24 +349,24 @@
 chr1	14444000	14445000	Eya1	673.0	144000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14445000	14446000	Eya1	673.0	145000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14446000	14447000	Eya1	673.0	146000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14447000	14448000	Eya1	673.0	147000	0.000594353640	0.000000000000	0.868328510517	0.400000000000
-chr1	14448000	14449000	Eya1	673.0	148000	0.000594353640	0.000000000000	0.899904092956	0.400000000000
-chr1	14449000	14450000	Eya1	673.0	149000	0.000891530461	0.000000000000	1.387702573545	0.600000000000
-chr1	14450000	14451000	Eya1	673.0	150000	0.001188707281	0.000000000000	1.721555655524	0.800000000000
-chr1	14451000	14452000	Eya1	673.0	151000	0.001188707281	0.000000000000	1.816320187745	0.800000000000
-chr1	14452000	14453000	Eya1	673.0	152000	0.000594353640	0.000000000000	0.879906224076	0.400000000000
-chr1	14453000	14454000	Eya1	673.0	153000	0.000594353640	0.000000000000	0.887797759777	0.400000000000
-chr1	14454000	14455000	Eya1	673.0	154000	0.000891530461	0.000000000000	1.356019866146	0.600000000000
-chr1	14455000	14456000	Eya1	673.0	155000	0.000594353640	0.000000000000	0.876012833675	0.400000000000
-chr1	14456000	14457000	Eya1	673.0	156000	0.000594353640	0.000000000000	0.876012833675	0.400000000000
-chr1	14457000	14458000	Eya1	673.0	157000	0.000594353640	0.000000000000	0.821489212945	0.400000000000
-chr1	14458000	14459000	Eya1	673.0	158000	0.001188707281	0.000000000000	1.583831204275	0.800000000000
-chr1	14459000	14460000	Eya1	673.0	159000	0.000594353640	0.000000000000	0.770345916308	0.400000000000
-chr1	14460000	14461000	Eya1	673.0	160000	0.001188707281	0.000000000000	1.517079697070	0.800000000000
-chr1	14461000	14462000	Eya1	673.0	161000	0.001188707281	0.000000000000	1.429450544260	0.800000000000
-chr1	14462000	14463000	Eya1	673.0	162000	0.001188707281	0.000000000000	1.616154290340	0.800000000000
-chr1	14463000	14464000	Eya1	673.0	163000	0.000594353640	0.000000000000	0.821489212945	0.400000000000
-chr1	14464000	14465000	Eya1	673.0	164000	0.000594353640	0.000000000000	0.857051516792	0.400000000000
+chr1	14447000	14448000	Eya1	673.0	147000	0.000594353640	1.000000000000	0.778751808649	0.400000000000
+chr1	14448000	14449000	Eya1	673.0	148000	0.000594353640	1.000000000000	0.838719862294	0.400000000000
+chr1	14449000	14450000	Eya1	673.0	149000	0.000891530461	1.000000000000	1.366561723305	0.600000000000
+chr1	14450000	14451000	Eya1	673.0	150000	0.001188707281	1.000000000000	1.755876200960	0.800000000000
+chr1	14451000	14452000	Eya1	673.0	151000	0.001188707281	1.000000000000	1.756709422634	0.800000000000
+chr1	14452000	14453000	Eya1	673.0	152000	0.000594353640	1.000000000000	0.835554881521	0.400000000000
+chr1	14453000	14454000	Eya1	673.0	153000	0.000594353640	1.000000000000	0.827436635112	0.400000000000
+chr1	14454000	14455000	Eya1	673.0	154000	0.000891530461	1.000000000000	1.192287216994	0.600000000000
+chr1	14455000	14456000	Eya1	673.0	155000	0.000594353640	1.000000000000	0.785643417147	0.400000000000
+chr1	14456000	14457000	Eya1	673.0	156000	0.000594353640	1.000000000000	0.831857736126	0.400000000000
+chr1	14457000	14458000	Eya1	673.0	157000	0.000594353640	1.000000000000	0.808974297441	0.400000000000
+chr1	14458000	14459000	Eya1	673.0	158000	0.001188707281	1.000000000000	1.559702445068	0.800000000000
+chr1	14459000	14460000	Eya1	673.0	159000	0.000594353640	1.000000000000	0.772156748785	0.400000000000
+chr1	14460000	14461000	Eya1	673.0	160000	0.001188707281	1.000000000000	1.493967860289	0.800000000000
+chr1	14461000	14462000	Eya1	673.0	161000	0.001188707281	1.000000000000	1.508221808665	0.800000000000
+chr1	14462000	14463000	Eya1	673.0	162000	0.001188707281	1.000000000000	1.591533108618	0.800000000000
+chr1	14463000	14464000	Eya1	673.0	163000	0.000594353640	1.000000000000	0.780082358626	0.400000000000
+chr1	14464000	14465000	Eya1	673.0	164000	0.000594353640	1.000000000000	0.813852157891	0.400000000000
 chr1	14465000	14466000	Eya1	673.0	165000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14466000	14467000	Eya1	673.0	166000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14467000	14468000	Eya1	673.0	167000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -378,28 +378,28 @@
 chr1	14473000	14474000	Eya1	673.0	173000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14474000	14475000	Eya1	673.0	174000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	14475000	14476000	Eya1	673.0	175000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	14476000	14477000	Eya1	673.0	176000	0.000297176820	0.000000000000	0.421231702882	0.200000000000
-chr1	14477000	14478000	Eya1	673.0	177000	0.000297176820	0.000000000000	0.449952046478	0.200000000000
-chr1	14478000	14479000	Eya1	673.0	178000	0.000594353640	0.000000000000	0.933862738240	0.400000000000
-chr1	14479000	14480000	Eya1	673.0	179000	0.000594353640	0.000000000000	0.951821637197	0.400000000000
-chr1	14480000	14481000	Eya1	673.0	180000	0.001485884101	0.000000000000	2.512422592521	1.000000000000
-chr1	14481000	14482000	Eya1	673.0	181000	0.001188707281	0.000000000000	2.020192860178	0.800000000000
-chr1	14482000	14483000	Eya1	673.0	182000	0.001188707281	0.000000000000	2.128805380321	0.800000000000
-chr1	14483000	14484000	Eya1	673.0	183000	0.001783060921	0.000000000000	3.093420317586	1.200000000000
-chr1	14484000	14485000	Eya1	673.0	184000	0.002080237741	0.000000000000	3.380127570538	1.400000000000
-chr1	14485000	14486000	Eya1	673.0	185000	0.001188707281	0.000000000000	1.903643274393	0.800000000000
-chr1	14486000	14487000	Eya1	673.0	186000	0.001188707281	0.000000000000	2.106158514412	0.800000000000
-chr1	14487000	14488000	Eya1	673.0	187000	0.001188707281	0.000000000000	2.140312436513	0.800000000000
-chr1	14488000	14489000	Eya1	673.0	188000	0.000594353640	0.000000000000	1.058710697124	0.400000000000
-chr1	14489000	14490000	Eya1	673.0	189000	0.000297176820	0.000000000000	0.575520059550	0.200000000000
-chr1	14490000	14491000	Eya1	673.0	190000	0.000297176820	0.000000000000	0.578885673960	0.200000000000
-chr1	14491000	14492000	Eya1	673.0	191000	0.002080237741	0.000000000000	3.849589730333	1.400000000000
-chr1	14492000	14493000	Eya1	673.0	192000	0.003268945022	0.000000000000	5.982878858272	2.200000000000
-chr1	14493000	14494000	Eya1	673.0	193000	0.002971768202	0.000000000000	5.892229182196	2.000000000000
-chr1	14494000	14495000	Eya1	673.0	194000	0.003268945022	0.000000000000	6.294126893758	2.200000000000
-chr1	14495000	14496000	Eya1	673.0	195000	0.003268945022	0.000000000000	6.680269651133	2.200000000000
-chr1	14496000	14497000	Eya1	673.0	196000	0.002971768202	0.000000000000	6.072972410121	2.000000000000
-chr1	14497000	14498000	Eya1	673.0	197000	0.002080237741	0.000000000000	3.937080406684	1.400000000000
-chr1	14498000	14499000	Eya1	673.0	198000	0.002971768202	0.000000000000	4.852424033528	2.000000000000
-chr1	14499000	14500000	Eya1	673.0	199000	0.003343239227	0.000000000000	5.830530441735	2.250000000000
-chr1	14500000	14501000	Eya1	673.0	200000	0.004457652303	0.000000000000	7.575723225668	3.000000000000
+chr1	14476000	14477000	Eya1	673.0	176000	0.000297176820	1.000000000000	0.377777473345	0.200000000000
+chr1	14477000	14478000	Eya1	673.0	177000	0.000297176820	1.000000000000	0.387710125250	0.200000000000
+chr1	14478000	14479000	Eya1	673.0	178000	0.000594353640	1.000000000000	0.804681391196	0.400000000000
+chr1	14479000	14480000	Eya1	673.0	179000	0.000594353640	1.000000000000	0.853631790099	0.400000000000
+chr1	14480000	14481000	Eya1	673.0	180000	0.001485884101	1.000000000000	2.209060071856	1.000000000000
+chr1	14481000	14482000	Eya1	673.0	181000	0.001188707281	1.000000000000	1.740739337114	0.800000000000
+chr1	14482000	14483000	Eya1	673.0	182000	0.001188707281	1.000000000000	1.946633238000	0.800000000000
+chr1	14483000	14484000	Eya1	673.0	183000	0.001783060921	1.000000000000	2.611109005672	1.200000000000
+chr1	14484000	14485000	Eya1	673.0	184000	0.002080237741	1.000000000000	3.150313631272	1.400000000000
+chr1	14485000	14486000	Eya1	673.0	185000	0.001188707281	1.000000000000	1.707263580199	0.800000000000
+chr1	14486000	14487000	Eya1	673.0	186000	0.001188707281	1.000000000000	1.814813352082	0.800000000000
+chr1	14487000	14488000	Eya1	673.0	187000	0.001188707281	1.000000000000	1.806605148755	0.800000000000
+chr1	14488000	14489000	Eya1	673.0	188000	0.000594353640	1.000000000000	0.912259118375	0.400000000000
+chr1	14489000	14490000	Eya1	673.0	189000	0.000297176820	1.000000000000	0.475667144687	0.200000000000
+chr1	14490000	14491000	Eya1	673.0	190000	0.000297176820	1.000000000000	0.488628585681	0.200000000000
+chr1	14491000	14492000	Eya1	673.0	191000	0.002080237741	1.000000000000	3.452466352281	1.400000000000
+chr1	14492000	14493000	Eya1	673.0	192000	0.003268945022	1.000000000000	5.155266499539	2.200000000000
+chr1	14493000	14494000	Eya1	673.0	193000	0.002971768202	1.000000000000	4.559079214345	2.000000000000
+chr1	14494000	14495000	Eya1	673.0	194000	0.003268945022	1.000000000000	5.423459548891	2.200000000000
+chr1	14495000	14496000	Eya1	673.0	195000	0.003268945022	1.000000000000	5.638713926662	2.200000000000
+chr1	14496000	14497000	Eya1	673.0	196000	0.002971768202	1.000000000000	5.019309740274	2.000000000000
+chr1	14497000	14498000	Eya1	673.0	197000	0.002080237741	1.000000000000	3.323229640928	1.400000000000
+chr1	14498000	14499000	Eya1	673.0	198000	0.002971768202	1.000000000000	4.181187622141	2.000000000000
+chr1	14499000	14500000	Eya1	673.0	199000	0.003343239227	1.000000000000	4.818931539295	2.250000000000
+chr1	14500000	14501000	Eya1	673.0	200000	0.004457652303	1.000000000000	6.794212212290	3.000000000000
--- a/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3
+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6
 # FL-E13-5_chr1.cool	chr1_4487435_4487435	4.29  Mbp	4.69  Mbp	Sox17	Sum of interactions in fixate range: 810.0
 # Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative Interactions	p-value	x-fold	Raw
 #
@@ -195,75 +195,75 @@
 chr1	4477000	4478000	Sox17	810.0	-10000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4478000	4479000	Sox17	810.0	-9000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4479000	4480000	Sox17	810.0	-8000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4480000	4481000	Sox17	810.0	-7000	0.002222222222	0.000185972288	0.779180117089	1.800000000000
-chr1	4481000	4482000	Sox17	810.0	-6000	0.002222222222	0.000185972288	0.537170617614	1.800000000000
-chr1	4482000	4483000	Sox17	810.0	-5000	0.002222222222	0.000185972288	0.379990303436	1.800000000000
-chr1	4483000	4484000	Sox17	810.0	-4000	0.012098765432	0.000000000000	1.215347622436	9.800000000000
-chr1	4484000	4485000	Sox17	810.0	-3000	0.032839506173	0.000000000000	1.523937459823	26.600000000000
-chr1	4485000	4486000	Sox17	810.0	-2000	0.092592592593	0.000000000000	1.384128990547	75.000000000000
-chr1	4486000	4487000	Sox17	810.0	-1000	0.111111111111	0.000000000000	1.453408818204	90.000000000000
-chr1	4487000	4488000	Sox17	810.0	0	0.114567901235	0.188793973612	1.440149085516	92.800000000000
-chr1	4488000	4489000	Sox17	810.0	1000	0.105432098765	0.000000000000	1.347376918585	85.400000000000
-chr1	4489000	4490000	Sox17	810.0	2000	0.086913580247	0.000000000000	1.270443659967	70.400000000000
-chr1	4490000	4491000	Sox17	810.0	3000	0.028395061728	0.000000000000	1.145359755892	23.000000000000
-chr1	4491000	4492000	Sox17	810.0	4000	0.014320987654	0.000000000000	0.915431553855	11.600000000000
-chr1	4492000	4493000	Sox17	810.0	5000	0.010864197531	0.000000000000	0.897089431163	8.800000000000
-chr1	4493000	4494000	Sox17	810.0	6000	0.012345679012	0.000000000000	1.180011336066	10.000000000000
-chr1	4494000	4495000	Sox17	810.0	7000	0.010123456790	0.000000000000	1.060081230757	8.200000000000
-chr1	4495000	4496000	Sox17	810.0	8000	0.009382716049	0.000000000000	1.076973819704	7.600000000000
-chr1	4496000	4497000	Sox17	810.0	9000	0.005432098765	0.000000000000	0.678705694908	4.400000000000
-chr1	4497000	4498000	Sox17	810.0	10000	0.006666666667	0.000000000000	0.919910245827	5.400000000000
-chr1	4498000	4499000	Sox17	810.0	11000	0.007407407407	0.000000000000	1.156776232338	6.000000000000
-chr1	4499000	4500000	Sox17	810.0	12000	0.009876543210	0.000000000000	1.659037622278	8.000000000000
-chr1	4500000	4501000	Sox17	810.0	13000	0.007654320988	0.000000000000	1.425181941894	6.200000000000
-chr1	4501000	4502000	Sox17	810.0	14000	0.007654320988	0.000000000000	1.576778289436	6.200000000000
-chr1	4502000	4503000	Sox17	810.0	15000	0.006666666667	0.000000000000	1.434537037015	5.400000000000
-chr1	4503000	4504000	Sox17	810.0	16000	0.003950617284	0.000000000000	0.867467792926	3.200000000000
-chr1	4504000	4505000	Sox17	810.0	17000	0.001975308642	0.000000000000	0.470317599024	1.600000000000
-chr1	4505000	4506000	Sox17	810.0	18000	0.001728395062	0.000000000000	0.423640567251	1.400000000000
-chr1	4506000	4507000	Sox17	810.0	19000	0.003456790123	0.000000000000	0.869022688092	2.800000000000
-chr1	4507000	4508000	Sox17	810.0	20000	0.005185185185	0.000000000000	1.383960410629	4.200000000000
-chr1	4508000	4509000	Sox17	810.0	21000	0.005432098765	0.000000000000	1.490469013972	4.400000000000
-chr1	4509000	4510000	Sox17	810.0	22000	0.006419753086	0.000000000000	1.835550680659	5.200000000000
-chr1	4510000	4511000	Sox17	810.0	23000	0.007160493827	0.000000000000	2.286823503223	5.800000000000
-chr1	4511000	4512000	Sox17	810.0	24000	0.005679012346	0.000000000000	1.847340012418	4.600000000000
-chr1	4512000	4513000	Sox17	810.0	25000	0.005679012346	0.000000000000	1.948173195509	4.600000000000
-chr1	4513000	4514000	Sox17	810.0	26000	0.005432098765	0.000000000000	2.082197218564	4.400000000000
-chr1	4514000	4515000	Sox17	810.0	27000	0.003950617284	0.000000000000	1.551826228615	3.200000000000
-chr1	4515000	4516000	Sox17	810.0	28000	0.002962962963	0.000000000000	1.119003947265	2.400000000000
-chr1	4516000	4517000	Sox17	810.0	29000	0.002222222222	0.000000000000	0.883318748347	1.800000000000
-chr1	4517000	4518000	Sox17	810.0	30000	0.000246913580	0.000000000000	0.099693078950	0.200000000000
+chr1	4480000	4481000	Sox17	810.0	-7000	0.002222222222	0.038292851627	0.698799956258	1.800000000000
+chr1	4481000	4482000	Sox17	810.0	-6000	0.002222222222	0.038292851627	0.547879529674	1.800000000000
+chr1	4482000	4483000	Sox17	810.0	-5000	0.002222222222	0.038292851627	0.414294373583	1.800000000000
+chr1	4483000	4484000	Sox17	810.0	-4000	0.012098765432	0.000000000241	1.496040625274	9.800000000000
+chr1	4484000	4485000	Sox17	810.0	-3000	0.032839506173	0.000000000000	2.063491579666	26.600000000000
+chr1	4485000	4486000	Sox17	810.0	-2000	0.092592592593	0.000000000000	1.947203687501	75.000000000000
+chr1	4486000	4487000	Sox17	810.0	-1000	0.111111111111	0.000000000000	2.095783778345	90.000000000000
+chr1	4487000	4488000	Sox17	810.0	0	0.114567901235	0.202097333611	2.076663533359	92.800000000000
+chr1	4488000	4489000	Sox17	810.0	1000	0.105432098765	1.000000000000	1.942888094450	85.400000000000
+chr1	4489000	4490000	Sox17	810.0	2000	0.086913580247	1.000000000000	1.742588502567	70.400000000000
+chr1	4490000	4491000	Sox17	810.0	3000	0.028395061728	1.000000000000	1.571018695947	23.000000000000
+chr1	4491000	4492000	Sox17	810.0	4000	0.014320987654	1.000000000000	1.239542535708	11.600000000000
+chr1	4492000	4493000	Sox17	810.0	5000	0.010864197531	1.000000000000	1.214706335669	8.800000000000
+chr1	4493000	4494000	Sox17	810.0	6000	0.012345679012	1.000000000000	1.556296261340	10.000000000000
+chr1	4494000	4495000	Sox17	810.0	7000	0.010123456790	1.000000000000	1.379480914429	8.200000000000
+chr1	4495000	4496000	Sox17	810.0	8000	0.009382716049	1.000000000000	1.420401887745	7.600000000000
+chr1	4496000	4497000	Sox17	810.0	9000	0.005432098765	1.000000000000	0.895133040954	4.400000000000
+chr1	4497000	4498000	Sox17	810.0	10000	0.006666666667	1.000000000000	1.197076780782	5.400000000000
+chr1	4498000	4499000	Sox17	810.0	11000	0.007407407407	1.000000000000	1.484967840270	6.000000000000
+chr1	4499000	4500000	Sox17	810.0	12000	0.009876543210	1.000000000000	2.129726947769	8.000000000000
+chr1	4500000	4501000	Sox17	810.0	13000	0.007654320988	1.000000000000	1.854585508199	6.200000000000
+chr1	4501000	4502000	Sox17	810.0	14000	0.007654320988	1.000000000000	2.051857436138	6.200000000000
+chr1	4502000	4503000	Sox17	810.0	15000	0.006666666667	1.000000000000	1.791079839261	5.400000000000
+chr1	4503000	4504000	Sox17	810.0	16000	0.003950617284	1.000000000000	1.083070032546	3.200000000000
+chr1	4504000	4505000	Sox17	810.0	17000	0.001975308642	1.000000000000	0.587211307837	1.600000000000
+chr1	4505000	4506000	Sox17	810.0	18000	0.001728395062	1.000000000000	0.551282354686	1.400000000000
+chr1	4506000	4507000	Sox17	810.0	19000	0.003456790123	1.000000000000	1.115575085533	2.800000000000
+chr1	4507000	4508000	Sox17	810.0	20000	0.005185185185	1.000000000000	1.776606956637	4.200000000000
+chr1	4508000	4509000	Sox17	810.0	21000	0.005432098765	1.000000000000	1.913333357465	4.400000000000
+chr1	4509000	4510000	Sox17	810.0	22000	0.006419753086	1.000000000000	2.356318926322	5.200000000000
+chr1	4510000	4511000	Sox17	810.0	23000	0.007160493827	1.000000000000	2.895409365136	5.800000000000
+chr1	4511000	4512000	Sox17	810.0	24000	0.005679012346	1.000000000000	2.338967378402	4.600000000000
+chr1	4512000	4513000	Sox17	810.0	25000	0.005679012346	1.000000000000	2.432376190506	4.600000000000
+chr1	4513000	4514000	Sox17	810.0	26000	0.005432098765	1.000000000000	2.526479531178	4.400000000000
+chr1	4514000	4515000	Sox17	810.0	27000	0.003950617284	1.000000000000	1.937520329511	3.200000000000
+chr1	4515000	4516000	Sox17	810.0	28000	0.002962962963	1.000000000000	1.377445707024	2.400000000000
+chr1	4516000	4517000	Sox17	810.0	29000	0.002222222222	1.000000000000	1.056260872459	1.800000000000
+chr1	4517000	4518000	Sox17	810.0	30000	0.000246913580	1.000000000000	0.122717890244	0.200000000000
 chr1	4518000	4519000	Sox17	810.0	31000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4519000	4520000	Sox17	810.0	32000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4520000	4521000	Sox17	810.0	33000	0.000987654321	0.000000000000	0.421238361763	0.800000000000
-chr1	4521000	4522000	Sox17	810.0	34000	0.001234567901	0.000000000000	0.549043992821	1.000000000000
-chr1	4522000	4523000	Sox17	810.0	35000	0.001234567901	0.000000000000	0.580838913290	1.000000000000
-chr1	4523000	4524000	Sox17	810.0	36000	0.001234567901	0.000000000000	0.596856241937	1.000000000000
-chr1	4524000	4525000	Sox17	810.0	37000	0.001728395062	0.000000000000	0.856737397024	1.400000000000
-chr1	4525000	4526000	Sox17	810.0	38000	0.000740740741	0.000000000000	0.376128613396	0.600000000000
-chr1	4526000	4527000	Sox17	810.0	39000	0.000493827160	0.000000000000	0.252290767279	0.400000000000
-chr1	4527000	4528000	Sox17	810.0	40000	0.000987654321	0.000000000000	0.474728947390	0.800000000000
-chr1	4528000	4529000	Sox17	810.0	41000	0.001481481481	0.000000000000	0.724641322521	1.200000000000
-chr1	4529000	4530000	Sox17	810.0	42000	0.001234567901	0.000000000000	0.595991232884	1.000000000000
-chr1	4530000	4531000	Sox17	810.0	43000	0.001481481481	0.000000000000	0.746566930025	1.200000000000
-chr1	4531000	4532000	Sox17	810.0	44000	0.001975308642	0.000000000000	1.071619415341	1.600000000000
-chr1	4532000	4533000	Sox17	810.0	45000	0.001481481481	0.000000000000	0.892370236674	1.200000000000
-chr1	4533000	4534000	Sox17	810.0	46000	0.000987654321	0.000000000000	0.595991232956	0.800000000000
-chr1	4534000	4535000	Sox17	810.0	47000	0.000740740741	0.000000000000	0.468198046261	0.600000000000
-chr1	4535000	4536000	Sox17	810.0	48000	0.000987654321	0.000000000000	0.633886629181	0.800000000000
-chr1	4536000	4537000	Sox17	810.0	49000	0.000740740741	0.000000000000	0.457774342000	0.600000000000
-chr1	4537000	4538000	Sox17	810.0	50000	0.000740740741	0.000000000000	0.458625223683	0.600000000000
-chr1	4538000	4539000	Sox17	810.0	51000	0.000740740741	0.000000000000	0.464671130632	0.600000000000
-chr1	4539000	4540000	Sox17	810.0	52000	0.000987654321	0.000000000000	0.605869540392	0.800000000000
-chr1	4540000	4541000	Sox17	810.0	53000	0.000987654321	0.000000000000	0.633886629181	0.800000000000
-chr1	4541000	4542000	Sox17	810.0	54000	0.000740740741	0.000000000000	0.517275409651	0.600000000000
-chr1	4542000	4543000	Sox17	810.0	55000	0.000740740741	0.000000000000	0.524979511557	0.600000000000
-chr1	4543000	4544000	Sox17	810.0	56000	0.001234567901	0.000000000000	0.878705022935	1.000000000000
-chr1	4544000	4545000	Sox17	810.0	57000	0.001234567901	0.000000000000	0.901828838855	1.000000000000
-chr1	4545000	4546000	Sox17	810.0	58000	0.000740740741	0.000000000000	0.539913282947	0.600000000000
-chr1	4546000	4547000	Sox17	810.0	59000	0.000740740741	0.000000000000	0.535228568961	0.600000000000
-chr1	4547000	4548000	Sox17	810.0	60000	0.000740740741	0.000000000000	0.508743031695	0.600000000000
-chr1	4548000	4549000	Sox17	810.0	61000	0.000246913580	0.000000000000	0.173883277251	0.200000000000
+chr1	4520000	4521000	Sox17	810.0	33000	0.000987654321	1.000000000000	0.525933815293	0.800000000000
+chr1	4521000	4522000	Sox17	810.0	34000	0.001234567901	1.000000000000	0.685504522305	1.000000000000
+chr1	4522000	4523000	Sox17	810.0	35000	0.001234567901	1.000000000000	0.714987708022	1.000000000000
+chr1	4523000	4524000	Sox17	810.0	36000	0.001234567901	1.000000000000	0.755695902960	1.000000000000
+chr1	4524000	4525000	Sox17	810.0	37000	0.001728395062	1.000000000000	1.084738494331	1.400000000000
+chr1	4525000	4526000	Sox17	810.0	38000	0.000740740741	1.000000000000	0.469612396844	0.600000000000
+chr1	4526000	4527000	Sox17	810.0	39000	0.000493827160	1.000000000000	0.301685961554	0.400000000000
+chr1	4527000	4528000	Sox17	810.0	40000	0.000987654321	1.000000000000	0.576022750156	0.800000000000
+chr1	4528000	4529000	Sox17	810.0	41000	0.001481481481	1.000000000000	0.841030726872	1.200000000000
+chr1	4529000	4530000	Sox17	810.0	42000	0.001234567901	1.000000000000	0.702197865842	1.000000000000
+chr1	4530000	4531000	Sox17	810.0	43000	0.001481481481	1.000000000000	0.918991764889	1.200000000000
+chr1	4531000	4532000	Sox17	810.0	44000	0.001975308642	1.000000000000	1.281428318878	1.600000000000
+chr1	4532000	4533000	Sox17	810.0	45000	0.001481481481	1.000000000000	1.067084522368	1.200000000000
+chr1	4533000	4534000	Sox17	810.0	46000	0.000987654321	1.000000000000	0.691717300513	0.800000000000
+chr1	4534000	4535000	Sox17	810.0	47000	0.000740740741	1.000000000000	0.535165101452	0.600000000000
+chr1	4535000	4536000	Sox17	810.0	48000	0.000987654321	1.000000000000	0.713405406576	0.800000000000
+chr1	4536000	4537000	Sox17	810.0	49000	0.000740740741	1.000000000000	0.499100457284	0.600000000000
+chr1	4537000	4538000	Sox17	810.0	50000	0.000740740741	1.000000000000	0.516158093850	0.600000000000
+chr1	4538000	4539000	Sox17	810.0	51000	0.000740740741	1.000000000000	0.506619861857	0.600000000000
+chr1	4539000	4540000	Sox17	810.0	52000	0.000987654321	1.000000000000	0.649910847275	0.800000000000
+chr1	4540000	4541000	Sox17	810.0	53000	0.000987654321	1.000000000000	0.668817568635	0.800000000000
+chr1	4541000	4542000	Sox17	810.0	54000	0.000740740741	1.000000000000	0.554876714112	0.600000000000
+chr1	4542000	4543000	Sox17	810.0	55000	0.000740740741	1.000000000000	0.572372652235	0.600000000000
+chr1	4543000	4544000	Sox17	810.0	56000	0.001234567901	1.000000000000	0.988935379175	1.000000000000
+chr1	4544000	4545000	Sox17	810.0	57000	0.001234567901	1.000000000000	1.030818744269	1.000000000000
+chr1	4545000	4546000	Sox17	810.0	58000	0.000740740741	1.000000000000	0.617137874082	0.600000000000
+chr1	4546000	4547000	Sox17	810.0	59000	0.000740740741	1.000000000000	0.611783098806	0.600000000000
+chr1	4547000	4548000	Sox17	810.0	60000	0.000740740741	1.000000000000	0.599401889648	0.600000000000
+chr1	4548000	4549000	Sox17	810.0	61000	0.000246913580	1.000000000000	0.192638548730	0.200000000000
 chr1	4549000	4550000	Sox17	810.0	62000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4550000	4551000	Sox17	810.0	63000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4551000	4552000	Sox17	810.0	64000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -272,134 +272,134 @@
 chr1	4554000	4555000	Sox17	810.0	67000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4555000	4556000	Sox17	810.0	68000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4556000	4557000	Sox17	810.0	69000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4557000	4558000	Sox17	810.0	70000	0.000740740741	0.000000000000	0.597434310652	0.600000000000
-chr1	4558000	4559000	Sox17	810.0	71000	0.000987654321	0.000000000000	0.770461734373	0.800000000000
-chr1	4559000	4560000	Sox17	810.0	72000	0.001234567901	0.000000000000	0.983813278620	1.000000000000
-chr1	4560000	4561000	Sox17	810.0	73000	0.001728395062	0.000000000000	1.425068145523	1.400000000000
-chr1	4561000	4562000	Sox17	810.0	74000	0.001975308642	0.000000000000	1.566605526763	1.600000000000
-chr1	4562000	4563000	Sox17	810.0	75000	0.002962962963	0.000000000000	2.289933832159	2.400000000000
-chr1	4563000	4564000	Sox17	810.0	76000	0.002716049383	0.000000000000	2.084596063304	2.200000000000
-chr1	4564000	4565000	Sox17	810.0	77000	0.002469135802	0.000000000000	1.835865850765	2.000000000000
-chr1	4565000	4566000	Sox17	810.0	78000	0.002222222222	0.000000000000	1.818725088396	1.800000000000
-chr1	4566000	4567000	Sox17	810.0	79000	0.001975308642	0.000000000000	1.640833718057	1.600000000000
-chr1	4567000	4568000	Sox17	810.0	80000	0.000246913580	0.000000000000	0.215870840288	0.200000000000
-chr1	4568000	4569000	Sox17	810.0	81000	0.000740740741	0.000000000000	0.631049540665	0.600000000000
-chr1	4569000	4570000	Sox17	810.0	82000	0.000740740741	0.000000000000	0.637572016588	0.600000000000
-chr1	4570000	4571000	Sox17	810.0	83000	0.000493827160	0.000000000000	0.372157421369	0.400000000000
-chr1	4571000	4572000	Sox17	810.0	84000	0.000493827160	0.000000000000	0.349986341038	0.400000000000
-chr1	4572000	4573000	Sox17	810.0	85000	0.000740740741	0.000000000000	0.523864905367	0.600000000000
-chr1	4573000	4574000	Sox17	810.0	86000	0.000740740741	0.000000000000	0.575152378611	0.600000000000
-chr1	4574000	4575000	Sox17	810.0	87000	0.000740740741	0.000000000000	0.548311934077	0.600000000000
-chr1	4575000	4576000	Sox17	810.0	88000	0.000740740741	0.000000000000	0.544680729189	0.600000000000
-chr1	4576000	4577000	Sox17	810.0	89000	0.000740740741	0.000000000000	0.601805781250	0.600000000000
-chr1	4577000	4578000	Sox17	810.0	90000	0.000493827160	0.000000000000	0.404161130755	0.400000000000
+chr1	4557000	4558000	Sox17	810.0	70000	0.000740740741	1.000000000000	0.651368393880	0.600000000000
+chr1	4558000	4559000	Sox17	810.0	71000	0.000987654321	1.000000000000	0.853564716482	0.800000000000
+chr1	4559000	4560000	Sox17	810.0	72000	0.001234567901	1.000000000000	1.107229084890	1.000000000000
+chr1	4560000	4561000	Sox17	810.0	73000	0.001728395062	1.000000000000	1.679017668933	1.400000000000
+chr1	4561000	4562000	Sox17	810.0	74000	0.001975308642	1.000000000000	1.845777247806	1.600000000000
+chr1	4562000	4563000	Sox17	810.0	75000	0.002962962963	1.000000000000	2.738272579788	2.400000000000
+chr1	4563000	4564000	Sox17	810.0	76000	0.002716049383	1.000000000000	2.492732392537	2.200000000000
+chr1	4564000	4565000	Sox17	810.0	77000	0.002469135802	1.000000000000	2.033884676872	2.000000000000
+chr1	4565000	4566000	Sox17	810.0	78000	0.002222222222	1.000000000000	1.982912628958	1.800000000000
+chr1	4566000	4567000	Sox17	810.0	79000	0.001975308642	1.000000000000	1.760107680637	1.600000000000
+chr1	4567000	4568000	Sox17	810.0	80000	0.000246913580	1.000000000000	0.227766612936	0.200000000000
+chr1	4568000	4569000	Sox17	810.0	81000	0.000740740741	1.000000000000	0.699115346589	0.600000000000
+chr1	4569000	4570000	Sox17	810.0	82000	0.000740740741	1.000000000000	0.683917810405	0.600000000000
+chr1	4570000	4571000	Sox17	810.0	83000	0.000493827160	1.000000000000	0.399209943509	0.400000000000
+chr1	4571000	4572000	Sox17	810.0	84000	0.000493827160	1.000000000000	0.393890857570	0.400000000000
+chr1	4572000	4573000	Sox17	810.0	85000	0.000740740741	1.000000000000	0.608006289918	0.600000000000
+chr1	4573000	4574000	Sox17	810.0	86000	0.000740740741	1.000000000000	0.637189045582	0.600000000000
+chr1	4574000	4575000	Sox17	810.0	87000	0.000740740741	1.000000000000	0.626737796725	0.600000000000
+chr1	4575000	4576000	Sox17	810.0	88000	0.000740740741	1.000000000000	0.622587215447	0.600000000000
+chr1	4576000	4577000	Sox17	810.0	89000	0.000740740741	1.000000000000	0.666717318381	0.600000000000
+chr1	4577000	4578000	Sox17	810.0	90000	0.000493827160	1.000000000000	0.447754464578	0.400000000000
 chr1	4578000	4579000	Sox17	810.0	91000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4579000	4580000	Sox17	810.0	92000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4580000	4581000	Sox17	810.0	93000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4581000	4582000	Sox17	810.0	94000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4582000	4583000	Sox17	810.0	95000	0.000246913580	0.000000000000	0.198663744199	0.200000000000
-chr1	4583000	4584000	Sox17	810.0	96000	0.000493827160	0.000000000000	0.386135165004	0.400000000000
-chr1	4584000	4585000	Sox17	810.0	97000	0.000493827160	0.000000000000	0.400227689064	0.400000000000
-chr1	4585000	4586000	Sox17	810.0	98000	0.002222222222	0.000000000000	1.758244920146	1.800000000000
-chr1	4586000	4587000	Sox17	810.0	99000	0.002222222222	0.000000000000	1.888319161188	1.800000000000
-chr1	4587000	4588000	Sox17	810.0	100000	0.001975308642	0.000000000000	1.874570715149	1.600000000000
-chr1	4588000	4589000	Sox17	810.0	101000	0.001728395062	0.000000000000	1.755266861622	1.400000000000
-chr1	4589000	4590000	Sox17	810.0	102000	0.001728395062	0.000000000000	1.708390299916	1.400000000000
+chr1	4582000	4583000	Sox17	810.0	95000	0.000246913580	1.000000000000	0.220091868359	0.200000000000
+chr1	4583000	4584000	Sox17	810.0	96000	0.000493827160	1.000000000000	0.434574420199	0.400000000000
+chr1	4584000	4585000	Sox17	810.0	97000	0.000493827160	1.000000000000	0.436358713169	0.400000000000
+chr1	4585000	4586000	Sox17	810.0	98000	0.002222222222	1.000000000000	1.916972540051	1.800000000000
+chr1	4586000	4587000	Sox17	810.0	99000	0.002222222222	1.000000000000	1.992376825966	1.800000000000
+chr1	4587000	4588000	Sox17	810.0	100000	0.001975308642	1.000000000000	1.911941732625	1.600000000000
+chr1	4588000	4589000	Sox17	810.0	101000	0.001728395062	1.000000000000	1.821126007670	1.400000000000
+chr1	4589000	4590000	Sox17	810.0	102000	0.001728395062	1.000000000000	1.802532808961	1.400000000000
 chr1	4590000	4591000	Sox17	810.0	103000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	4591000	4592000	Sox17	810.0	104000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4592000	4593000	Sox17	810.0	105000	0.000493827160	0.000000000000	0.492495749455	0.400000000000
-chr1	4593000	4594000	Sox17	810.0	106000	0.000493827160	0.000000000000	0.480975380957	0.400000000000
-chr1	4594000	4595000	Sox17	810.0	107000	0.000740740741	0.000000000000	0.693090927964	0.600000000000
-chr1	4595000	4596000	Sox17	810.0	108000	0.000740740741	0.000000000000	0.676001014547	0.600000000000
-chr1	4596000	4597000	Sox17	810.0	109000	0.000987654321	0.000000000000	0.934622615061	0.800000000000
-chr1	4597000	4598000	Sox17	810.0	110000	0.000493827160	0.000000000000	0.483804647926	0.400000000000
-chr1	4598000	4599000	Sox17	810.0	111000	0.000493827160	0.000000000000	0.458199387818	0.400000000000
-chr1	4599000	4600000	Sox17	810.0	112000	0.000740740741	0.000000000000	0.704972486820	0.600000000000
-chr1	4600000	4601000	Sox17	810.0	113000	0.000987654321	0.000000000000	0.964771731912	0.800000000000
-chr1	4601000	4602000	Sox17	810.0	114000	0.001234567901	0.000000000000	1.188537429714	1.000000000000
-chr1	4602000	4603000	Sox17	810.0	115000	0.001234567901	0.000000000000	1.198932800900	1.000000000000
-chr1	4603000	4604000	Sox17	810.0	116000	0.001728395062	0.000000000000	1.931971580617	1.400000000000
-chr1	4604000	4605000	Sox17	810.0	117000	0.001234567901	0.000000000000	1.408335447937	1.000000000000
-chr1	4605000	4606000	Sox17	810.0	118000	0.000987654321	0.000000000000	1.142316530120	0.800000000000
-chr1	4606000	4607000	Sox17	810.0	119000	0.000987654321	0.000000000000	1.115210713937	0.800000000000
-chr1	4607000	4608000	Sox17	810.0	120000	0.000987654321	0.000000000000	1.100291506945	0.800000000000
-chr1	4608000	4609000	Sox17	810.0	121000	0.000493827160	0.000000000000	0.541097303510	0.400000000000
-chr1	4609000	4610000	Sox17	810.0	122000	0.000493827160	0.000000000000	0.555721555072	0.400000000000
-chr1	4610000	4611000	Sox17	810.0	123000	0.000987654321	0.000000000000	1.134438485021	0.800000000000
-chr1	4611000	4612000	Sox17	810.0	124000	0.000493827160	0.000000000000	0.602540586849	0.400000000000
-chr1	4612000	4613000	Sox17	810.0	125000	0.000493827160	0.000000000000	0.657974321282	0.400000000000
-chr1	4613000	4614000	Sox17	810.0	126000	0.000493827160	0.000000000000	0.613782015792	0.400000000000
-chr1	4614000	4615000	Sox17	810.0	127000	0.000493827160	0.000000000000	0.627838092596	0.400000000000
-chr1	4615000	4616000	Sox17	810.0	128000	0.000246913580	0.000000000000	0.328987160641	0.200000000000
-chr1	4616000	4617000	Sox17	810.0	129000	0.000246913580	0.000000000000	0.317555174276	0.200000000000
-chr1	4617000	4618000	Sox17	810.0	130000	0.000246913580	0.000000000000	0.296919819842	0.200000000000
-chr1	4618000	4619000	Sox17	810.0	131000	0.000246913580	0.000000000000	0.322536431950	0.200000000000
-chr1	4619000	4620000	Sox17	810.0	132000	0.000246913580	0.000000000000	0.330308394228	0.200000000000
-chr1	4620000	4621000	Sox17	810.0	133000	0.000493827160	0.000000000000	0.595991232596	0.400000000000
-chr1	4621000	4622000	Sox17	810.0	134000	0.000493827160	0.000000000000	0.620730491495	0.400000000000
-chr1	4622000	4623000	Sox17	810.0	135000	0.000493827160	0.000000000000	0.650172254170	0.400000000000
-chr1	4623000	4624000	Sox17	810.0	136000	0.000740740741	0.000000000000	0.893986848895	0.600000000000
-chr1	4624000	4625000	Sox17	810.0	137000	0.001234567901	0.000000000000	1.389303887680	1.000000000000
-chr1	4625000	4626000	Sox17	810.0	138000	0.000740740741	0.000000000000	0.927595377301	0.600000000000
-chr1	4626000	4627000	Sox17	810.0	139000	0.000740740741	0.000000000000	0.868804120580	0.600000000000
-chr1	4627000	4628000	Sox17	810.0	140000	0.000740740741	0.000000000000	0.780823956737	0.600000000000
-chr1	4628000	4629000	Sox17	810.0	141000	0.000493827160	0.000000000000	0.561411536910	0.400000000000
-chr1	4629000	4630000	Sox17	810.0	142000	0.000493827160	0.000000000000	0.627838092596	0.400000000000
-chr1	4630000	4631000	Sox17	810.0	143000	0.000493827160	0.000000000000	0.598158473458	0.400000000000
-chr1	4631000	4632000	Sox17	810.0	144000	0.000493827160	0.000000000000	0.679725537759	0.400000000000
-chr1	4632000	4633000	Sox17	810.0	145000	0.000493827160	0.000000000000	0.822467901876	0.400000000000
-chr1	4633000	4634000	Sox17	810.0	146000	0.000493827160	0.000000000000	0.758034932111	0.400000000000
+chr1	4592000	4593000	Sox17	810.0	105000	0.000493827160	1.000000000000	0.519635206783	0.400000000000
+chr1	4593000	4594000	Sox17	810.0	106000	0.000493827160	1.000000000000	0.499021997452	0.400000000000
+chr1	4594000	4595000	Sox17	810.0	107000	0.000740740741	1.000000000000	0.706908232214	0.600000000000
+chr1	4595000	4596000	Sox17	810.0	108000	0.000740740741	1.000000000000	0.689477618542	0.600000000000
+chr1	4596000	4597000	Sox17	810.0	109000	0.000987654321	1.000000000000	0.920384176886	0.800000000000
+chr1	4597000	4598000	Sox17	810.0	110000	0.000493827160	1.000000000000	0.467926409440	0.400000000000
+chr1	4598000	4599000	Sox17	810.0	111000	0.000493827160	1.000000000000	0.451218983681	0.400000000000
+chr1	4599000	4600000	Sox17	810.0	112000	0.000740740741	1.000000000000	0.743820682014	0.600000000000
+chr1	4600000	4601000	Sox17	810.0	113000	0.000987654321	1.000000000000	1.000970810233	0.800000000000
+chr1	4601000	4602000	Sox17	810.0	114000	0.001234567901	1.000000000000	1.316734588696	1.000000000000
+chr1	4602000	4603000	Sox17	810.0	115000	0.001234567901	1.000000000000	1.307167864566	1.000000000000
+chr1	4603000	4604000	Sox17	810.0	116000	0.001728395062	1.000000000000	2.140356491792	1.400000000000
+chr1	4604000	4605000	Sox17	810.0	117000	0.001234567901	1.000000000000	1.411645986369	1.000000000000
+chr1	4605000	4606000	Sox17	810.0	118000	0.000987654321	1.000000000000	1.185177244024	0.800000000000
+chr1	4606000	4607000	Sox17	810.0	119000	0.000987654321	1.000000000000	1.157054393276	0.800000000000
+chr1	4607000	4608000	Sox17	810.0	120000	0.000987654321	1.000000000000	1.199621611602	0.800000000000
+chr1	4608000	4609000	Sox17	810.0	121000	0.000493827160	1.000000000000	0.532853997380	0.400000000000
+chr1	4609000	4610000	Sox17	810.0	122000	0.000493827160	1.000000000000	0.566800293976	0.400000000000
+chr1	4610000	4611000	Sox17	810.0	123000	0.000987654321	1.000000000000	1.177003607595	0.800000000000
+chr1	4611000	4612000	Sox17	810.0	124000	0.000493827160	1.000000000000	0.593361227267	0.400000000000
+chr1	4612000	4613000	Sox17	810.0	125000	0.000493827160	1.000000000000	0.671091548352	0.400000000000
+chr1	4613000	4614000	Sox17	810.0	126000	0.000493827160	1.000000000000	0.615224817761	0.400000000000
+chr1	4614000	4615000	Sox17	810.0	127000	0.000493827160	1.000000000000	0.596192149436	0.400000000000
+chr1	4615000	4616000	Sox17	810.0	128000	0.000246913580	1.000000000000	0.323975230102	0.200000000000
+chr1	4616000	4617000	Sox17	810.0	129000	0.000246913580	1.000000000000	0.312717403895	0.200000000000
+chr1	4617000	4618000	Sox17	810.0	130000	0.000246913580	1.000000000000	0.271510958907	0.200000000000
+chr1	4618000	4619000	Sox17	810.0	131000	0.000246913580	1.000000000000	0.311950939528	0.200000000000
+chr1	4619000	4620000	Sox17	810.0	132000	0.000246913580	1.000000000000	0.296233805775	0.200000000000
+chr1	4620000	4621000	Sox17	810.0	133000	0.000493827160	1.000000000000	0.524028257842	0.400000000000
+chr1	4621000	4622000	Sox17	810.0	134000	0.000493827160	1.000000000000	0.534864766691	0.400000000000
+chr1	4622000	4623000	Sox17	810.0	135000	0.000493827160	1.000000000000	0.571667190483	0.400000000000
+chr1	4623000	4624000	Sox17	810.0	136000	0.000740740741	1.000000000000	0.786042386763	0.600000000000
+chr1	4624000	4625000	Sox17	810.0	137000	0.001234567901	1.000000000000	1.245983405577	1.000000000000
+chr1	4625000	4626000	Sox17	810.0	138000	0.000740740741	1.000000000000	0.831904709719	0.600000000000
+chr1	4626000	4627000	Sox17	810.0	139000	0.000740740741	1.000000000000	0.763900348373	0.600000000000
+chr1	4627000	4628000	Sox17	810.0	140000	0.000740740741	1.000000000000	0.714005084532	0.600000000000
+chr1	4628000	4629000	Sox17	810.0	141000	0.000493827160	1.000000000000	0.513368843800	0.400000000000
+chr1	4629000	4630000	Sox17	810.0	142000	0.000493827160	1.000000000000	0.596192149436	0.400000000000
+chr1	4630000	4631000	Sox17	810.0	143000	0.000493827160	1.000000000000	0.557489844270	0.400000000000
+chr1	4631000	4632000	Sox17	810.0	144000	0.000493827160	1.000000000000	0.657417268942	0.400000000000
+chr1	4632000	4633000	Sox17	810.0	145000	0.000493827160	1.000000000000	0.752085356070	0.400000000000
+chr1	4633000	4634000	Sox17	810.0	146000	0.000493827160	1.000000000000	0.679836106744	0.400000000000
 chr1	4634000	4635000	Sox17	810.0	147000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4635000	4636000	Sox17	810.0	148000	0.000246913580	0.000000000000	0.373849046024	0.200000000000
-chr1	4636000	4637000	Sox17	810.0	149000	0.000246913580	0.000000000000	0.384330795060	0.200000000000
-chr1	4637000	4638000	Sox17	810.0	150000	0.000246913580	0.000000000000	0.357594739558	0.200000000000
-chr1	4638000	4639000	Sox17	810.0	151000	0.000246913580	0.000000000000	0.377278853812	0.200000000000
-chr1	4639000	4640000	Sox17	810.0	152000	0.000246913580	0.000000000000	0.365541289385	0.200000000000
+chr1	4635000	4636000	Sox17	810.0	148000	0.000246913580	1.000000000000	0.348431152669	0.200000000000
+chr1	4636000	4637000	Sox17	810.0	149000	0.000246913580	1.000000000000	0.378475736537	0.200000000000
+chr1	4637000	4638000	Sox17	810.0	150000	0.000246913580	1.000000000000	0.364723667669	0.200000000000
+chr1	4638000	4639000	Sox17	810.0	151000	0.000246913580	1.000000000000	0.364896741183	0.200000000000
+chr1	4639000	4640000	Sox17	810.0	152000	0.000246913580	1.000000000000	0.347116318064	0.200000000000
 chr1	4640000	4641000	Sox17	810.0	153000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4641000	4642000	Sox17	810.0	154000	0.000246913580	0.000000000000	0.375556119307	0.200000000000
-chr1	4642000	4643000	Sox17	810.0	155000	0.000246913580	0.000000000000	0.363923850039	0.200000000000
-chr1	4643000	4644000	Sox17	810.0	156000	0.000246913580	0.000000000000	0.363923850039	0.200000000000
-chr1	4644000	4645000	Sox17	810.0	157000	0.000246913580	0.000000000000	0.341272987847	0.200000000000
-chr1	4645000	4646000	Sox17	810.0	158000	0.000246913580	0.000000000000	0.328987160641	0.200000000000
-chr1	4646000	4647000	Sox17	810.0	159000	0.000246913580	0.000000000000	0.320026420787	0.200000000000
-chr1	4647000	4648000	Sox17	810.0	160000	0.000246913580	0.000000000000	0.315121801274	0.200000000000
-chr1	4648000	4649000	Sox17	810.0	161000	0.000493827160	0.000000000000	0.593839639683	0.400000000000
-chr1	4649000	4650000	Sox17	810.0	162000	0.000493827160	0.000000000000	0.671402368765	0.400000000000
-chr1	4650000	4651000	Sox17	810.0	163000	0.000493827160	0.000000000000	0.682545975694	0.400000000000
-chr1	4651000	4652000	Sox17	810.0	164000	0.000493827160	0.000000000000	0.712093420742	0.400000000000
-chr1	4652000	4653000	Sox17	810.0	165000	0.000987654321	0.000000000000	1.516069864221	0.800000000000
-chr1	4653000	4654000	Sox17	810.0	166000	0.000987654321	0.000000000000	1.644935803753	0.800000000000
-chr1	4654000	4655000	Sox17	810.0	167000	0.000987654321	0.000000000000	1.574101247046	0.800000000000
-chr1	4655000	4656000	Sox17	810.0	168000	0.001481481481	0.000000000000	2.295259259717	1.200000000000
-chr1	4656000	4657000	Sox17	810.0	169000	0.001728395062	0.000000000000	2.419023237597	1.400000000000
-chr1	4657000	4658000	Sox17	810.0	170000	0.001234567901	0.000000000000	1.671682727052	1.000000000000
-chr1	4658000	4659000	Sox17	810.0	171000	0.000987654321	0.000000000000	1.353856628464	0.800000000000
-chr1	4659000	4660000	Sox17	810.0	172000	0.000987654321	0.000000000000	1.270220697103	0.800000000000
-chr1	4660000	4661000	Sox17	810.0	173000	0.000493827160	0.000000000000	0.647612520865	0.400000000000
-chr1	4661000	4662000	Sox17	810.0	174000	0.000246913580	0.000000000000	0.342694958640	0.200000000000
-chr1	4662000	4663000	Sox17	810.0	175000	0.000246913580	0.000000000000	0.354512026264	0.200000000000
-chr1	4663000	4664000	Sox17	810.0	176000	0.000246913580	0.000000000000	0.349986340790	0.200000000000
-chr1	4664000	4665000	Sox17	810.0	177000	0.000246913580	0.000000000000	0.373849046024	0.200000000000
-chr1	4665000	4666000	Sox17	810.0	178000	0.000493827160	0.000000000000	0.775913114612	0.400000000000
-chr1	4666000	4667000	Sox17	810.0	179000	0.000246913580	0.000000000000	0.395417260391	0.200000000000
-chr1	4667000	4668000	Sox17	810.0	180000	0.000246913580	0.000000000000	0.417496396239	0.200000000000
-chr1	4668000	4669000	Sox17	810.0	181000	0.000246913580	0.000000000000	0.419626479907	0.200000000000
-chr1	4669000	4670000	Sox17	810.0	182000	0.000246913580	0.000000000000	0.442187043505	0.200000000000
+chr1	4641000	4642000	Sox17	810.0	154000	0.000246913580	1.000000000000	0.330209587258	0.200000000000
+chr1	4642000	4643000	Sox17	810.0	155000	0.000246913580	1.000000000000	0.326381493667	0.200000000000
+chr1	4643000	4644000	Sox17	810.0	156000	0.000246913580	1.000000000000	0.345580405193	0.200000000000
+chr1	4644000	4645000	Sox17	810.0	157000	0.000246913580	1.000000000000	0.336073890233	0.200000000000
+chr1	4645000	4646000	Sox17	810.0	158000	0.000246913580	1.000000000000	0.323975230102	0.200000000000
+chr1	4646000	4647000	Sox17	810.0	159000	0.000246913580	1.000000000000	0.320778698724	0.200000000000
+chr1	4647000	4648000	Sox17	810.0	160000	0.000246913580	1.000000000000	0.310321101844	0.200000000000
+chr1	4648000	4649000	Sox17	810.0	161000	0.000493827160	1.000000000000	0.626563751378	0.400000000000
+chr1	4649000	4650000	Sox17	810.0	162000	0.000493827160	1.000000000000	0.661173939568	0.400000000000
+chr1	4650000	4651000	Sox17	810.0	163000	0.000493827160	1.000000000000	0.648142502908	0.400000000000
+chr1	4651000	4652000	Sox17	810.0	164000	0.000493827160	1.000000000000	0.676200620074	0.400000000000
+chr1	4652000	4653000	Sox17	810.0	165000	0.000987654321	1.000000000000	1.386332452855	0.800000000000
+chr1	4653000	4654000	Sox17	810.0	166000	0.000987654321	1.000000000000	1.243833473318	0.800000000000
+chr1	4654000	4655000	Sox17	810.0	167000	0.000987654321	1.000000000000	1.245632721235	0.800000000000
+chr1	4655000	4656000	Sox17	810.0	168000	0.001481481481	1.000000000000	1.897031040397	1.200000000000
+chr1	4656000	4657000	Sox17	810.0	169000	0.001728395062	1.000000000000	1.999321931024	1.400000000000
+chr1	4657000	4658000	Sox17	810.0	170000	0.001234567901	1.000000000000	1.499232064694	1.000000000000
+chr1	4658000	4659000	Sox17	810.0	171000	0.000987654321	1.000000000000	1.166577475118	0.800000000000
+chr1	4659000	4660000	Sox17	810.0	172000	0.000987654321	1.000000000000	1.116847870700	0.800000000000
+chr1	4660000	4661000	Sox17	810.0	173000	0.000493827160	1.000000000000	0.614969855182	0.400000000000
+chr1	4661000	4662000	Sox17	810.0	174000	0.000246913580	1.000000000000	0.301316248499	0.200000000000
+chr1	4662000	4663000	Sox17	810.0	175000	0.000246913580	1.000000000000	0.317940593070	0.200000000000
+chr1	4663000	4664000	Sox17	810.0	176000	0.000246913580	1.000000000000	0.313881777236	0.200000000000
+chr1	4664000	4665000	Sox17	810.0	177000	0.000246913580	1.000000000000	0.322134462090	0.200000000000
+chr1	4665000	4666000	Sox17	810.0	178000	0.000493827160	1.000000000000	0.668580958364	0.400000000000
+chr1	4666000	4667000	Sox17	810.0	179000	0.000246913580	1.000000000000	0.354626046134	0.200000000000
+chr1	4667000	4668000	Sox17	810.0	180000	0.000246913580	1.000000000000	0.367085784780	0.200000000000
+chr1	4668000	4669000	Sox17	810.0	181000	0.000246913580	1.000000000000	0.361579498110	0.200000000000
+chr1	4669000	4670000	Sox17	810.0	182000	0.000246913580	1.000000000000	0.404346965794	0.200000000000
 chr1	4670000	4671000	Sox17	810.0	183000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	4671000	4672000	Sox17	810.0	184000	0.000246913580	0.000000000000	0.401203854492	0.200000000000
-chr1	4672000	4673000	Sox17	810.0	185000	0.000246913580	0.000000000000	0.395417260391	0.200000000000
-chr1	4673000	4674000	Sox17	810.0	186000	0.000246913580	0.000000000000	0.437482925987	0.200000000000
-chr1	4674000	4675000	Sox17	810.0	187000	0.000246913580	0.000000000000	0.444577243757	0.200000000000
-chr1	4675000	4676000	Sox17	810.0	188000	0.000493827160	0.000000000000	0.879644813784	0.400000000000
-chr1	4676000	4677000	Sox17	810.0	189000	0.000246913580	0.000000000000	0.478179012441	0.200000000000
-chr1	4677000	4678000	Sox17	810.0	190000	0.000246913580	0.000000000000	0.480975380957	0.200000000000
-chr1	4678000	4679000	Sox17	810.0	191000	0.000740740741	0.000000000000	1.370779835192	0.600000000000
-chr1	4679000	4680000	Sox17	810.0	192000	0.000740740741	0.000000000000	1.355716320410	0.600000000000
-chr1	4680000	4681000	Sox17	810.0	193000	0.000740740741	0.000000000000	1.468692681340	0.600000000000
-chr1	4681000	4682000	Sox17	810.0	194000	0.000740740741	0.000000000000	1.426244915656	0.600000000000
-chr1	4682000	4683000	Sox17	810.0	195000	0.000740740741	0.000000000000	1.513744604449	0.600000000000
-chr1	4683000	4684000	Sox17	810.0	196000	0.000493827160	0.000000000000	1.009163069632	0.400000000000
-chr1	4684000	4685000	Sox17	810.0	197000	0.000493827160	0.000000000000	0.934622615061	0.400000000000
-chr1	4685000	4686000	Sox17	810.0	198000	0.000246913580	0.000000000000	0.403170540070	0.200000000000
-chr1	4686000	4687000	Sox17	810.0	199000	0.000308641975	0.000000000000	0.538264332961	0.250000000000
-chr1	4687000	4688000	Sox17	810.0	200000	0.000411522634	0.000000000000	0.699377466512	0.333333333333
+chr1	4671000	4672000	Sox17	810.0	184000	0.000246913580	1.000000000000	0.373926115317	0.200000000000
+chr1	4672000	4673000	Sox17	810.0	185000	0.000246913580	1.000000000000	0.354626046134	0.200000000000
+chr1	4673000	4674000	Sox17	810.0	186000	0.000246913580	1.000000000000	0.376965859861	0.200000000000
+chr1	4674000	4675000	Sox17	810.0	187000	0.000246913580	1.000000000000	0.375260884294	0.200000000000
+chr1	4675000	4676000	Sox17	810.0	188000	0.000493827160	1.000000000000	0.757963440329	0.400000000000
+chr1	4676000	4677000	Sox17	810.0	189000	0.000246913580	1.000000000000	0.395214800462	0.200000000000
+chr1	4677000	4678000	Sox17	810.0	190000	0.000246913580	1.000000000000	0.405983997732	0.200000000000
+chr1	4678000	4679000	Sox17	810.0	191000	0.000740740741	1.000000000000	1.229370293696	0.600000000000
+chr1	4679000	4680000	Sox17	810.0	192000	0.000740740741	1.000000000000	1.168179917236	0.600000000000
+chr1	4680000	4681000	Sox17	810.0	193000	0.000740740741	1.000000000000	1.136392707872	0.600000000000
+chr1	4681000	4682000	Sox17	810.0	194000	0.000740740741	1.000000000000	1.228952281617	0.600000000000
+chr1	4682000	4683000	Sox17	810.0	195000	0.000740740741	1.000000000000	1.277728778668	0.600000000000
+chr1	4683000	4684000	Sox17	810.0	196000	0.000493827160	1.000000000000	0.834072951902	0.400000000000
+chr1	4684000	4685000	Sox17	810.0	197000	0.000493827160	1.000000000000	0.788900722520	0.400000000000
+chr1	4685000	4686000	Sox17	810.0	198000	0.000246913580	1.000000000000	0.347399909840	0.200000000000
+chr1	4686000	4687000	Sox17	810.0	199000	0.000308641975	1.000000000000	0.444875298484	0.250000000000
+chr1	4687000	4688000	Sox17	810.0	200000	0.000411522634	1.000000000000	0.627229741958	0.333333333333
--- a/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt	Fri Dec 11 21:16:12 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt	Tue Mar 16 15:21:53 2021 +0000
@@ -1,4 +1,4 @@
-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3
+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6
 # MB-E10-5_chr1.cool	chr1_19093103_19093103	18.89  Mbp	19.29  Mbp	Tfap2d	Sum of interactions in fixate range: 800.0
 # Chromosome	Start	End	Gene	Sum of interactions	Relative position	Relative Interactions	p-value	x-fold	Raw
 #
@@ -95,18 +95,18 @@
 chr1	18983000	18984000	Tfap2d	800.0	-110000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	18984000	18985000	Tfap2d	800.0	-109000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	18985000	18986000	Tfap2d	800.0	-108000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	18986000	18987000	Tfap2d	800.0	-107000	0.000500000000	0.023000625561	1.387914584417	0.400000000000
-chr1	18987000	18988000	Tfap2d	800.0	-106000	0.000500000000	0.023000625561	1.682320705695	0.400000000000
-chr1	18988000	18989000	Tfap2d	800.0	-105000	0.000500000000	0.023000625561	1.734893228113	0.400000000000
-chr1	18989000	18990000	Tfap2d	800.0	-104000	0.000500000000	0.023000625561	2.081871876625	0.400000000000
-chr1	18990000	18991000	Tfap2d	800.0	-103000	0.000500000000	0.023000625561	2.281503428260	0.400000000000
+chr1	18986000	18987000	Tfap2d	800.0	-107000	0.000500000000	0.299067125362	0.829824948245	0.400000000000
+chr1	18987000	18988000	Tfap2d	800.0	-106000	0.000500000000	0.299067125362	0.946680867864	0.400000000000
+chr1	18988000	18989000	Tfap2d	800.0	-105000	0.000500000000	0.299067125362	0.915248104257	0.400000000000
+chr1	18989000	18990000	Tfap2d	800.0	-104000	0.000500000000	0.299067125362	1.134907650442	0.400000000000
+chr1	18990000	18991000	Tfap2d	800.0	-103000	0.000500000000	0.299067125362	1.243734411173	0.400000000000
 chr1	18991000	18992000	Tfap2d	800.0	-102000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	18992000	18993000	Tfap2d	800.0	-101000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	18993000	18994000	Tfap2d	800.0	-100000	0.000250000000	0.042850447268	1.028084877240	0.200000000000
-chr1	18994000	18995000	Tfap2d	800.0	-99000	0.000250000000	0.042850447268	0.946305397749	0.200000000000
-chr1	18995000	18996000	Tfap2d	800.0	-98000	0.000250000000	0.042850447268	0.885902925125	0.200000000000
-chr1	18996000	18997000	Tfap2d	800.0	-97000	0.000250000000	0.042850447268	0.832748749263	0.200000000000
-chr1	18997000	18998000	Tfap2d	800.0	-96000	0.000250000000	0.042850447268	0.763989677803	0.200000000000
+chr1	18993000	18994000	Tfap2d	800.0	-100000	0.000250000000	0.378306706409	0.614685146810	0.200000000000
+chr1	18994000	18995000	Tfap2d	800.0	-99000	0.000250000000	0.378306706409	0.632353235816	0.200000000000
+chr1	18995000	18996000	Tfap2d	800.0	-98000	0.000250000000	0.378306706409	0.591990263285	0.200000000000
+chr1	18996000	18997000	Tfap2d	800.0	-97000	0.000250000000	0.378306706409	0.497894968781	0.200000000000
+chr1	18997000	18998000	Tfap2d	800.0	-96000	0.000250000000	0.378306706409	0.470219209914	0.200000000000
 chr1	18998000	18999000	Tfap2d	800.0	-95000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	18999000	19000000	Tfap2d	800.0	-94000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19000000	19001000	Tfap2d	800.0	-93000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -125,11 +125,11 @@
 chr1	19013000	19014000	Tfap2d	800.0	-80000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19014000	19015000	Tfap2d	800.0	-79000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19015000	19016000	Tfap2d	800.0	-78000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
-chr1	19016000	19017000	Tfap2d	800.0	-77000	0.000250000000	0.042850447268	0.578297742704	0.200000000000
-chr1	19017000	19018000	Tfap2d	800.0	-76000	0.000250000000	0.042850447268	0.551489237898	0.200000000000
-chr1	19018000	19019000	Tfap2d	800.0	-75000	0.000250000000	0.042850447268	0.603441123004	0.200000000000
-chr1	19019000	19020000	Tfap2d	800.0	-74000	0.000250000000	0.042850447268	0.590601950083	0.200000000000
-chr1	19020000	19021000	Tfap2d	800.0	-73000	0.000250000000	0.042850447268	0.465222765315	0.200000000000
+chr1	19016000	19017000	Tfap2d	800.0	-77000	0.000250000000	0.378306706409	0.325421548405	0.200000000000
+chr1	19017000	19018000	Tfap2d	800.0	-76000	0.000250000000	0.378306706409	0.329731767322	0.200000000000
+chr1	19018000	19019000	Tfap2d	800.0	-75000	0.000250000000	0.378306706409	0.339570311341	0.200000000000
+chr1	19019000	19020000	Tfap2d	800.0	-74000	0.000250000000	0.378306706409	0.342731205316	0.200000000000
+chr1	19020000	19021000	Tfap2d	800.0	-73000	0.000250000000	0.378306706409	0.286334602634	0.200000000000
 chr1	19021000	19022000	Tfap2d	800.0	-72000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19022000	19023000	Tfap2d	800.0	-71000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19023000	19024000	Tfap2d	800.0	-70000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
@@ -186,220 +186,220 @@
 chr1	19074000	19075000	Tfap2d	800.0	-19000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19075000	19076000	Tfap2d	800.0	-18000	0.000000000000	1.000000000000	0.000000000000	0.000000000000
 chr1	19076000	19077000	T