Repository 'hicexplorer_hicaggregatecontacts'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaggregatecontacts

Changeset 5:ce16a538ab46 (2019-12-16)
Previous changeset 4:0c812ed34277 (2019-12-16) Next changeset 6:f922a8d5e897 (2020-02-05)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
modified:
hicAggregateContacts.xml
macros.xml
added:
test-data/Li_et_al_2015.cool
test-data/cHi-C/FL-E13-5_chr1.cool
test-data/cHi-C/MB-E10-5_chr1.cool
test-data/cHi-C/background.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt
test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt
test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png
test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png
test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png
test-data/cHi-C/chicQualityControl/histogram.png
test-data/cHi-C/chicQualityControl/new_referencepoints.bed
test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter
test-data/cHi-C/chicQualityControl/sparsity.png
test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt
test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt
test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt
test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt
test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt
test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
test-data/cHi-C/referencePoints.bed
test-data/cHi-C/referencePoints_chicViewpoint.bed
test-data/distVsCounts.txt
test-data/find_TADs/multiFDR_boundaries.bed
test-data/find_TADs/multiFDR_boundaries.gff
test-data/find_TADs/multiFDR_score.bedgraph
test-data/find_TADs/multiFDR_tad_score.bm
test-data/find_TADs/multiFDR_zscore_matrix.h5
test-data/hicAggregateContacts/test_regions.bed
test-data/hicAggregateContacts_results1.png
test-data/hicAverageRegions/regions.bed
test-data/hicAverageRegions/result.npz
test-data/hicAverageRegions/result_rangeInBins_100.npz
test-data/hicAverageRegions/result_range_100000.npz
test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png
test-data/hicCompartmentsPolarization/pca1.bedgraph
test-data/hicConvertFormat/small_test_matrix_chr4.cool
test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv
test-data/hicConvertFormat/small_test_matrix_chr4.homer
test-data/hicConvertFormat/test_matrix.bed
test-data/hicCorrectMatrix/diagnostic_plot.png
test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5
test-data/hicCorrelate_heatmap_result1.png
test-data/hicCorrelate_scatter_result1.png
test-data/hicDetectLoops/loops.bedgraph
test-data/hicFindRestrictionSites/reference_genome.fasta
test-data/hicFindRestrictionSites/restriction_sites.bed
test-data/hicInfo/hicInfo_output.txt
test-data/hicInfo_output.txt
test-data/hicMergeLoops/gm12878_10kb.bedgraph
test-data/hicMergeLoops/gm12878_25kb.bedgraph
test-data/hicMergeLoops/gm12878_5kb.bedgraph
test-data/hicMergeLoops/gm12878_all.bedgraph
test-data/hicPCA/pca1_test1.bw
test-data/hicPCA/pca1_test2.bw
test-data/hicPCA/pca1_test3.bw
test-data/hicPCA/pca2_test1.bw
test-data/hicPCA/pca2_test2.bw
test-data/hicPCA/pca2_test3.bw
test-data/hicPlotAverageRegions/defaults.png
test-data/hicPlotAverageRegions/defaults_log.png
test-data/hicPlotAverageRegions/defaults_log1p.png
test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png
test-data/hicPlotDistVsCounts_result1.png
test-data/hicPlotDistVsCounts_result2.png
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/hicTransform/obs_exp_norm.h5
test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak
test-data/hicValidateLocations/loops_1.bedgraph
test-data/hicValidateLocations/overlap_smc3_matched_locations
test-data/hicValidateLocations/overlap_smc3_statistics
test-data/li_32-33mb_interactions.bedgraph
test-data/li_viewpoint_32-33Mb.png
test-data/li_viewpoint_32Mb.png
test-data/raw_qc_report
test-data/regions.bed
test-data/small_test_matrix.cool
test-data/small_test_matrix_result_sorted.bam
b
diff -r 0c812ed34277 -r ce16a538ab46 hicAggregateContacts.xml
--- a/hicAggregateContacts.xml Mon Dec 16 08:38:26 2019 -0500
+++ b/hicAggregateContacts.xml Mon Dec 16 15:27:02 2019 -0500
[
@@ -7,16 +7,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-@BINARY@
-    --matrix '$matrix_h5_cooler'
+    ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+    @BINARY@
+    --matrix 'matrix.$matrix_h5_cooler.ext'
     --BED $BED
     #if $BED2:
         --BED2 $BED2
     #end if
 
-    --range $range_min:$range_max
+    --range '$range_min:$range_max'
 
-    --numberOfBins $numberOfBins
+    --numberOfBins '$numberOfBins'
 
     --transform $transform
     --avgType $avgType
@@ -128,6 +129,8 @@
         <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">
@@ -141,6 +144,8 @@
         <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}: Plot">
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+
             </change_format>
         </data>
         <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
@@ -155,13 +160,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/>
-            <param name="BED" value="test_regions.bed" ftype="bed"/>
+            <param name="matrix_h5_cooler" value="Li_et_al_2015.cool" ftype="cool"/>
+            <param name="BED" value="hicAggregateContacts/test_regions.bed" ftype="bed"/>
             <param name="numberOfBins" value="30" />
             <param name="range_max" value="900000" />
             <param name="range_min" value="50000" />
             <param name="image_file_format" value="png" />
-            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" />
+            <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" delta='35000'/>
         </test>
     </tests>
     <help><![CDATA[
b
diff -r 0c812ed34277 -r ce16a538ab46 macros.xml
--- a/macros.xml Mon Dec 16 08:38:26 2019 -0500
+++ b/macros.xml Mon Dec 16 15:27:02 2019 -0500
[
b'@@ -1,6 +1,6 @@\n <macros>\n     <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n-    <token name="@WRAPPER_VERSION@">2.1.4</token>\n+    <token name="@WRAPPER_VERSION@">3.3.1</token>\n     <token name="@USE_RANGE@">\n         #if $use_range.select_use_range == "yes_use_range":\n             --range $range_min:$range_max\n@@ -15,6 +15,25 @@\n         <version_command>@BINARY@ --version</version_command>\n     </xml>\n \n+    <token name="@CHROMOSOME_LIST@">\n+        #if $chromosome_list:\n+            #set $chromosomes = []\n+            #for $chrom in $chromosome_list:\n+                #silent $chromosomes.append("\'%s\'" % $chrom.chromosomes)\n+            #end for\n+            #set $chromosome_string = \' \'.join($chromosomes)\n+            --chromosomes $chromosome_string\n+        #end if\n+    </token>\n+\n+    <xml name="chromosome_list">\n+        <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">\n+            <param argument="--chromosomes" type="text" value="" >\n+                <validator type="empty_field" />\n+            </param>\n+        </repeat>\n+    </xml>\n+\n     <xml name="citations">\n         <citations>\n             <citation type="doi">10.5281/zenodo.1133705</citation>\n@@ -114,6 +133,7 @@\n             <option value="brg">brg</option>\n             <option value="jet">jet</option>\n             <option value="afmhot">afmhot</option>\n+            <option value="plasma">plasma</option>\n             <option value="Accent_r">Accent reversed</option>\n             <option value="Spectral_r">Spectral reversed</option>\n             <option value="Set1_r">Set1 reversed</option>\n@@ -183,10 +203,10 @@\n             <option value="brg_r">brg reversed</option>\n             <option value="jet_r">jet reversed</option>\n             <option value="afmhot_r">afmhot reversed</option>\n+            <option value="plasma_r">plasma reversed</option>\n         </param>\n     </xml>\n \n-\n     <xml name="multiple_input_matrices">\n         <repeat name="input_files" title="Hi-C Matrix files" min="2">\n             <param name="matrix" type="data" format="h5,cool"\n@@ -202,19 +222,22 @@\n         #set $matrices = []\n         #set $mlabels = []\n         #for $counter, $i in enumerate($input_files):\n-            ln -s $i.matrix #echo str($counter)+\'_matrix\'#;\n-            #silent $matrices.append( \'%s_matrix\' % $counter )\n+            ln -s \'$i.matrix\' \'${counter}_matrix.$i.matrix.ext\'; \n+            #silent $matrices.append( \'\\\'%s_matrix.%s\\\'\' % ($counter,  $i.matrix.ext))\n \n             #if str($i.mlabel.value) != "":\n-                #set $mlabels += [\'"%s"\' % ($i.mlabel.value)]\n+                #set $mlabels += [\'\\\'%s\\\'\' % ($i.mlabel.value)]\n             #else\n-                #set $mlabels += [\'"%s"\' % ($i.matrix.name)]\n+                #set $mlabels += [\'\\\'%s\\\'\' % ($i.matrix.name)]\n             #end if\n         #end for\n         #set $mlabels = \' \'.join($mlabels)\n         #set $matrices = \' \'.join($matrices)\n     </token>\n \n+    <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($file.element_identifier))]]></token>\n+    <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($matrix.element_identifier))]]></token>\n+    <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($m.element_identifier))]]></token>\n \n     <xml name="region">\n         <param name="region" type="text" label="Region of the genome to limit the operation"\n@@ -330,6 +353,96 @@\n         <param name=\'matrix_h5_cooler_multiple\' type="data" format="h5,cool"\n             label="Matricies to compute on" multiple="true"/>\n     </xml>\n+\n+    \n+\n+    <xml name=\'convertFormat_single_macro\'>\n+        <conditional name="inputFormat_conditional">\n+            <param name="inputFormat_selector" type="select" label="Choose input file type">\n+                <option value="optionCool" selected="True">cool</option>\n+        '..b'n" truevalue="yes" falsevalue="" label=\'Apply correction factors with a division instead multiplication\'/>\n+                <param name=\'chromosome\' type=\'text\' label=\'Load only one chromosome\'/>\n+                <param name=\'loadRawValues\' type="boolean" truevalue="yes" falsevalue="" label=\'Load raw data\'/>\n+\n+            </when>\n+            <when value="optionH5">\n+                <expand macro=\'matrix_h5_cooler_macro\' />\n+            </when>\n+            <!-- <when value="optionHic">\n+                <param name=\'matrixHic\' type=\'data\' format=\'binary\' label=\'.hic matrix\'/>\n+                <param name=\'resolutions\' type=\'text\' label=\'List of resolutions\'/>\n+            </when> --> \n+\n+            <when value="optionHomer">\n+                <param name=\'matrixHomer\' type=\'data\' format=\'txt\' label=\'Homer interaction matrix\'/>\n+            </when>\n+\n+            <when value="optionHicpro">\n+                <param name=\'matrixHicpro\' type=\'data\' format=\'txt\' label=\'.hic matrix\'/>\n+                <param name=\'bedHicpro\' type=\'data\' format=\'bed\' label=\'HicPro bed file\'/>\n+            </when>\n+        </conditional>\n+    </xml>\n+\n+    <xml name=\'convertFormat_multiple_macro\'>\n+        <conditional name="inputFormat_conditional">\n+            <param name="inputFormat_selector" type="select" label="Choose input file type">\n+                <option value="optionCool" selected="True">cool</option>\n+                <option value="optionH5">h5</option>\n+                <option value="optionHomer">Homer</option>\n+                <option value="optionHicpro">HiCPro</option>\n+            </param>\n+            <when value="optionCool">\n+                <expand macro=\'matrix_h5_cooler_multiple_macro\' />\n+                <param name=\'correctionName\' type=\'text\' label=\'Correction factors column name\'/>\n+                <param name=\'correctionDivision\' type="boolean" truevalue="yes" falsevalue="" label=\'Apply correction factors with a division instead multiplication\'/>\n+                <param name=\'chromosome\' type=\'text\' label=\'Load only one chromosome\'/>\n+                <param name=\'loadRawValues\' type="boolean" truevalue="yes" falsevalue="" label=\'Load raw data\'/>\n+\n+            </when>\n+            <when value="optionH5">\n+                <expand macro=\'matrix_h5_cooler_multiple_macro\' />\n+            </when>\n+           \n+            <when value="optionHomer">\n+                <param name=\'matrixHomer\' type=\'data\' format=\'txt\' label=\'Homer interaction matrix\' multiple="true"/>\n+            </when>\n+\n+            <when value="optionHicpro">\n+                <param name=\'matrixHicpro\' type=\'data\' format=\'txt\' label=\'.hic matrix\' multiple="true"/>\n+                <param name=\'bedHicpro\' type=\'data\' format=\'bed\' label=\'HicPro bed file\' multiple="true"/>\n+            </when>\n+        </conditional>\n+    </xml>\n+    <xml name=\'convertFormat_single_output_macro\'>\n+        <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == \'optionCool\'</filter> -->\n+\n+        <conditional name="outputFormat_conditional">\n+            <param name="outputFormat_selector" type="select" label="Choose output file type">\n+                <option value="cool" selected="True">cool</option>\n+                <option value="h5">h5</option>\n+                <option value="homer">Homer</option>\n+                <option value="ginteractions">ginteractions</option>\n+\n+            </param>\n+            <when value="cool">\n+                <param name=\'storeAppliedCorrection\' type="boolean" truevalue="yes" falsevalue=""   label=\'Store applied correction factors in column count\'/>\n+                <param name=\'enforceInteger\' type="boolean" truevalue="yes" falsevalue=""  label=\'Enforce integer for count column\'/>\n+            </when>\n+            <when value=\'h5\'/>\n+            <when value=\'homer\'/>\n+            <when value=\'ginteractions\'/>\n+\n+        </conditional>\n+    </xml>\n     <token name="@REFERENCES@">\n \n .. class:: infomark\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/Li_et_al_2015.cool
b
Binary file test-data/Li_et_al_2015.cool has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/FL-E13-5_chr1.cool
b
Binary file test-data/cHi-C/FL-E13-5_chr1.cool has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/MB-E10-5_chr1.cool
b
Binary file test-data/cHi-C/MB-E10-5_chr1.cool has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/background.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/background.bed Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,1002 @@\n+Relative position\tsize nbinom\tprob nbinom\tmax value\tmean value\n+-500000\t58.254577634279\t0.998604709282\t1.333333333333\t0.000105073709\n+-499000\t10.000013353187\t0.991925224088\t1.500000000000\t0.000105073709\n+-498000\t72.266262784304\t0.998828265884\t1.200000000000\t0.000111077921\n+-497000\t51.093422441771\t0.998183086351\t1.000000000000\t0.000120084239\n+-496000\t86.575220693033\t0.998899865570\t0.800000000000\t0.000123086345\n+-495000\t72.441590407550\t0.998655447638\t0.800000000000\t0.000126088451\n+-494000\t75.085350270547\t0.998668414055\t1.000000000000\t0.000129090557\n+-493000\t71.967411178924\t0.998612779641\t1.000000000000\t0.000129090557\n+-492000\t77.026231982211\t0.998763649786\t1.200000000000\t0.000123086345\n+-491000\t96.154018360868\t0.999129584825\t1.000000000000\t0.000108075815\n+-490000\t70.641792331241\t0.998918479365\t1.400000000000\t0.000099069497\n+-489000\t72.297114570842\t0.998971709245\t0.800000000000\t0.000096067391\n+-488000\t55.276417890737\t0.998907322028\t0.800000000000\t0.000078054755\n+-487000\t75.866231077639\t0.999020037562\t0.600000000000\t0.000096067391\n+-486000\t77.908114872120\t0.999075493568\t0.600000000000\t0.000093065285\n+-485000\t70.196050128375\t0.998940963837\t0.600000000000\t0.000096067391\n+-484000\t48.306835304302\t0.998789125810\t0.600000000000\t0.000078054755\n+-483000\t65.826727385050\t0.999115985283\t0.600000000000\t0.000075052649\n+-482000\t10.000003651221\t0.996523342626\t0.400000000000\t0.000045031590\n+-481000\t48.188933357556\t0.999179280048\t0.400000000000\t0.000051035802\n+-480000\t10.000001173914\t0.997216871755\t0.400000000000\t0.000036025272\n+-479000\t10.000002160096\t0.996985563716\t0.400000000000\t0.000039027378\n+-478000\t61.980720096540\t0.999287603012\t0.800000000000\t0.000057040014\n+-477000\t47.193502172887\t0.999138448161\t0.600000000000\t0.000054037908\n+-476000\t75.435666576826\t0.999477638616\t0.600000000000\t0.000051035802\n+-475000\t83.258498044933\t0.999385868055\t0.600000000000\t0.000066046332\n+-474000\t64.452927063111\t0.999206823435\t0.600000000000\t0.000066046332\n+-473000\t68.592799621533\t0.999390093904\t0.600000000000\t0.000054037908\n+-472000\t48.567204011739\t0.999139405277\t0.600000000000\t0.000054037908\n+-471000\t10.000004448331\t0.996292395667\t0.600000000000\t0.000048033696\n+-470000\t10.000000920405\t0.995831238986\t1.400000000000\t0.000054037908\n+-469000\t10.000003872489\t0.994909340544\t1.400000000000\t0.000066046332\n+-468000\t63.250123985231\t0.999022818205\t1.400000000000\t0.000081056861\n+-467000\t51.399551404579\t0.998558644000\t1.400000000000\t0.000096067391\n+-466000\t64.883458129266\t0.998762977849\t1.000000000000\t0.000105073709\n+-465000\t86.383451689662\t0.999139519880\t0.800000000000\t0.000096067391\n+-464000\t64.657320565128\t0.998830168725\t1.000000000000\t0.000099069497\n+-463000\t69.011442263596\t0.998889631783\t1.000000000000\t0.000099069497\n+-462000\t120.365580780362\t0.999304923056\t1.000000000000\t0.000108075815\n+-461000\t83.873478804403\t0.999085832019\t1.000000000000\t0.000099069497\n+-460000\t76.791436688795\t0.998822607239\t0.800000000000\t0.000117082133\n+-459000\t71.300309154477\t0.998707418591\t1.000000000000\t0.000120084239\n+-458000\t70.551044686671\t0.998794143443\t0.600000000000\t0.000111077921\n+-457000\t88.657625851365\t0.999084917164\t0.800000000000\t0.000105073709\n+-456000\t66.985331452249\t0.998825498193\t0.800000000000\t0.000102071603\n+-455000\t212.376735013798\t0.999710065148\t0.600000000000\t0.000078054755\n+-454000\t62.703317289439\t0.999261443476\t0.600000000000\t0.000060042120\n+-453000\t45.696967611307\t0.998932417121\t0.600000000000\t0.000063044226\n+-452000\t82.313181248075\t0.999548168551\t0.600000000000\t0.000048033696\n+-451000\t61.955802866608\t0.999249835457\t0.600000000000\t0.000060042120\n+-450000\t71.163546816639\t0.999118429295\t1.000000000000\t0.000081056861\n+-449000\t57.404577886000\t0.998868956077\t1.000000000000\t0.000084058967\n+-448000\t78.889496868591\t0.999175114488\t1.000000000000\t0.000084058967\n+-447000\t59.455705064746\t0.998872066360\t1.000000000000\t0.000087061073\n+-446000\t69.521205032032\t0.998763823049\t1.000000000000\t0.000111077921\n+-445000\t99.901425243691\t0.999325366218\t0.800000000000\t0.0000870'..b'92515295592\t0.998432747334\t1.400000000000\t0.000222155842\n+444000\t82.443622273366\t0.997719903159\t1.400000000000\t0.000243170584\n+445000\t70.933399279725\t0.997396373546\t1.400000000000\t0.000243170584\n+446000\t95.161892262226\t0.998095770809\t1.600000000000\t0.000234164266\n+447000\t124.614672839908\t0.998565069417\t1.200000000000\t0.000231162160\n+448000\t77.860490008359\t0.997704488044\t1.400000000000\t0.000231162160\n+449000\t65.217115835699\t0.997403641809\t1.400000000000\t0.000219153736\n+450000\t75.445932132698\t0.998007293338\t1.200000000000\t0.000198138995\n+451000\t95.181162634818\t0.998473187366\t1.000000000000\t0.000186130571\n+452000\t94.977236808895\t0.998461455130\t1.000000000000\t0.000189132677\n+453000\t71.519354123232\t0.997988008873\t1.000000000000\t0.000186130571\n+454000\t75.038048093362\t0.998148510684\t1.000000000000\t0.000183128465\n+455000\t66.094167095466\t0.997699897371\t1.000000000000\t0.000198138995\n+456000\t111.325708146664\t0.998498182775\t1.000000000000\t0.000216151630\n+457000\t102.171886886530\t0.998454607629\t1.000000000000\t0.000204143206\n+458000\t88.125308869888\t0.998313915544\t1.000000000000\t0.000192134783\n+459000\t70.605027521073\t0.997930191387\t0.800000000000\t0.000189132677\n+460000\t100.268739339170\t0.998772290781\t0.600000000000\t0.000159111617\n+461000\t74.543018827171\t0.998473634038\t0.800000000000\t0.000147103193\n+462000\t63.337319446090\t0.998204073767\t0.800000000000\t0.000147103193\n+463000\t117.089896011864\t0.999027727546\t0.800000000000\t0.000147103193\n+464000\t91.138003901288\t0.998496746777\t1.800000000000\t0.000177124253\n+465000\t92.914491189803\t0.998350787907\t1.800000000000\t0.000198138995\n+466000\t52.209334348546\t0.997159438011\t2.400000000000\t0.000192134783\n+467000\t77.918569531358\t0.998034146232\t2.800000000000\t0.000198138995\n+468000\t40.028010375624\t0.996410794913\t2.800000000000\t0.000186130571\n+469000\t52.807401795042\t0.997408431862\t1.400000000000\t0.000177124253\n+470000\t105.325058737937\t0.998676526339\t1.400000000000\t0.000180126359\n+471000\t97.395447231439\t0.998474152554\t1.000000000000\t0.000192134783\n+472000\t71.036732364957\t0.998055374489\t1.200000000000\t0.000183128465\n+473000\t58.839853998831\t0.997768804625\t1.200000000000\t0.000174122147\n+474000\t109.506948227434\t0.998942877974\t1.000000000000\t0.000150105299\n+475000\t73.687080792836\t0.998676219719\t0.600000000000\t0.000126088451\n+476000\t86.562200266338\t0.998926533547\t0.600000000000\t0.000120084239\n+477000\t78.601283549403\t0.998670347780\t0.600000000000\t0.000135094769\n+478000\t77.287682759273\t0.998311780993\t1.000000000000\t0.000168117935\n+479000\t80.196363250368\t0.998336155363\t0.800000000000\t0.000174122147\n+480000\t95.618679354949\t0.998538823715\t0.800000000000\t0.000180126359\n+481000\t71.324679124414\t0.998079961192\t1.000000000000\t0.000177124253\n+482000\t98.947326582471\t0.998662082026\t1.200000000000\t0.000171120041\n+483000\t98.312778915279\t0.998677055532\t1.000000000000\t0.000168117935\n+484000\t80.536358888257\t0.998500685590\t1.200000000000\t0.000156109511\n+485000\t75.299149742118\t0.998174557637\t1.200000000000\t0.000177124253\n+486000\t80.676043504302\t0.998160484267\t1.600000000000\t0.000192134783\n+487000\t65.456290718619\t0.997731312445\t1.600000000000\t0.000192134783\n+488000\t135.605664962437\t0.998837097471\t1.400000000000\t0.000204143206\n+489000\t78.041126983216\t0.997890938542\t1.600000000000\t0.000213149524\n+490000\t73.842941938827\t0.998020155259\t1.200000000000\t0.000192134783\n+491000\t135.330452041151\t0.998884251454\t1.000000000000\t0.000195136889\n+492000\t70.441325198247\t0.997891524929\t1.000000000000\t0.000192134783\n+493000\t93.145208276513\t0.998579085962\t1.200000000000\t0.000171120041\n+494000\t93.195291870240\t0.998579645775\t1.200000000000\t0.000171120041\n+495000\t66.167995861224\t0.997615723218\t1.200000000000\t0.000204143206\n+496000\t68.869469387443\t0.998039511367\t1.200000000000\t0.000174122147\n+497000\t61.393255588548\t0.997958646123\t1.400000000000\t0.000162113723\n+498000\t64.393702971434\t0.998089554455\t1.200000000000\t0.000159111617\n+499000\t64.222140571019\t0.998102497389\t1.000000000000\t0.000157610564\n+500000\t10.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 14274000 14279000 Eya1 673.0 -22000    7.00000
+chr1 14285000 14308000 Eya1 673.0 7000  389.40000
+chr1 14310000 14322000 Eya1 673.0 21000   54.80000
+chr1 14361000 14407000 Eya1 673.0 106000   21.20000
+chr1 14426000 14432000 Eya1 673.0 131000    2.40000
+chr1 14447000 14455000 Eya1 673.0 154000    4.40000
+chr1 14460000 14465000 Eya1 673.0 164000    3.20000
+chr1 14491000 14500000 Eya1 673.0 199000   17.65000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 19077000 19114000 Tfap2d 472.0 20000  344.80000
+chr1 19125000 19129000 Tfap2d 472.0 35000    7.80000
+chr1 19134000 19139000 Tfap2d 472.0 45000    8.40000
+chr1 19141000 19238000 Tfap2d 472.0 144000   47.40000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,9 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 4472000 4503000 Sox17 810.0 15000  566.20000
+chr1 4507000 4516000 Sox17 810.0 28000   38.80000
+chr1 4520000 4531000 Sox17 810.0 43000   10.40000
+chr1 4533000 4543000 Sox17 810.0 55000    6.80000
+chr1 4562000 4593000 Sox17 810.0 105000   25.00000
+chr1 4664000 4669000 Sox17 810.0 181000    1.20000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 14274000 14279000 Eya1 832.0 -22000    0.00000
+chr1 14285000 14308000 Eya1 832.0 7000  479.80000
+chr1 14310000 14322000 Eya1 832.0 21000   52.80000
+chr1 14361000 14407000 Eya1 832.0 106000   36.00000
+chr1 14426000 14432000 Eya1 832.0 131000    9.00000
+chr1 14447000 14455000 Eya1 832.0 154000   12.40000
+chr1 14460000 14465000 Eya1 832.0 164000    7.60000
+chr1 14491000 14500000 Eya1 832.0 199000   15.75000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 19077000 19114000 Tfap2d 800.0 20000  527.80000
+chr1 19125000 19129000 Tfap2d 800.0 35000    8.80000
+chr1 19134000 19139000 Tfap2d 800.0 45000   11.20000
+chr1 19141000 19238000 Tfap2d 800.0 144000  163.00000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,9 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 4472000 4503000 Sox17 978.0 15000  724.40000
+chr1 4507000 4516000 Sox17 978.0 28000   19.00000
+chr1 4520000 4531000 Sox17 978.0 43000   22.20000
+chr1 4533000 4543000 Sox17 978.0 55000   12.20000
+chr1 4562000 4593000 Sox17 978.0 105000   23.20000
+chr1 4664000 4669000 Sox17 978.0 181000    5.40000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 14274000 14279000 Eya1 673.0 -22000    7.00000
+chr1 14285000 14308000 Eya1 673.0 7000  389.40000
+chr1 14310000 14322000 Eya1 673.0 21000   54.80000
+chr1 14361000 14407000 Eya1 673.0 106000   21.20000
+chr1 14426000 14432000 Eya1 673.0 131000    2.40000
+chr1 14447000 14455000 Eya1 673.0 154000    4.40000
+chr1 14460000 14465000 Eya1 673.0 164000    3.20000
+chr1 14491000 14500000 Eya1 673.0 199000   17.65000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# 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 distance Raw target
+chr1 14274000 14279000 Eya1 832.0 -22000    0.00000
+chr1 14285000 14308000 Eya1 832.0 7000  479.80000
+chr1 14310000 14322000 Eya1 832.0 21000   52.80000
+chr1 14361000 14407000 Eya1 832.0 106000   36.00000
+chr1 14426000 14432000 Eya1 832.0 131000    9.00000
+chr1 14447000 14455000 Eya1 832.0 154000   12.40000
+chr1 14460000 14465000 Eya1 832.0 164000    7.60000
+chr1 14491000 14500000 Eya1 832.0 199000   15.75000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,17 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.43072
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00105
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.12754
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.40725
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.36639
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.16231
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.43072
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00105
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.12754
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.40725
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.36639
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.16231
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+# 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 Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png
b
Binary file test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png
b
Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png
b
Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png
b
Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicQualityControl/histogram.png
b
Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicQualityControl/new_referencepoints.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,35 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+chr1 24202042 24202042 Col9a1
+chr1 33776741 33776741 Rab23
+chr1 38684089 38684089 Aff3
+chr1 42753991 42753991 Pou3f3
+chr1 52176282 52176282 Stat1
+chr1 53118507 53118507 Mstn
+chr1 57028178 57028178 Satb2
+chr1 59821123 59821123 Bmpr2
+chr1 66991630 66991630 Myl1
+chr1 74648029 74648029 Stk36
+chr1 74818466 74818466 Wnt6
+chr1 75356867 75356867 Des
+chr1 77511663 77511663 Epha4
+chr1 78193711 78193711 Pax3
+chr1 89102386 89102386 Chrng
+chr1 93355905 93355905 Per2
+chr1 93698054 93698054 Twist2
+chr1 107677300 107677300 Tnfrsf11a
+chr1 120950196 120950196 Gli2
+chr1 122499064 122499064 En1
+chr1 127808791 127808791 Lypd1
+chr1 135934092 135934092 Fmod
+chr1 136186581 136186581 MyoG
+chr1 164004278 164006270 mm712
+chr1 164147754 164147754 Dnm3os
+chr1 165243781 165243781 Prrx1
+chr1 165333772 165333772 Gorab
+chr1 169619689 169619689 Lmx1a
+chr1 182823250 182823250 Lefty2
+chr1 182865170 182865170 Lefty1
+chr1 188529871 188529871 Tgfb2
+chr1 194979306 194979306 Irf6
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,45 @@
+# Created with chicQualityControl version 3.3
+# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
+chr1 4487435 4487435 Sox17 0.14485514485514486 0.16083916083916083
+chr1 14300280 14300280 Eya1 0.14285714285714285 0.1938061938061938
+chr1 19093103 19093103 Tfap2d 0.1048951048951049 0.16683316683316685
+chr1 19198995 19198995 Tfap2b 0.01898101898101898 0.016983016983016984
+chr1 24202042 24202042 Col9a1 0.10589410589410589 0.12787212787212787
+chr1 33776741 33776741 Rab23 0.15484515484515485 0.2137862137862138
+chr1 38684089 38684089 Aff3 0.11588411588411589 0.11388611388611389
+chr1 42753991 42753991 Pou3f3 0.04995004995004995 0.07592407592407592
+chr1 52176282 52176282 Stat1 0.19080919080919082 0.22777222777222778
+chr1 52557292 52557292 Nab1 0.02197802197802198 0.024975024975024976
+chr1 53118507 53118507 Mstn 0.3116883116883117 0.37462537462537465
+chr1 57028178 57028178 Satb2 0.12287712287712288 0.14385614385614387
+chr1 59821123 59821123 Bmpr2 0.14085914085914086 0.16983016983016982
+chr1 66991630 66991630 Myl1 0.0919080919080919 0.09290709290709291
+chr1 74648029 74648029 Stk36 0.2777222777222777 0.3356643356643357
+chr1 74818466 74818466 Wnt6 0.29270729270729273 0.34165834165834164
+chr1 74838593 74838593 Wnt10a 0.00999000999000999 0.008991008991008992
+chr1 74998246 74998246 Ihh 0.008991008991008992 0.003996003996003996
+chr1 75356867 75356867 Des 0.18081918081918083 0.21678321678321677
+chr1 77511663 77511663 Epha4 0.15684315684315683 0.22277722277722278
+chr1 78193711 78193711 Pax3 0.24375624375624375 0.3096903096903097
+chr1 89102386 89102386 Chrng 0.16783216783216784 0.2217782217782218
+chr1 93355905 93355905 Per2 0.15384615384615385 0.16483516483516483
+chr1 93698054 93698054 Twist2 0.22277722277722278 0.23476523476523475
+chr1 94076918 94076918 Hdac4 0.0 0.0
+chr1 107677300 107677300 Tnfrsf11a 0.14685314685314685 0.16383616383616384
+chr1 120950196 120950196 Gli2 0.13986013986013987 0.2007992007992008
+chr1 122499064 122499064 En1 0.1008991008991009 0.11988011988011989
+chr1 127808791 127808791 Lypd1 0.18681318681318682 0.22977022977022976
+chr1 135934092 135934092 Fmod 0.3516483516483517 0.4145854145854146
+chr1 136186581 136186581 MyoG 0.07392607392607392 0.09090909090909091
+chr1 152313295 152313295 Prg4 0.00999000999000999 0.006993006993006993
+chr1 164004278 164006270 mm712 0.26173826173826176 0.2867132867132867
+chr1 164147754 164147754 Dnm3os 0.24875124875124874 0.24675324675324675
+chr1 165243781 165243781 Prrx1 0.36063936063936064 0.34065934065934067
+chr1 165333772 165333772 Gorab 0.36863136863136864 0.3956043956043956
+chr1 169619689 169619689 Lmx1a 0.11888111888111888 0.16783216783216784
+chr1 170362300 170362300 Pbx1 0.003996003996003996 0.002997002997002997
+chr1 180249284 180249284 Gm16586 0.0 0.0
+chr1 182823250 182823250 Lefty2 0.27472527472527475 0.33266733266733267
+chr1 182865170 182865170 Lefty1 0.25674325674325676 0.3086913086913087
+chr1 188529871 188529871 Tgfb2 0.13486513486513488 0.16583416583416583
+chr1 194979306 194979306 Irf6 0.12987012987012986 0.15284715284715283
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,8 @@
+chr1 19198995 19198995 Tfap2b
+chr1 52557292 52557292 Nab1
+chr1 74838593 74838593 Wnt10a
+chr1 74998246 74998246 Ihh
+chr1 94076918 94076918 Hdac4
+chr1 152313295 152313295 Prg4
+chr1 170362300 170362300 Pbx1
+chr1 180249284 180249284 Gm16586
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicQualityControl/sparsity.png
b
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655
+chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000
+chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605
+chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109
+chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783
+chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109
+chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 14274000 14279000
+chr1 14285000 14308000
+chr1 14310000 14322000
+chr1 14361000 14395000
+chr1 14491000 14500000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655
+chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,7 @@
+# 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 14295000 14298000 Eya1 832.0 -3000 0.05985576923100000002 0.06113759528369666629 4.79015312599299925012 49.79999999999999715783
+chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000
+chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891
+chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473
+chr1 14491000 14501000 Eya1 832.0 200000 0.02253605769199999720 0.00000000000003064216 41.39757163433100117800 18.75000000000000000000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14295000 14298000
+chr1 14426000 14432000
+chr1 14447000 14455000
+chr1 14460000 14465000
+chr1 14491000 14501000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655
+chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 19089000 19091000 Tfap2d 472.0 -3000 0.06101694915199999680 0.18835888966198111039 4.06818820852600016025 28.80000000000000071054
+chr1 19104000 19106000 Tfap2d 472.0 11000 0.02245762711799999950 0.11671915718551462149 3.62722049649999966903 10.59999999999999964473
+chr1 19109000 19114000 Tfap2d 472.0 18000 0.03940677966200000631 0.00080680261510490681 9.61739201792699915927 18.60000000000000142109
+chr1 19125000 19129000 Tfap2d 472.0 33000 0.01652542372999999884 0.00829653069244939978 7.28507499155399962376 7.79999999999999982236
+chr1 19133000 19138000 Tfap2d 472.0 41000 0.01949152542399999744 0.00041957482022692005 9.72184228688099949522 9.19999999999999928946
+chr1 19197000 19202000 Tfap2d 472.0 108000 0.01059322033899999863 0.00398884532051024809 10.24326734149200035517 5.00000000000000000000
+chr1 19227000 19233000 Tfap2d 472.0 137000 0.01186440677899999914 0.00244241040005155341 14.41899403645599875290 5.59999999999999964473
+chr1 19254000 19261000 Tfap2d 472.0 163000 0.01355932203300000069 0.00004326025137579848 19.68794216164500454624 6.39999999999999946709
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,8 @@
+# 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 target
+chr1 4509000 4515000 Sox17 810.0 23000 0.03432098765399999724 0.00000160319175224188 11.55191083898800030738 27.80000000000000071054
+chr1 4561000 4567000 Sox17 810.0 75000 0.01432098765400000029 0.00000102319718320310 11.23656007944399881637 11.59999999999999964473
+chr1 4585000 4590000 Sox17 810.0 98000 0.00987654320999999807 0.00037019878415911478 8.98479195802099894763 8.00000000000000000000
+chr1 4652000 4658000 Sox17 810.0 169000 0.00740740740700000008 0.00005538687174366785 11.12107213938599947767 6.00000000000000000000
+chr1 4499000 4500000 Sox17 810.0 12000 0.00987654320999999981 0.15859163588059266292 1.65903762227799989049 8.00000000000000000000
+chr1 4501000 4502000 Sox17 810.0 14000 0.00765432098799999957 0.17926099806325068720 1.57677828943600006895 6.20000000000000017764
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,13 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 19089000 19091000
+chr1 19104000 19106000
+chr1 19109000 19114000
+chr1 19125000 19129000
+chr1 19133000 19138000
+chr1 19197000 19202000
+chr1 19227000 19233000
+chr1 19254000 19261000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 4499000 4502000
+chr1 4509000 4515000
+chr1 4561000 4567000
+chr1 4585000 4590000
+chr1 4652000 4658000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +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 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000
+chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605
+chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109
+chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783
+chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109
+chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,8 @@
+# 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 19097000 19099000 Tfap2d 472.0 4000 0.04322033898299999788 0.18510915606880684603 3.09466471690400002359 20.39999999999999857891
+chr1 19103000 19106000 Tfap2d 472.0 11000 0.03305084745700000159 0.03717817323565530963 5.08894228542100002244 15.60000000000000142109
+chr1 19110000 19114000 Tfap2d 472.0 18000 0.03135593220400000047 0.00456343459440844423 7.84960476513000049437 14.79999999999999893419
+chr1 19126000 19129000 Tfap2d 472.0 33000 0.01271186440799999991 0.01781395819889997068 5.68520760692500015665 6.00000000000000000000
+chr1 19134000 19137000 Tfap2d 472.0 41000 0.01271186440799999991 0.00778984492262324579 6.25346808942800080899 6.00000000000000000000
+chr1 19162000 19198000 Tfap2d 472.0 69000 0.02966101695299999674 0.00000060908645727054 24.93693789855100106934 14.00000000000000532907
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,8 @@
+# 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 target
+chr1 4483000 4496000 Sox17 810.0 0 0.64098765432000004427 0.00000017949046104970 15.90973968251499925941 519.20000000000004547474
+chr1 4497000 4503000 Sox17 810.0 12000 0.04592592592699999698 0.00009501601454375841 8.17222136878799965132 37.19999999999999573674
+chr1 4507000 4516000 Sox17 810.0 23000 0.04790123456699999643 0.00000000479943529363 15.54534421085400097695 38.80000000000000426326
+chr1 4533000 4543000 Sox17 810.0 46000 0.00839506173000000022 0.00536916279076038450 5.36115769549400056349 6.79999999999999893419
+chr1 4562000 4565000 Sox17 810.0 75000 0.00814814814800000030 0.00087160464483748701 6.21039574622800039094 6.59999999999999964473
+chr1 4567000 4585000 Sox17 810.0 81000 0.00814814814699999987 0.00084968562666110081 6.38963961746400066488 6.60000000000000053291
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# 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 14295000 14303000 Eya1 832.0 -1000 0.51754807692400006669 0.00019954744684358428 10.99424166368200062038 430.60000000000002273737
+chr1 14304000 14307000 Eya1 832.0 4000 0.03052884615399999862 0.12043367620410594387 2.40926082355099957510 25.39999999999999857891
+chr1 14311000 14322000 Eya1 832.0 11000 0.05841346153899999727 0.00001294028787446333 12.63215080382700250539 48.59999999999999431566
+chr1 14369000 14382000 Eya1 832.0 69000 0.00793269231000000123 0.00220510219722336309 6.44339861264899926852 6.59999999999999875655
+chr1 14391000 14407000 Eya1 832.0 106000 0.01201923077000000006 0.00000515283260571486 11.00547257592000072179 10.00000000000000000000
+chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000
+chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891
+chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473
+chr1 14491000 14500000 Eya1 832.0 199000 0.01893028846099999857 0.00000000000000932587 35.26961282318300305860 15.75000000000000000000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# 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 19082000 Tfap2d 800.0 -15000 0.01675000000000000100 0.00195382844240210574 8.20856302019300088091 13.40000000000000035527
+chr1 19083000 19095000 Tfap2d 800.0 0 0.41274999999999995026 0.00011621308769860228 18.49630381537900092326 330.19999999999998863132
+chr1 19096000 19114000 Tfap2d 800.0 3000 0.17700000000000001843 0.00042447176642534945 22.86014655871399980924 141.59999999999999431566
+chr1 19125000 19129000 Tfap2d 800.0 33000 0.01099999999999999936 0.00379145119303403444 4.83882643603000062171 8.80000000000000071054
+chr1 19135000 19139000 Tfap2d 800.0 43000 0.01175000000000000003 0.00015657417058367873 6.23967021246500053167 9.40000000000000035527
+chr1 19141000 19170000 Tfap2d 800.0 49000 0.02125000000000001193 0.00000543603606051324 15.65207577841900032922 17.00000000000000355271
+chr1 19195000 19208000 Tfap2d 800.0 105000 0.04900000000000001577 0.00000000000000000000 47.90516101420298866742 39.20000000000000284217
+chr1 19209000 19238000 Tfap2d 800.0 124000 0.09275000000000004075 0.00000000000000000000 112.06129567939001390187 74.20000000000000284217
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,9 @@
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 4472000 4492000 Sox17 978.0 0 0.66196319018500004994 0.00000000202165995056 17.41734930604599895787 647.40000000000009094947
+chr1 4493000 4496000 Sox17 978.0 6000 0.02576687116499999652 0.03614683764250059550 2.69049295166299984317 25.20000000000000284217
+chr1 4497000 4503000 Sox17 978.0 12000 0.03946830265799999848 0.00007297810251505332 7.02344214143100042946 38.60000000000000142109
+chr1 4520000 4531000 Sox17 978.0 37000 0.02269938650399999994 0.00000000003034350549 10.91808266157200080215 22.20000000000000284217
+chr1 4562000 4566000 Sox17 978.0 78000 0.00920245398800000058 0.00000732123325153378 7.15040494335099996448 9.00000000000000000000
+chr1 4569000 4593000 Sox17 978.0 93000 0.01022494887899999885 0.00001986913191398543 8.54218878677400006438 9.99999999999999822364
+chr1 4664000 4669000 Sox17 978.0 179000 0.00552147239400000052 0.00001416173948909361 8.93206575494200016863 5.40000000000000035527
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,13 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 14274000 14279000
+chr1 14285000 14308000
+chr1 14310000 14322000
+chr1 14361000 14407000
+chr1 14426000 14432000
+chr1 14447000 14455000
+chr1 14460000 14465000
+chr1 14491000 14500000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,9 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 19077000 19114000
+chr1 19125000 19129000
+chr1 19134000 19139000
+chr1 19141000 19238000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,11 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 4472000 4503000
+chr1 4507000 4516000
+chr1 4520000 4531000
+chr1 4533000 4543000
+chr1 4562000 4593000
+chr1 4664000 4669000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10  Mbp\t14.50  Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89  Mbp\t19.29  Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29  Mbp\t4.69  Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10  Mbp\t14.50  Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89  Mbp\t19.29  Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29  Mbp\t4.69  Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10  Mbp\t14.50  Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89  Mbp\t19.29  Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29  Mbp\t4.69  Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10  Mbp\t14.50  Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89  Mbp\t19.29  Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:27:02 2019 -0500
b
b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29  Mbp\t4.69  Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/referencePoints.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/referencePoints.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,43 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+chr1 19198995 19198995 Tfap2b
+chr1 24202042 24202042 Col9a1
+chr1 33776741 33776741 Rab23
+chr1 38684089 38684089 Aff3
+chr1 42753991 42753991 Pou3f3
+chr1 52176282 52176282 Stat1
+chr1 52557292 52557292 Nab1
+chr1 53118507 53118507 Mstn
+chr1 57028178 57028178 Satb2
+chr1 59821123 59821123 Bmpr2
+chr1 66991630 66991630 Myl1
+chr1 74648029 74648029 Stk36
+chr1 74818466 74818466 Wnt6
+chr1 74838593 74838593 Wnt10a
+chr1 74998246 74998246 Ihh
+chr1 75356867 75356867 Des
+chr1 77511663 77511663 Epha4
+chr1 78193711 78193711 Pax3
+chr1 89102386 89102386 Chrng
+chr1 93355905 93355905 Per2
+chr1 93698054 93698054 Twist2
+chr1 94076918 94076918 Hdac4
+chr1 107677300 107677300 Tnfrsf11a
+chr1 120950196 120950196 Gli2
+chr1 122499064 122499064 En1
+chr1 127808791 127808791 Lypd1
+chr1 135934092 135934092 Fmod
+chr1 136186581 136186581 MyoG
+chr1 152313295 152313295 Prg4
+chr1 164004278 164006270 mm712
+chr1 164147754 164147754 Dnm3os
+chr1 165243781 165243781 Prrx1
+chr1 165333772 165333772 Gorab
+chr1 169619689 169619689 Lmx1a
+chr1 170362300 170362300 Pbx1
+chr1 180249284 180249284 Gm16586
+chr1 182823250 182823250 Lefty2
+chr1 182865170 182865170 Lefty1
+chr1 188529871 188529871 Tgfb2
+chr1 194979306 194979306 Irf6
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/cHi-C/referencePoints_chicViewpoint.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,4 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/distVsCounts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/distVsCounts.txt Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,600 @@\n+\tMatrix\tChromosome\tDistance\tContacts\n+0\tsmall_test_matrix_h5\tall\t0\t0.09142620133910055\n+1\tsmall_test_matrix_h5\tall\t5000\t0.07741782506891134\n+2\tsmall_test_matrix_h5\tall\t10000\t0.04433044715929309\n+3\tsmall_test_matrix_h5\tall\t15000\t0.03461983446557299\n+4\tsmall_test_matrix_h5\tall\t20000\t0.027541995607526563\n+5\tsmall_test_matrix_h5\tall\t25000\t0.023782660332541568\n+6\tsmall_test_matrix_h5\tall\t30000\t0.02002019841977069\n+7\tsmall_test_matrix_h5\tall\t35000\t0.01967193628907643\n+8\tsmall_test_matrix_h5\tall\t40000\t0.017480230691479873\n+9\tsmall_test_matrix_h5\tall\t45000\t0.015494884606233642\n+10\tsmall_test_matrix_h5\tall\t50000\t0.014013686402856293\n+11\tsmall_test_matrix_h5\tall\t55000\t0.012799142755089891\n+12\tsmall_test_matrix_h5\tall\t60000\t0.011404919302007028\n+13\tsmall_test_matrix_h5\tall\t65000\t0.011588417540514775\n+14\tsmall_test_matrix_h5\tall\t70000\t0.01084818501519938\n+15\tsmall_test_matrix_h5\tall\t75000\t0.010554561717352416\n+16\tsmall_test_matrix_h5\tall\t80000\t0.008769313368728748\n+17\tsmall_test_matrix_h5\tall\t85000\t0.00907137741704464\n+18\tsmall_test_matrix_h5\tall\t90000\t0.008328855454056958\n+19\tsmall_test_matrix_h5\tall\t95000\t0.009049098076693346\n+20\tsmall_test_matrix_h5\tall\t100000\t0.007140723035554228\n+21\tsmall_test_matrix_h5\tall\t105000\t0.006874701099952176\n+22\tsmall_test_matrix_h5\tall\t110000\t0.006488846360863585\n+23\tsmall_test_matrix_h5\tall\t115000\t0.005354792389613497\n+24\tsmall_test_matrix_h5\tall\t120000\t0.006584066558927396\n+25\tsmall_test_matrix_h5\tall\t125000\t0.005598802395209581\n+26\tsmall_test_matrix_h5\tall\t130000\t0.005990534954771461\n+27\tsmall_test_matrix_h5\tall\t135000\t0.005393743257820928\n+28\tsmall_test_matrix_h5\tall\t140000\t0.0048564062593680676\n+29\tsmall_test_matrix_h5\tall\t145000\t0.005338291746641075\n+30\tsmall_test_matrix_h5\tall\t150000\t0.0047404740474047405\n+31\tsmall_test_matrix_h5\tall\t155000\t0.004892544122943931\n+32\tsmall_test_matrix_h5\tall\t160000\t0.004864572698336437\n+33\tsmall_test_matrix_h5\tall\t165000\t0.004025474645517904\n+34\tsmall_test_matrix_h5\tall\t170000\t0.004538077778445633\n+35\tsmall_test_matrix_h5\tall\t175000\t0.0036380036079374624\n+36\tsmall_test_matrix_h5\tall\t180000\t0.003970402454430608\n+37\tsmall_test_matrix_h5\tall\t185000\t0.0030994222436206064\n+38\tsmall_test_matrix_h5\tall\t190000\t0.0034318742850261907\n+39\tsmall_test_matrix_h5\tall\t195000\t0.0034333212865919767\n+40\tsmall_test_matrix_h5\tall\t200000\t0.0031334739379331126\n+41\tsmall_test_matrix_h5\tall\t205000\t0.0035869303110682422\n+42\tsmall_test_matrix_h5\tall\t210000\t0.0030154087386545245\n+43\tsmall_test_matrix_h5\tall\t215000\t0.002865761689291101\n+44\tsmall_test_matrix_h5\tall\t220000\t0.0026254639828590396\n+45\tsmall_test_matrix_h5\tall\t225000\t0.0027774423378818984\n+46\tsmall_test_matrix_h5\tall\t230000\t0.0027483313702394976\n+47\tsmall_test_matrix_h5\tall\t235000\t0.002265997945495196\n+48\tsmall_test_matrix_h5\tall\t240000\t0.0025691400936980503\n+49\tsmall_test_matrix_h5\tall\t245000\t0.001904934687953556\n+50\tsmall_test_matrix_h5\tall\t250000\t0.00266190749871442\n+51\tsmall_test_matrix_h5\tall\t255000\t0.002511650426677964\n+52\tsmall_test_matrix_h5\tall\t260000\t0.0026942754215481487\n+53\tsmall_test_matrix_h5\tall\t265000\t0.0026650514839491215\n+54\tsmall_test_matrix_h5\tall\t270000\t0.002120762262550368\n+55\tsmall_test_matrix_h5\tall\t275000\t0.002697460144268655\n+56\tsmall_test_matrix_h5\tall\t280000\t0.0020314726660804706\n+57\tsmall_test_matrix_h5\tall\t285000\t0.002062606163552536\n+58\tsmall_test_matrix_h5\tall\t290000\t0.0020937642239417385\n+59\tsmall_test_matrix_h5\tall\t295000\t0.001973164956590371\n+60\tsmall_test_matrix_h5\tall\t300000\t0.0017917337301466792\n+61\tsmall_test_matrix_h5\tall\t305000\t0.0018532020901689148\n+62\tsmall_test_matrix_h5\tall\t310000\t0.0016107953682035073\n+63\tsmall_test_matrix_h5\tall\t315000\t0.002158710854363028\n+64\tsmall_test_matrix_h5\tall\t320000\t0.001429570824588618\n+65\tsmall_test_matrix_h5\tall\t325000\t0.0014301363193768258\n+66\tsmall_test_matrix_h5\tall\t330000\t0.0016133451036498129\n+67\tsmall_test_matrix_h5\tall\t335000\t0.0017966989463426518\n+68\tsmall_test_matrix_h5\tall\t340000\t0.0013709063214013709\n+69\tsmall_test_matrix_h5\tall\t3'..b'15\n+533\tsmall_test_matrix_h5\tall\t2670000\t7.141326858530314e-05\n+534\tsmall_test_matrix_h5\tall\t2675000\t0.0001785841845846132\n+535\tsmall_test_matrix_h5\tall\t2680000\t0.0001786352268667381\n+536\tsmall_test_matrix_h5\tall\t2685000\t0.0002858980773354299\n+537\tsmall_test_matrix_h5\tall\t2690000\t0.00010724243940802173\n+538\tsmall_test_matrix_h5\tall\t2695000\t0.00021454623471358077\n+539\tsmall_test_matrix_h5\tall\t2700000\t0.00021460762572430073\n+540\tsmall_test_matrix_h5\tall\t2705000\t0.00017889087656529517\n+541\tsmall_test_matrix_h5\tall\t2710000\t0.00010736525660296328\n+542\tsmall_test_matrix_h5\tall\t2715000\t3.579866828953963e-05\n+543\tsmall_test_matrix_h5\tall\t2720000\t0.0001432356943350283\n+544\tsmall_test_matrix_h5\tall\t2725000\t3.581918475535497e-05\n+545\tsmall_test_matrix_h5\tall\t2730000\t0.00014331780723754928\n+546\tsmall_test_matrix_h5\tall\t2735000\t0.00021503834850548347\n+547\tsmall_test_matrix_h5\tall\t2740000\t7.170000717000071e-05\n+548\tsmall_test_matrix_h5\tall\t2745000\t0.0003586028831671807\n+549\tsmall_test_matrix_h5\tall\t2750000\t0.00014348231580457708\n+550\tsmall_test_matrix_h5\tall\t2755000\t0.00014352350197344816\n+551\tsmall_test_matrix_h5\tall\t2760000\t7.178235589692053e-05\n+552\tsmall_test_matrix_h5\tall\t2765000\t0.00014360594528613484\n+553\tsmall_test_matrix_h5\tall\t2770000\t0.00025138260432378077\n+554\tsmall_test_matrix_h5\tall\t2775000\t0.00014368848336805806\n+555\tsmall_test_matrix_h5\tall\t2780000\t0.00014372978799856272\n+556\tsmall_test_matrix_h5\tall\t2785000\t0.0001437711163827187\n+557\tsmall_test_matrix_h5\tall\t2790000\t0.00025167181994678936\n+558\tsmall_test_matrix_h5\tall\t2795000\t0.0001438538444939941\n+559\tsmall_test_matrix_h5\tall\t2800000\t0.00010792143319663285\n+560\tsmall_test_matrix_h5\tall\t2805000\t0.00021590500179920834\n+561\tsmall_test_matrix_h5\tall\t2810000\t0.00017997264415808796\n+562\tsmall_test_matrix_h5\tall\t2815000\t3.600489666594657e-05\n+563\tsmall_test_matrix_h5\tall\t2820000\t0.0002160916228480876\n+564\tsmall_test_matrix_h5\tall\t2825000\t0.000144102601051949\n+565\tsmall_test_matrix_h5\tall\t2830000\t0.00014414414414414415\n+566\tsmall_test_matrix_h5\tall\t2835000\t0.0002523249945930358\n+567\tsmall_test_matrix_h5\tall\t2840000\t0.00018028412778538978\n+568\tsmall_test_matrix_h5\tall\t2845000\t0.00010820168794633196\n+569\tsmall_test_matrix_h5\tall\t2850000\t0.00018038819539649325\n+570\tsmall_test_matrix_h5\tall\t2855000\t7.217610970768675e-05\n+571\tsmall_test_matrix_h5\tall\t2860000\t0.0003248862897985705\n+572\tsmall_test_matrix_h5\tall\t2865000\t0.00018054452227919405\n+573\tsmall_test_matrix_h5\tall\t2870000\t0.0002889547063497797\n+574\tsmall_test_matrix_h5\tall\t2875000\t0.00036129778163162076\n+575\tsmall_test_matrix_h5\tall\t2880000\t0.00014456089627755693\n+576\tsmall_test_matrix_h5\tall\t2890000\t0.00021696680407897592\n+577\tsmall_test_matrix_h5\tall\t2895000\t0.0001808579903060117\n+578\tsmall_test_matrix_h5\tall\t2900000\t7.236413633403285e-05\n+579\tsmall_test_matrix_h5\tall\t2905000\t0.0002533478103510677\n+580\tsmall_test_matrix_h5\tall\t2910000\t0.00010860907971906451\n+581\tsmall_test_matrix_h5\tall\t2915000\t0.00010864054465126386\n+582\tsmall_test_matrix_h5\tall\t2920000\t0.00021734405564007825\n+583\tsmall_test_matrix_h5\tall\t2925000\t0.00010870352924124937\n+584\tsmall_test_matrix_h5\tall\t2930000\t0.0001812250815512867\n+585\tsmall_test_matrix_h5\tall\t2935000\t0.00010876658690450294\n+586\tsmall_test_matrix_h5\tall\t2940000\t0.00014506419090447523\n+587\tsmall_test_matrix_h5\tall\t2945000\t0.000290212580715374\n+588\tsmall_test_matrix_h5\tall\t2950000\t0.0001451484142535743\n+589\tsmall_test_matrix_h5\tall\t2955000\t0.00025408348457350274\n+590\tsmall_test_matrix_h5\tall\t2960000\t0.00010892455159392927\n+591\tsmall_test_matrix_h5\tall\t2965000\t7.263746640517178e-05\n+592\tsmall_test_matrix_h5\tall\t2970000\t3.6329288672527794e-05\n+593\tsmall_test_matrix_h5\tall\t2975000\t7.26797005596337e-05\n+594\tsmall_test_matrix_h5\tall\t2980000\t0.00010905125408942203\n+595\tsmall_test_matrix_h5\tall\t2985000\t0.00021816595156715876\n+596\tsmall_test_matrix_h5\tall\t2990000\t0.00010911471593802284\n+597\tsmall_test_matrix_h5\tall\t2995000\t0.00014552863275849522\n+598\tsmall_test_matrix_h5\tall\t3000000\t0.00029114200451270107\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/find_TADs/multiFDR_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_score.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,24097 @@\n+chr2L\t2500\t7500\t-0.245086500000\n+chr2L\t7500\t12500\t-0.231015500000\n+chr2L\t12500\t17500\t0.248282500000\n+chr2L\t17500\t22500\t0.222277500000\n+chr2L\t22500\t27500\t0.285627500000\n+chr2L\t27500\t32500\t0.003759500000\n+chr2L\t32500\t37500\t0.390073000000\n+chr2L\t37500\t42500\t0.210737500000\n+chr2L\t42500\t47500\t0.220971500000\n+chr2L\t47500\t52500\t0.115526500000\n+chr2L\t52500\t57500\t0.220971500000\n+chr2L\t57500\t62500\t0.220971500000\n+chr2L\t62500\t67500\t0.153475000000\n+chr2L\t67500\t72500\t-0.212048000000\n+chr2L\t72500\t77500\t-0.145684500000\n+chr2L\t77500\t82500\t-0.145684500000\n+chr2L\t82500\t87500\t0.186132000000\n+chr2L\t87500\t92500\t0.177488000000\n+chr2L\t92500\t97500\t0.442941000000\n+chr2L\t97500\t102500\t0.024936000000\n+chr2L\t102500\t107500\t-0.145684500000\n+chr2L\t107500\t112500\t-0.151675000000\n+chr2L\t112500\t117500\t0.161949000000\n+chr2L\t117500\t122500\t0.161949000000\n+chr2L\t122500\t127500\t-0.079542500000\n+chr2L\t127500\t132500\t0.116894000000\n+chr2L\t132500\t137500\t0.116894000000\n+chr2L\t137500\t142500\t0.136150000000\n+chr2L\t142500\t147500\t0.487624500000\n+chr2L\t147500\t152500\t0.146384000000\n+chr2L\t152500\t157500\t-0.129681500000\n+chr2L\t157500\t162500\t-0.129681500000\n+chr2L\t162500\t167500\t-0.085311500000\n+chr2L\t167500\t172500\t0.156180000000\n+chr2L\t172500\t177500\t0.421633000000\n+chr2L\t177500\t182500\t0.190754000000\n+chr2L\t182500\t187500\t0.387190000000\n+chr2L\t187500\t192500\t0.320826500000\n+chr2L\t192500\t197500\t-0.212048000000\n+chr2L\t197500\t202500\t-0.041427000000\n+chr2L\t202500\t207500\t-0.151675000000\n+chr2L\t207500\t212500\t0.089816500000\n+chr2L\t212500\t217500\t0.311779000000\n+chr2L\t217500\t222500\t0.222321500000\n+chr2L\t222500\t227500\t0.222321500000\n+chr2L\t227500\t232500\t0.222321500000\n+chr2L\t232500\t237500\t0.161949000000\n+chr2L\t237500\t242500\t-0.079542500000\n+chr2L\t242500\t247500\t-0.139915500000\n+chr2L\t247500\t252500\t-0.065328000000\n+chr2L\t252500\t257500\t0.191481000000\n+chr2L\t257500\t262500\t0.191481000000\n+chr2L\t262500\t267500\t0.453490500000\n+chr2L\t267500\t272500\t0.282870000000\n+chr2L\t272500\t277500\t0.136150000000\n+chr2L\t277500\t282500\t-0.139915500000\n+chr2L\t282500\t287500\t0.116894000000\n+chr2L\t287500\t292500\t0.191481000000\n+chr2L\t292500\t297500\t-0.137460500000\n+chr2L\t297500\t302500\t-0.137460500000\n+chr2L\t302500\t307500\t0.376157500000\n+chr2L\t307500\t312500\t0.376157500000\n+chr2L\t312500\t317500\t0.024936000000\n+chr2L\t317500\t322500\t0.281745000000\n+chr2L\t322500\t327500\t0.376578000000\n+chr2L\t327500\t332500\t-0.145684500000\n+chr2L\t332500\t337500\t-0.145684500000\n+chr2L\t337500\t342500\t-0.212048000000\n+chr2L\t342500\t347500\t-0.212048000000\n+chr2L\t347500\t352500\t-0.129681500000\n+chr2L\t352500\t357500\t-0.129681500000\n+chr2L\t357500\t362500\t-0.129681500000\n+chr2L\t362500\t367500\t-0.129681500000\n+chr2L\t367500\t372500\t0.044761500000\n+chr2L\t372500\t377500\t0.044761500000\n+chr2L\t377500\t382500\t0.044761500000\n+chr2L\t382500\t387500\t0.320826500000\n+chr2L\t387500\t392500\t0.064018000000\n+chr2L\t392500\t397500\t0.064018000000\n+chr2L\t397500\t402500\t-0.145684500000\n+chr2L\t402500\t407500\t0.024936000000\n+chr2L\t407500\t412500\t0.467966500000\n+chr2L\t412500\t417500\t0.202513500000\n+chr2L\t417500\t422500\t0.202513500000\n+chr2L\t422500\t427500\t0.390073000000\n+chr2L\t427500\t432500\t0.279825000000\n+chr2L\t432500\t437500\t0.521316000000\n+chr2L\t437500\t442500\t0.089816500000\n+chr2L\t442500\t447500\t-0.151675000000\n+chr2L\t447500\t452500\t0.044761500000\n+chr2L\t452500\t457500\t0.044761500000\n+chr2L\t457500\t462500\t-0.151675000000\n+chr2L\t462500\t467500\t0.173118500000\n+chr2L\t467500\t472500\t0.173118500000\n+chr2L\t472500\t477500\t0.102247500000\n+chr2L\t477500\t482500\t0.320826500000\n+chr2L\t482500\t487500\t0.320826500000\n+chr2L\t487500\t492500\t0.575879000000\n+chr2L\t492500\t497500\t-0.212048000000\n+chr2L\t497500\t502500\t-0.212048000000\n+chr2L\t502500\t507500\t-0.041427000000\n+chr2L\t507500\t512500\t-0.212048000000\n+chr2L\t512500\t517500\t-0.034517500000\n+chr2L\t517500\t522500\t-0.123974500000\n+chr2L\t522500\t527500\t-0.212048000000\n+chr2L\t527500\t532500\t-0.212048000000\n+chr2L\t532500\t537500\t-0.212048000000\n+chr2L\t537500\t542500\t-0.212048000000\n+chr2L\t542500\t547500\t-0.212048000000\n+chr2L\t547500\t552500\t0.044761500000\n+chr2L\t552500\t55750'..b'X\t21927500\t21932500\t-0.123078500000\n+chrX\t21932500\t21937500\t-0.123078500000\n+chrX\t21937500\t21942500\t-0.123078500000\n+chrX\t21942500\t21947500\t-0.123078500000\n+chrX\t21947500\t21952500\t-0.123078500000\n+chrX\t21952500\t21957500\t-0.123078500000\n+chrX\t21957500\t21962500\t-0.123078500000\n+chrX\t21962500\t21967500\t0.417830000000\n+chrX\t21967500\t21972500\t0.417830000000\n+chrX\t21972500\t21977500\t0.417830000000\n+chrX\t21977500\t21982500\t-0.123078500000\n+chrX\t21982500\t21987500\t-0.123078500000\n+chrX\t21987500\t21992500\t-0.123078500000\n+chrX\t21992500\t21997500\t-0.123078500000\n+chrX\t21997500\t22002500\t-0.123078500000\n+chrX\t22002500\t22007500\t-0.123078500000\n+chrX\t22007500\t22012500\t-0.123078500000\n+chrX\t22012500\t22017500\t-0.123078500000\n+chrX\t22017500\t22022500\t-0.123078500000\n+chrX\t22022500\t22027500\t-0.123078500000\n+chrX\t22027500\t22032500\t-0.123078500000\n+chrX\t22032500\t22037500\t-0.123078500000\n+chrX\t22037500\t22042500\t0.314729500000\n+chrX\t22042500\t22047500\t0.422962000000\n+chrX\t22047500\t22052500\t0.534135000000\n+chrX\t22052500\t22057500\t0.566234000000\n+chrX\t22057500\t22062500\t0.870595500000\n+chrX\t22062500\t22067500\t-0.011905500000\n+chrX\t22067500\t22072500\t-0.123078500000\n+chrX\t22072500\t22077500\t-0.123078500000\n+chrX\t22077500\t22082500\t-0.123078500000\n+chrX\t22082500\t22087500\t-0.123078500000\n+chrX\t22087500\t22092500\t-0.123078500000\n+chrX\t22092500\t22097500\t-0.123078500000\n+chrX\t22097500\t22102500\t-0.123078500000\n+chrX\t22102500\t22107500\t-0.123078500000\n+chrX\t22107500\t22112500\t0.181282500000\n+chrX\t22112500\t22117500\t-0.123078500000\n+chrX\t22117500\t22122500\t-0.123078500000\n+chrX\t22122500\t22127500\t-0.123078500000\n+chrX\t22127500\t22132500\t-0.123078500000\n+chrX\t22132500\t22137500\t-0.123078500000\n+chrX\t22137500\t22142500\t0.026382500000\n+chrX\t22142500\t22147500\t0.026382500000\n+chrX\t22147500\t22152500\t0.026382500000\n+chrX\t22152500\t22157500\t0.026382500000\n+chrX\t22157500\t22162500\t-0.123078500000\n+chrX\t22162500\t22167500\t0.328783000000\n+chrX\t22167500\t22172500\t0.024421500000\n+chrX\t22172500\t22177500\t-0.123078500000\n+chrX\t22177500\t22182500\t-0.123078500000\n+chrX\t22182500\t22187500\t-0.123078500000\n+chrX\t22187500\t22192500\t-0.123078500000\n+chrX\t22192500\t22197500\t0.032313000000\n+chrX\t22197500\t22202500\t-0.123078500000\n+chrX\t22202500\t22207500\t-0.123078500000\n+chrX\t22207500\t22212500\t-0.123078500000\n+chrX\t22212500\t22217500\t-0.123078500000\n+chrX\t22217500\t22222500\t-0.123078500000\n+chrX\t22222500\t22227500\t-0.123078500000\n+chrX\t22227500\t22232500\t-0.123078500000\n+chrX\t22232500\t22237500\t0.026382500000\n+chrX\t22237500\t22242500\t0.026382500000\n+chrX\t22242500\t22247500\t0.026382500000\n+chrX\t22247500\t22252500\t0.026382500000\n+chrX\t22252500\t22257500\t-0.123078500000\n+chrX\t22257500\t22262500\t-0.123078500000\n+chrX\t22262500\t22267500\t-0.123078500000\n+chrX\t22267500\t22272500\t-0.123078500000\n+chrX\t22272500\t22277500\t-0.123078500000\n+chrX\t22277500\t22282500\t-0.123078500000\n+chrX\t22282500\t22287500\t-0.123078500000\n+chrX\t22287500\t22292500\t-0.123078500000\n+chrX\t22292500\t22297500\t-0.123078500000\n+chrX\t22297500\t22302500\t0.024421500000\n+chrX\t22302500\t22307500\t0.177868500000\n+chrX\t22307500\t22312500\t0.030368500000\n+chrX\t22312500\t22317500\t0.030368500000\n+chrX\t22317500\t22322500\t0.554135000000\n+chrX\t22322500\t22327500\t0.998827500000\n+chrX\t22327500\t22332500\t0.998827500000\n+chrX\t22332500\t22337500\t0.400688000000\n+chrX\t22337500\t22342500\t-0.123078500000\n+chrX\t22342500\t22347500\t-0.123078500000\n+chrX\t22347500\t22352500\t-0.123078500000\n+chrX\t22352500\t22357500\t-0.123078500000\n+chrX\t22357500\t22362500\t-0.123078500000\n+chrX\t22362500\t22367500\t-0.123078500000\n+chrX\t22367500\t22372500\t-0.123078500000\n+chrX\t22372500\t22377500\t-0.123078500000\n+chrX\t22377500\t22382500\t-0.123078500000\n+chrX\t22382500\t22387500\t-0.123078500000\n+chrX\t22387500\t22392500\t-0.123078500000\n+chrX\t22392500\t22397500\t-0.124675500000\n+chrX\t22397500\t22402500\t-0.126415000000\n+chrX\t22402500\t22407500\t-0.128395000000\n+chrX\t22407500\t22412500\t-0.135287500000\n+chrX\t22412500\t22417500\t-0.144761000000\n+chrX\t22417500\t22421413\t0.000000000000\n+chrXHet\t2500\t202056\t0.000000000000\n+chrYHet\t2500\t346019\t0.000000000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/find_TADs/multiFDR_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_tad_score.bm Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,24113 @@\n+#{"step":15000,"minDepth":15000,"maxDepth":30000,"binsize":5000}\n+chr2L\t0\t5000\t0.000000\t0.000000\n+chr2L\t5000\t10000\t-0.260846\t-0.229327\n+chr2L\t10000\t15000\t-0.244737\t-0.217294\n+chr2L\t15000\t20000\t0.038826\t0.457739\n+chr2L\t20000\t25000\t0.248816\t0.195739\n+chr2L\t25000\t30000\t0.248816\t0.322439\n+chr2L\t30000\t35000\t-0.234167\t0.241686\n+chr2L\t35000\t40000\t0.480531\t0.299615\n+chr2L\t40000\t45000\t0.207538\t0.213937\n+chr2L\t45000\t50000\t0.207538\t0.234405\n+chr2L\t50000\t55000\t0.038826\t0.192227\n+chr2L\t55000\t60000\t0.207538\t0.234405\n+chr2L\t60000\t65000\t0.207538\t0.234405\n+chr2L\t65000\t70000\t0.207538\t0.099412\n+chr2L\t70000\t75000\t-0.234167\t-0.189929\n+chr2L\t75000\t80000\t-0.234167\t-0.057202\n+chr2L\t80000\t85000\t-0.234167\t-0.057202\n+chr2L\t85000\t90000\t0.296739\t0.075525\n+chr2L\t90000\t95000\t0.176728\t0.178248\n+chr2L\t95000\t100000\t0.707634\t0.178248\n+chr2L\t100000\t105000\t0.038826\t0.011046\n+chr2L\t105000\t110000\t-0.234167\t-0.057202\n+chr2L\t110000\t115000\t-0.234167\t-0.069183\n+chr2L\t115000\t120000\t0.248816\t0.075082\n+chr2L\t120000\t125000\t0.248816\t0.075082\n+chr2L\t125000\t130000\t-0.234167\t0.075082\n+chr2L\t130000\t135000\t0.176728\t0.057060\n+chr2L\t135000\t140000\t0.176728\t0.057060\n+chr2L\t140000\t145000\t0.207538\t0.064762\n+chr2L\t145000\t150000\t0.753523\t0.221726\n+chr2L\t150000\t155000\t0.207538\t0.085230\n+chr2L\t155000\t160000\t-0.234167\t-0.025196\n+chr2L\t160000\t165000\t-0.234167\t-0.025196\n+chr2L\t165000\t170000\t-0.234167\t0.063544\n+chr2L\t170000\t175000\t0.248816\t0.063544\n+chr2L\t175000\t180000\t0.779722\t0.063544\n+chr2L\t180000\t185000\t0.207538\t0.173970\n+chr2L\t185000\t190000\t0.618432\t0.155948\n+chr2L\t190000\t195000\t0.618432\t0.023221\n+chr2L\t195000\t200000\t-0.234167\t-0.189929\n+chr2L\t200000\t205000\t0.038826\t-0.121680\n+chr2L\t205000\t210000\t-0.234167\t-0.069183\n+chr2L\t210000\t215000\t0.248816\t-0.069183\n+chr2L\t215000\t220000\t0.248816\t0.374742\n+chr2L\t220000\t225000\t0.248816\t0.195827\n+chr2L\t225000\t230000\t0.248816\t0.195827\n+chr2L\t230000\t235000\t0.248816\t0.195827\n+chr2L\t235000\t240000\t0.248816\t0.075082\n+chr2L\t240000\t245000\t-0.234167\t0.075082\n+chr2L\t245000\t250000\t-0.234167\t-0.045664\n+chr2L\t250000\t255000\t-0.234167\t0.103511\n+chr2L\t255000\t260000\t0.176728\t0.206234\n+chr2L\t260000\t265000\t0.176728\t0.206234\n+chr2L\t265000\t270000\t0.480531\t0.426450\n+chr2L\t270000\t275000\t0.207538\t0.358202\n+chr2L\t275000\t280000\t0.207538\t0.064762\n+chr2L\t280000\t285000\t-0.234167\t-0.045664\n+chr2L\t285000\t290000\t0.176728\t0.057060\n+chr2L\t290000\t295000\t0.176728\t0.206234\n+chr2L\t295000\t300000\t-0.234167\t-0.040754\n+chr2L\t300000\t305000\t-0.234167\t-0.040754\n+chr2L\t305000\t310000\t0.587622\t0.164693\n+chr2L\t310000\t315000\t0.587622\t0.164693\n+chr2L\t315000\t320000\t0.038826\t0.011046\n+chr2L\t320000\t325000\t0.449720\t0.113770\n+chr2L\t325000\t330000\t0.707634\t0.045522\n+chr2L\t330000\t335000\t-0.234167\t-0.057202\n+chr2L\t335000\t340000\t-0.234167\t-0.057202\n+chr2L\t340000\t345000\t-0.234167\t-0.189929\n+chr2L\t345000\t350000\t-0.234167\t-0.189929\n+chr2L\t350000\t355000\t-0.234167\t-0.025196\n+chr2L\t355000\t360000\t-0.234167\t-0.025196\n+chr2L\t360000\t365000\t-0.234167\t-0.025196\n+chr2L\t365000\t370000\t-0.234167\t-0.025196\n+chr2L\t370000\t375000\t0.176728\t-0.087205\n+chr2L\t375000\t380000\t0.176728\t-0.087205\n+chr2L\t380000\t385000\t0.176728\t-0.087205\n+chr2L\t385000\t390000\t0.618432\t0.023221\n+chr2L\t390000\t395000\t0.207538\t-0.079502\n+chr2L\t395000\t400000\t0.207538\t-0.079502\n+chr2L\t400000\t405000\t-0.234167\t-0.057202\n+chr2L\t405000\t410000\t0.038826\t0.011046\n+chr2L\t410000\t415000\t0.738444\t0.197489\n+chr2L\t415000\t420000\t0.207538\t0.197489\n+chr2L\t420000\t425000\t0.207538\t0.197489\n+chr2L\t425000\t430000\t0.480531\t0.299615\n+chr2L\t430000\t435000\t0.207538\t0.352112\n+chr2L\t435000\t440000\t0.690520\t0.352112\n+chr2L\t440000\t445000\t0.248816\t-0.069183\n+chr2L\t445000\t450000\t-0.234167\t-0.069183\n+chr2L\t450000\t455000\t0.176728\t-0.087205\n+chr2L\t455000\t460000\t0.176728\t-0.087205\n+chr2L\t460000\t465000\t-0.234167\t-0.069183\n+chr2L\t465000\t470000\t0.248816\t0.097421\n+chr2L\t470000\t475000\t0.248816\t0.097421\n+chr2L\t475000\t480000\t0.038826\t0.165669\n+chr2L\t480000\t485000\t0.618432\t0.023221\n+chr2L\t485000\t490000\t0.618432\t0.023221\n+chr2L\t490000\t495000\t1.026516\t0.125242\n+chr2L\t495000\t500000\t-0.234167'..b'36915\t-0.109242\n+chrX\t21985000\t21990000\t-0.136915\t-0.109242\n+chrX\t21990000\t21995000\t-0.136915\t-0.109242\n+chrX\t21995000\t22000000\t-0.136915\t-0.109242\n+chrX\t22000000\t22005000\t-0.136915\t-0.109242\n+chrX\t22005000\t22010000\t-0.136915\t-0.109242\n+chrX\t22010000\t22015000\t-0.136915\t-0.109242\n+chrX\t22015000\t22020000\t-0.136915\t-0.109242\n+chrX\t22020000\t22025000\t-0.136915\t-0.109242\n+chrX\t22025000\t22030000\t-0.136915\t-0.109242\n+chrX\t22030000\t22035000\t-0.136915\t-0.109242\n+chrX\t22035000\t22040000\t-0.136915\t-0.109242\n+chrX\t22040000\t22045000\t0.350063\t0.279396\n+chrX\t22045000\t22050000\t0.523235\t0.322689\n+chrX\t22050000\t22055000\t0.523235\t0.545035\n+chrX\t22055000\t22060000\t0.752470\t0.379998\n+chrX\t22060000\t22065000\t1.239449\t0.501742\n+chrX\t22065000\t22070000\t-0.136915\t0.113104\n+chrX\t22070000\t22075000\t-0.136915\t-0.109242\n+chrX\t22075000\t22080000\t-0.136915\t-0.109242\n+chrX\t22080000\t22085000\t-0.136915\t-0.109242\n+chrX\t22085000\t22090000\t-0.136915\t-0.109242\n+chrX\t22090000\t22095000\t-0.136915\t-0.109242\n+chrX\t22095000\t22100000\t-0.136915\t-0.109242\n+chrX\t22100000\t22105000\t-0.136915\t-0.109242\n+chrX\t22105000\t22110000\t-0.136915\t-0.109242\n+chrX\t22110000\t22115000\t0.350063\t0.012502\n+chrX\t22115000\t22120000\t-0.136915\t-0.109242\n+chrX\t22120000\t22125000\t-0.136915\t-0.109242\n+chrX\t22125000\t22130000\t-0.136915\t-0.109242\n+chrX\t22130000\t22135000\t-0.136915\t-0.109242\n+chrX\t22135000\t22140000\t-0.136915\t-0.109242\n+chrX\t22140000\t22145000\t-0.136915\t0.189680\n+chrX\t22145000\t22150000\t-0.136915\t0.189680\n+chrX\t22150000\t22155000\t-0.136915\t0.189680\n+chrX\t22155000\t22160000\t-0.136915\t0.189680\n+chrX\t22160000\t22165000\t-0.136915\t-0.109242\n+chrX\t22165000\t22170000\t0.350063\t0.307503\n+chrX\t22170000\t22175000\t-0.136915\t0.185758\n+chrX\t22175000\t22180000\t-0.136915\t-0.109242\n+chrX\t22180000\t22185000\t-0.136915\t-0.109242\n+chrX\t22185000\t22190000\t-0.136915\t-0.109242\n+chrX\t22190000\t22195000\t-0.136915\t-0.109242\n+chrX\t22195000\t22200000\t-0.136915\t0.201541\n+chrX\t22200000\t22205000\t-0.136915\t-0.109242\n+chrX\t22205000\t22210000\t-0.136915\t-0.109242\n+chrX\t22210000\t22215000\t-0.136915\t-0.109242\n+chrX\t22215000\t22220000\t-0.136915\t-0.109242\n+chrX\t22220000\t22225000\t-0.136915\t-0.109242\n+chrX\t22225000\t22230000\t-0.136915\t-0.109242\n+chrX\t22230000\t22235000\t-0.136915\t-0.109242\n+chrX\t22235000\t22240000\t-0.136915\t0.189680\n+chrX\t22240000\t22245000\t-0.136915\t0.189680\n+chrX\t22245000\t22250000\t-0.136915\t0.189680\n+chrX\t22250000\t22255000\t-0.136915\t0.189680\n+chrX\t22255000\t22260000\t-0.136915\t-0.109242\n+chrX\t22260000\t22265000\t-0.136915\t-0.109242\n+chrX\t22265000\t22270000\t-0.136915\t-0.109242\n+chrX\t22270000\t22275000\t-0.136915\t-0.109242\n+chrX\t22275000\t22280000\t-0.136915\t-0.109242\n+chrX\t22280000\t22285000\t-0.136915\t-0.109242\n+chrX\t22285000\t22290000\t-0.136915\t-0.109242\n+chrX\t22290000\t22295000\t-0.136915\t-0.109242\n+chrX\t22295000\t22300000\t-0.136915\t-0.109242\n+chrX\t22300000\t22305000\t-0.136915\t0.185758\n+chrX\t22305000\t22310000\t-0.136915\t0.492652\n+chrX\t22310000\t22315000\t-0.136915\t0.197652\n+chrX\t22315000\t22320000\t-0.136915\t0.197652\n+chrX\t22320000\t22325000\t0.523235\t0.585035\n+chrX\t22325000\t22330000\t1.412620\t0.585035\n+chrX\t22330000\t22335000\t1.412620\t0.585035\n+chrX\t22335000\t22340000\t0.523235\t0.278141\n+chrX\t22340000\t22345000\t-0.136915\t-0.109242\n+chrX\t22345000\t22350000\t-0.136915\t-0.109242\n+chrX\t22350000\t22355000\t-0.136915\t-0.109242\n+chrX\t22355000\t22360000\t-0.136915\t-0.109242\n+chrX\t22360000\t22365000\t-0.136915\t-0.109242\n+chrX\t22365000\t22370000\t-0.136915\t-0.109242\n+chrX\t22370000\t22375000\t-0.136915\t-0.109242\n+chrX\t22375000\t22380000\t-0.136915\t-0.109242\n+chrX\t22380000\t22385000\t-0.136915\t-0.109242\n+chrX\t22385000\t22390000\t-0.136915\t-0.109242\n+chrX\t22390000\t22395000\t-0.136915\t-0.109242\n+chrX\t22395000\t22400000\t-0.136915\t-0.112436\n+chrX\t22400000\t22405000\t-0.136915\t-0.115915\n+chrX\t22405000\t22410000\t-0.136915\t-0.119875\n+chrX\t22410000\t22415000\t-0.144847\t-0.125728\n+chrX\t22415000\t22420000\t-0.156233\t-0.133289\n+chrX\t22420000\t22422827\t0.000000\t0.000000\n+chrXHet\t0\t5000\t0.000000\t0.000000\n+chrXHet\t200000\t204112\t0.000000\t0.000000\n+chrYHet\t0\t5000\t0.000000\t0.000000\n+chrYHet\t345000\t347038\t0.000000\t0.000000\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/find_TADs/multiFDR_zscore_matrix.h5
b
Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAggregateContacts/test_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAggregateContacts/test_regions.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,55 @@
+2R 5441451 5441452 msl2_peak_1532 9.54697
+2R 8291271 8291272 msl2_peak_1644 7.36770
+2R 14575573 14575574 msl2_peak_1947 4.41313
+3L 628463 628464 msl2_peak_2780 11.60203
+3L 3903421 3903422 msl2_peak_2958 4.32242
+3L 8759529 8759530 msl2_peak_3195 4.10429
+3R 2901523 2901524 msl2_peak_4559 2.22040
+3R 3932152 3932153 msl2_peak_4603 9.59945
+3R 11851634 11851635 msl2_peak_4969 8.43238
+3R 20545331 20545332 msl2_peak_5267 4.72876
+X 147841 147842 msl2_peak_22671 16.59036
+X 366894 366895 msl2_peak_22686 25.37647
+X 517100 517101 msl2_peak_22694 8.54298
+X 548547 548548 msl2_peak_22696 27.53758
+X 656427 656428 msl2_peak_22697 14.11897
+X 692287 692288 msl2_peak_22698 15.96065
+X 818016 818017 msl2_peak_22713 10.66184
+X 937135 937136 msl2_peak_22717 67.84654
+X 1112721 1112722 msl2_peak_22727 26.81313
+X 1268823 1268824 msl2_peak_22735 29.73846
+X 1356647 1356648 msl2_peak_22736 9.58288
+X 1375009 1375010 msl2_peak_22738 4.49598
+X 1375616 1375617 msl2_peak_22739 128.36397
+X 1409093 1409094 msl2_peak_22742 14.72497
+X 1588015 1588016 msl2_peak_22757 102.61334
+X 1679121 1679122 msl2_peak_22767 16.12354
+X 1754043 1754044 msl2_peak_22769 20.51431
+X 1775025 1775026 msl2_peak_22773 43.05813
+X 1787755 1787756 msl2_peak_22774 142.73460
+X 1798236 1798237 msl2_peak_22775 80.66115
+X 1819545 1819546 msl2_peak_22777 11.21560
+X 1918989 1918990 msl2_peak_22793 74.48118
+X 1956476 1956477 msl2_peak_22794 32.73601
+X 1972291 1972292 msl2_peak_22795 37.39349
+X 2007235 2007236 msl2_peak_22798 11.21560
+X 2015927 2015928 msl2_peak_22799 68.80555
+X 2044335 2044336 msl2_peak_22804 36.60362
+X 2050114 2050115 msl2_peak_22805 47.23102
+X 2072937 2072938 msl2_peak_22807 52.37415
+X 2126007 2126008 msl2_peak_22808 42.23372
+X 2162302 2162303 msl2_peak_22810 78.64520
+X 2237610 2237611 msl2_peak_22817 43.05813
+X 2340287 2340288 msl2_peak_22825 14.72497
+X 2493295 2493296 msl2_peak_22827 23.47760
+X 2503119 2503120 msl2_peak_22828 80.83590
+X 2520611 2520612 msl2_peak_22839 17.87077
+X 2521079 2521080 msl2_peak_22840 60.08352
+X 2613112 2613113 msl2_peak_22844 43.87985
+X 2628624 2628625 msl2_peak_22847 115.37079
+X 3382405 3382406 msl2_peak_22879 6.13203
+X 3593688 3593689 msl2_peak_22908 10.66184
+X 3596515 3596516 msl2_peak_22909 6.59200
+X 3755342 3755343 msl2_peak_22919 164.76546
+X 3848197 3848198 msl2_peak_22920 74.65739
+X 4021813 4021814 msl2_peak_22929 32.73601
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAggregateContacts_results1.png
b
Binary file test-data/hicAggregateContacts_results1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAverageRegions/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAverageRegions/regions.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,6 @@
+chr2L 2500000
+chr2L 3500000
+chr2L 4500000
+chr2L 5500000
+chr2L 7000000
+chr2L 19000000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAverageRegions/result.npz
b
Binary file test-data/hicAverageRegions/result.npz has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAverageRegions/result_rangeInBins_100.npz
b
Binary file test-data/hicAverageRegions/result_rangeInBins_100.npz has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicAverageRegions/result_range_100000.npz
b
Binary file test-data/hicAverageRegions/result_range_100000.npz has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png
b
Binary file test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCompartmentsPolarization/pca1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicCompartmentsPolarization/pca1.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,449 @@\n+chrX\t0\t50000\t-0.001950268891\n+chrX\t50000\t100000\t0.004039333365\n+chrX\t150000\t200000\t-0.004150079458\n+chrX\t200000\t250000\t0.077532321648\n+chrX\t250000\t300000\t0.013162235059\n+chrX\t300000\t350000\t-0.010570170513\n+chrX\t350000\t400000\t-0.006386912627\n+chrX\t400000\t450000\t0.000348354523\n+chrX\t450000\t500000\t-0.002191464759\n+chrX\t500000\t550000\t0.034823907107\n+chrX\t550000\t600000\t-0.001240094255\n+chrX\t600000\t650000\t-0.000229749119\n+chrX\t650000\t700000\t-0.006317260062\n+chrX\t700000\t750000\t-0.002565261791\n+chrX\t750000\t800000\t-0.004311642764\n+chrX\t800000\t850000\t0.041284600526\n+chrX\t850000\t900000\t-0.001206205197\n+chrX\t900000\t950000\t0.004206457668\n+chrX\t950000\t1000000\t0.000000000000\n+chrX\t1000000\t1050000\t-0.002344340704\n+chrX\t1050000\t1100000\t-0.003197692841\n+chrX\t1100000\t1150000\t0.004195129694\n+chrX\t1150000\t1200000\t0.000621806104\n+chrX\t1200000\t1250000\t-0.003285597309\n+chrX\t1250000\t1300000\t0.076828548177\n+chrX\t1300000\t1350000\t-0.010697220075\n+chrX\t1350000\t1400000\t0.416262439056\n+chrX\t1400000\t1450000\t-0.009560094422\n+chrX\t1450000\t1500000\t0.000365175544\n+chrX\t1500000\t1550000\t-0.004096594539\n+chrX\t1550000\t1600000\t0.031524755415\n+chrX\t1600000\t1650000\t-0.004378928052\n+chrX\t1650000\t1700000\t-0.003028959081\n+chrX\t1700000\t1750000\t0.000462699373\n+chrX\t1750000\t1800000\t-0.003895237855\n+chrX\t1800000\t1850000\t-0.011390750254\n+chrX\t1850000\t1900000\t-0.019371497852\n+chrX\t1900000\t1950000\t-0.019303635122\n+chrX\t1950000\t2000000\t-0.003072862657\n+chrX\t2000000\t2050000\t0.426941553649\n+chrX\t2050000\t2100000\t-0.008142799642\n+chrX\t2100000\t2150000\t-0.005175407952\n+chrX\t2150000\t2200000\t-0.004879520091\n+chrX\t2200000\t2250000\t0.003878381414\n+chrX\t2250000\t2300000\t-0.010525540521\n+chrX\t2300000\t2350000\t-0.006908266316\n+chrX\t2350000\t2400000\t-0.016957291626\n+chrX\t2400000\t2450000\t-0.011568145873\n+chrX\t2450000\t2500000\t-0.002393277901\n+chrX\t2500000\t2550000\t-0.004360707817\n+chrX\t2550000\t2600000\t0.009573130188\n+chrX\t2600000\t2650000\t0.018342700509\n+chrX\t2650000\t2700000\t-0.005767802666\n+chrX\t2700000\t2750000\t-0.005017890458\n+chrX\t2750000\t2800000\t0.006550346751\n+chrX\t2800000\t2850000\t-0.003855852841\n+chrX\t2850000\t2900000\t-0.008714181700\n+chrX\t2900000\t2950000\t-0.028685776873\n+chrX\t2950000\t3000000\t-0.002385659352\n+chrX\t3000000\t3050000\t-0.003655480667\n+chrX\t3050000\t3100000\t-0.032800223632\n+chrX\t3100000\t3150000\t-0.003747377987\n+chrX\t3150000\t3200000\t-0.017915223328\n+chrX\t3200000\t3250000\t-0.003754593793\n+chrX\t3250000\t3300000\t-0.004671494041\n+chrX\t3300000\t3350000\t-0.006455053039\n+chrX\t3350000\t3400000\t-0.008604273625\n+chrX\t3400000\t3450000\t-0.003040237722\n+chrX\t3450000\t3500000\t-0.004303299624\n+chrX\t3500000\t3550000\t-0.004902250248\n+chrX\t3550000\t3600000\t-0.004581094820\n+chrX\t3600000\t3650000\t0.019156317567\n+chrX\t3650000\t3700000\t-0.002166080628\n+chrX\t3700000\t3750000\t-0.000481896350\n+chrX\t3750000\t3800000\t-0.009569770797\n+chrX\t3800000\t3850000\t-0.003338969958\n+chrX\t3850000\t3900000\t-0.011773255276\n+chrX\t3900000\t3950000\t-0.008847512200\n+chrX\t3950000\t4000000\t-0.007784475913\n+chrX\t4000000\t4050000\t-0.001558790514\n+chrX\t4050000\t4100000\t-0.009136763597\n+chrX\t4100000\t4150000\t0.004393960600\n+chrX\t4150000\t4200000\t-0.010129062603\n+chrX\t4200000\t4250000\t-0.003471639817\n+chrX\t4250000\t4300000\t-0.030715717878\n+chrX\t4300000\t4350000\t-0.001707151907\n+chrX\t4350000\t4400000\t0.040416368868\n+chrX\t4400000\t4450000\t-0.006496816404\n+chrX\t4450000\t4500000\t-0.004509415975\n+chrX\t4500000\t4550000\t-0.003751041995\n+chrX\t4550000\t4600000\t-0.001721307777\n+chrX\t4600000\t4650000\t-0.016064202375\n+chrX\t4650000\t4700000\t-0.004886880327\n+chrX\t4700000\t4750000\t-0.009686363742\n+chrX\t4750000\t4800000\t-0.004757063036\n+chrX\t4800000\t4850000\t-0.000291087448\n+chrX\t4850000\t4900000\t-0.009414513708\n+chrX\t4900000\t4950000\t0.006904458726\n+chrX\t4950000\t5000000\t-0.000209215809\n+chrX\t5000000\t5050000\t-0.004828582394\n+chrX\t5050000\t5100000\t-0.004968977275\n+chrX\t5100000\t5150000\t-0.001178977521\n+chrX\t5150000\t5200000\t-0.006528513078\n+chrX\t5200000\t5250000\t0.043603051711\n+chrX\t5250000\t5300000\t-0.008545750187\n+chrX\t5300000\t5350000\t0.004704260708\n+chrX\t5350000\t5400000\t-'..b'0000\t17500000\t0.026176829549\n+chrX\t17500000\t17550000\t-0.007676818502\n+chrX\t17550000\t17600000\t-0.010194895446\n+chrX\t17600000\t17650000\t0.003272666853\n+chrX\t17650000\t17700000\t-0.008543963076\n+chrX\t17700000\t17750000\t-0.033067814804\n+chrX\t17750000\t17800000\t-0.005216617982\n+chrX\t17800000\t17850000\t-0.007128902326\n+chrX\t17850000\t17900000\t0.004491811817\n+chrX\t17900000\t17950000\t-0.009182273159\n+chrX\t17950000\t18000000\t-0.001411096233\n+chrX\t18000000\t18050000\t-0.012135159354\n+chrX\t18050000\t18100000\t-0.012889660944\n+chrX\t18100000\t18150000\t-0.011600603087\n+chrX\t18150000\t18200000\t-0.002783990355\n+chrX\t18200000\t18250000\t-0.004049922767\n+chrX\t18250000\t18300000\t-0.003809328569\n+chrX\t18300000\t18350000\t-0.001981026029\n+chrX\t18350000\t18400000\t0.009114374027\n+chrX\t18400000\t18450000\t-0.003819231590\n+chrX\t18450000\t18500000\t-0.015875671966\n+chrX\t18500000\t18550000\t-0.002489442945\n+chrX\t18550000\t18600000\t-0.005267679819\n+chrX\t18600000\t18650000\t-0.005137813667\n+chrX\t18650000\t18700000\t0.000952856827\n+chrX\t18700000\t18750000\t-0.013910874190\n+chrX\t18750000\t18800000\t-0.012123009185\n+chrX\t18800000\t18850000\t-0.007538538144\n+chrX\t18850000\t18900000\t-0.003668466069\n+chrX\t18900000\t18950000\t-0.011925135389\n+chrX\t18950000\t19000000\t0.000663835810\n+chrX\t19000000\t19050000\t-0.005829240341\n+chrX\t19050000\t19100000\t0.008455719900\n+chrX\t19100000\t19150000\t-0.010811696304\n+chrX\t19150000\t19200000\t-0.005968135017\n+chrX\t19200000\t19250000\t-0.003232695436\n+chrX\t19250000\t19300000\t-0.000015686406\n+chrX\t19300000\t19350000\t-0.003128615981\n+chrX\t19350000\t19400000\t-0.003203152238\n+chrX\t19400000\t19450000\t-0.003764554364\n+chrX\t19450000\t19500000\t-0.002403681148\n+chrX\t19500000\t19550000\t0.005425385755\n+chrX\t19550000\t19600000\t-0.016571619789\n+chrX\t19600000\t19650000\t-0.002656867028\n+chrX\t19650000\t19700000\t-0.014794729718\n+chrX\t19700000\t19750000\t-0.005658424837\n+chrX\t19750000\t19800000\t0.001090613488\n+chrX\t19800000\t19850000\t-0.005070736648\n+chrX\t19850000\t19900000\t-0.023701433181\n+chrX\t19900000\t19950000\t0.022056014970\n+chrX\t19950000\t20000000\t-0.005472350746\n+chrX\t20000000\t20050000\t-0.006526748195\n+chrX\t20050000\t20100000\t-0.004537628831\n+chrX\t20100000\t20150000\t-0.004054836753\n+chrX\t20150000\t20200000\t-0.001042600796\n+chrX\t20200000\t20250000\t-0.004783296645\n+chrX\t20250000\t20300000\t-0.003251957151\n+chrX\t20300000\t20350000\t0.054661022316\n+chrX\t20350000\t20400000\t-0.003961439372\n+chrX\t20400000\t20450000\t-0.005281811188\n+chrX\t20450000\t20500000\t-0.005204549361\n+chrX\t20500000\t20550000\t-0.004739600508\n+chrX\t20550000\t20600000\t-0.001486223614\n+chrX\t20600000\t20650000\t-0.003893437681\n+chrX\t20650000\t20700000\t-0.005909648304\n+chrX\t20700000\t20750000\t-0.004901728963\n+chrX\t20750000\t20800000\t-0.022366323681\n+chrX\t20800000\t20850000\t-0.014851220883\n+chrX\t20850000\t20900000\t-0.005979228301\n+chrX\t20900000\t20950000\t-0.002678465469\n+chrX\t20950000\t21000000\t-0.000837267099\n+chrX\t21000000\t21050000\t-0.005240758707\n+chrX\t21050000\t21100000\t0.008094281576\n+chrX\t21100000\t21150000\t-0.012173892530\n+chrX\t21150000\t21200000\t-0.009963024884\n+chrX\t21200000\t21250000\t-0.007099167097\n+chrX\t21250000\t21300000\t-0.027394159923\n+chrX\t21300000\t21350000\t-0.006812301752\n+chrX\t21350000\t21400000\t-0.004767405867\n+chrX\t21400000\t21450000\t0.000000000000\n+chrX\t21450000\t21500000\t-0.011016146286\n+chrX\t21500000\t21550000\t-0.002220183435\n+chrX\t21550000\t21600000\t0.000000000000\n+chrX\t21600000\t21650000\t0.010847097910\n+chrX\t21800000\t21850000\t0.000000000000\n+chrX\t21850000\t21900000\t-0.004203947422\n+chrX\t21900000\t21950000\t-0.003779034055\n+chrX\t21950000\t22000000\t-0.003865322501\n+chrX\t22000000\t22050000\t0.005700071718\n+chrX\t22050000\t22100000\t-0.002209909697\n+chrX\t22100000\t22150000\t-0.011412614059\n+chrX\t22150000\t22200000\t-0.002407124600\n+chrX\t22200000\t22250000\t-0.001909149896\n+chrX\t22250000\t22300000\t0.009260278990\n+chrX\t22300000\t22350000\t0.415034242513\n+chrX\t22350000\t22400000\t-0.001005473337\n+chrX\t22400000\t22422827\t-0.018885834822\n+chrXHet\t0\t50000\t0.866025403784\n+chrXHet\t50000\t100000\t-0.288675134595\n+chrXHet\t100000\t150000\t-0.288675134595\n+chrXHet\t150000\t200000\t-0.288675134595\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicConvertFormat/small_test_matrix_chr4.cool
b
Binary file test-data/hicConvertFormat/small_test_matrix_chr4.cool has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,326 @@\n+chr4\t70000\t75000\tchr4\t70000\t75000\t1\n+chr4\t70000\t75000\tchr4\t185000\t190000\t1\n+chr4\t75000\t80000\tchr4\t80000\t85000\t1\n+chr4\t80000\t85000\tchr4\t80000\t85000\t2\n+chr4\t80000\t85000\tchr4\t85000\t90000\t1\n+chr4\t80000\t85000\tchr4\t185000\t190000\t1\n+chr4\t85000\t90000\tchr4\t185000\t190000\t1\n+chr4\t85000\t90000\tchr4\t750000\t755000\t1\n+chr4\t90000\t95000\tchr4\t100000\t105000\t1\n+chr4\t90000\t95000\tchr4\t255000\t260000\t1\n+chr4\t90000\t95000\tchr4\t1030000\t1035000\t1\n+chr4\t95000\t100000\tchr4\t280000\t285000\t1\n+chr4\t100000\t105000\tchr4\t140000\t145000\t1\n+chr4\t105000\t110000\tchr4\t110000\t115000\t2\n+chr4\t105000\t110000\tchr4\t155000\t160000\t1\n+chr4\t105000\t110000\tchr4\t200000\t205000\t1\n+chr4\t105000\t110000\tchr4\t1110000\t1115000\t1\n+chr4\t110000\t115000\tchr4\t125000\t130000\t1\n+chr4\t110000\t115000\tchr4\t210000\t215000\t1\n+chr4\t120000\t125000\tchr4\t190000\t195000\t1\n+chr4\t120000\t125000\tchr4\t250000\t255000\t1\n+chr4\t125000\t130000\tchr4\t175000\t180000\t1\n+chr4\t125000\t130000\tchr4\t220000\t225000\t1\n+chr4\t125000\t130000\tchr4\t330000\t335000\t1\n+chr4\t130000\t135000\tchr4\t135000\t140000\t1\n+chr4\t130000\t135000\tchr4\t150000\t155000\t1\n+chr4\t135000\t140000\tchr4\t135000\t140000\t1\n+chr4\t135000\t140000\tchr4\t145000\t150000\t1\n+chr4\t135000\t140000\tchr4\t195000\t200000\t1\n+chr4\t140000\t145000\tchr4\t150000\t155000\t1\n+chr4\t140000\t145000\tchr4\t165000\t170000\t1\n+chr4\t145000\t150000\tchr4\t145000\t150000\t1\n+chr4\t145000\t150000\tchr4\t210000\t215000\t1\n+chr4\t150000\t155000\tchr4\t150000\t155000\t1\n+chr4\t150000\t155000\tchr4\t155000\t160000\t1\n+chr4\t150000\t155000\tchr4\t170000\t175000\t2\n+chr4\t150000\t155000\tchr4\t270000\t275000\t1\n+chr4\t150000\t155000\tchr4\t385000\t390000\t1\n+chr4\t150000\t155000\tchr4\t590000\t595000\t1\n+chr4\t150000\t155000\tchr4\t935000\t940000\t1\n+chr4\t155000\t160000\tchr4\t155000\t160000\t5\n+chr4\t155000\t160000\tchr4\t175000\t180000\t1\n+chr4\t155000\t160000\tchr4\t585000\t590000\t1\n+chr4\t160000\t165000\tchr4\t220000\t225000\t1\n+chr4\t160000\t165000\tchr4\t805000\t810000\t1\n+chr4\t170000\t175000\tchr4\t185000\t190000\t1\n+chr4\t170000\t175000\tchr4\t605000\t610000\t1\n+chr4\t175000\t180000\tchr4\t175000\t180000\t1\n+chr4\t175000\t180000\tchr4\t185000\t190000\t1\n+chr4\t175000\t180000\tchr4\t200000\t205000\t1\n+chr4\t175000\t180000\tchr4\t210000\t215000\t1\n+chr4\t175000\t180000\tchr4\t280000\t285000\t1\n+chr4\t175000\t180000\tchr4\t315000\t320000\t1\n+chr4\t180000\t185000\tchr4\t260000\t265000\t1\n+chr4\t180000\t185000\tchr4\t270000\t275000\t1\n+chr4\t180000\t185000\tchr4\t645000\t650000\t1\n+chr4\t185000\t190000\tchr4\t185000\t190000\t3\n+chr4\t185000\t190000\tchr4\t640000\t645000\t1\n+chr4\t190000\t195000\tchr4\t190000\t195000\t1\n+chr4\t195000\t200000\tchr4\t205000\t210000\t1\n+chr4\t195000\t200000\tchr4\t270000\t275000\t1\n+chr4\t195000\t200000\tchr4\t955000\t960000\t1\n+chr4\t195000\t200000\tchr4\t1085000\t1090000\t1\n+chr4\t200000\t205000\tchr4\t255000\t260000\t1\n+chr4\t200000\t205000\tchr4\t330000\t335000\t1\n+chr4\t200000\t205000\tchr4\t390000\t395000\t1\n+chr4\t205000\t210000\tchr4\t210000\t215000\t1\n+chr4\t205000\t210000\tchr4\t240000\t245000\t1\n+chr4\t205000\t210000\tchr4\t595000\t600000\t1\n+chr4\t210000\t215000\tchr4\t220000\t225000\t1\n+chr4\t220000\t225000\tchr4\t225000\t230000\t1\n+chr4\t220000\t225000\tchr4\t350000\t355000\t1\n+chr4\t235000\t240000\tchr4\t240000\t245000\t1\n+chr4\t235000\t240000\tchr4\t250000\t255000\t1\n+chr4\t235000\t240000\tchr4\t590000\t595000\t1\n+chr4\t245000\t250000\tchr4\t415000\t420000\t1\n+chr4\t260000\t265000\tchr4\t320000\t325000\t1\n+chr4\t265000\t270000\tchr4\t265000\t270000\t1\n+chr4\t265000\t270000\tchr4\t330000\t335000\t1\n+chr4\t270000\t275000\tchr4\t270000\t275000\t1\n+chr4\t275000\t280000\tchr4\t275000\t280000\t2\n+chr4\t275000\t280000\tchr4\t280000\t285000\t1\n+chr4\t290000\t295000\tchr4\t515000\t520000\t1\n+chr4\t300000\t305000\tchr4\t315000\t320000\t1\n+chr4\t305000\t310000\tchr4\t325000\t330000\t1\n+chr4\t305000\t310000\tchr4\t440000\t445000\t1\n+chr4\t310000\t315000\tchr4\t395000\t400000\t1\n+chr4\t320000\t325000\tchr4\t335000\t340000\t1\n+chr4\t320000\t325000\tchr4\t380000\t385000\t1\n+chr4\t320000\t325000\tchr4\t585000\t590000\t1\n+chr4\t330000\t335000\tchr4\t345000\t350000\t1\n+chr4\t335000\t340000\tchr4\t335000\t340000\t1\n+chr4\t335000\t340000\tchr4\t345000\t350000\t1\n+chr4\t345000\t350000\tchr4\t705000\t710000\t1\n+chr4\t350000\t355000\tchr4\t355000\t360000\t1\n+chr4\t350000\t355000\tchr4\t365000\t370000\t1\n+chr4\t350000\t355000\tchr4\t370000\t375000\t1\n+chr4\t370000\t375000\tchr4\t3950'..b'000\t1\n+chr4\t955000\t960000\tchr4\t960000\t965000\t1\n+chr4\t955000\t960000\tchr4\t1205000\t1210000\t1\n+chr4\t960000\t965000\tchr4\t960000\t965000\t1\n+chr4\t960000\t965000\tchr4\t975000\t980000\t1\n+chr4\t965000\t970000\tchr4\t1025000\t1030000\t1\n+chr4\t965000\t970000\tchr4\t1095000\t1100000\t1\n+chr4\t970000\t975000\tchr4\t975000\t980000\t2\n+chr4\t970000\t975000\tchr4\t1100000\t1105000\t1\n+chr4\t975000\t980000\tchr4\t975000\t980000\t1\n+chr4\t975000\t980000\tchr4\t1070000\t1075000\t1\n+chr4\t975000\t980000\tchr4\t1110000\t1115000\t1\n+chr4\t980000\t985000\tchr4\t990000\t995000\t1\n+chr4\t985000\t990000\tchr4\t990000\t995000\t1\n+chr4\t985000\t990000\tchr4\t1000000\t1005000\t1\n+chr4\t985000\t990000\tchr4\t1030000\t1035000\t1\n+chr4\t985000\t990000\tchr4\t1045000\t1050000\t1\n+chr4\t990000\t995000\tchr4\t990000\t995000\t1\n+chr4\t990000\t995000\tchr4\t995000\t1000000\t1\n+chr4\t990000\t995000\tchr4\t1025000\t1030000\t1\n+chr4\t990000\t995000\tchr4\t1055000\t1060000\t1\n+chr4\t1000000\t1005000\tchr4\t1000000\t1005000\t1\n+chr4\t1000000\t1005000\tchr4\t1105000\t1110000\t1\n+chr4\t1005000\t1010000\tchr4\t1010000\t1015000\t1\n+chr4\t1005000\t1010000\tchr4\t1020000\t1025000\t1\n+chr4\t1010000\t1015000\tchr4\t1020000\t1025000\t1\n+chr4\t1010000\t1015000\tchr4\t1040000\t1045000\t1\n+chr4\t1015000\t1020000\tchr4\t1020000\t1025000\t1\n+chr4\t1015000\t1020000\tchr4\t1025000\t1030000\t1\n+chr4\t1020000\t1025000\tchr4\t1020000\t1025000\t2\n+chr4\t1020000\t1025000\tchr4\t1025000\t1030000\t2\n+chr4\t1020000\t1025000\tchr4\t1035000\t1040000\t1\n+chr4\t1020000\t1025000\tchr4\t1080000\t1085000\t1\n+chr4\t1020000\t1025000\tchr4\t1205000\t1210000\t1\n+chr4\t1030000\t1035000\tchr4\t1035000\t1040000\t4\n+chr4\t1030000\t1035000\tchr4\t1040000\t1045000\t1\n+chr4\t1030000\t1035000\tchr4\t1060000\t1065000\t1\n+chr4\t1030000\t1035000\tchr4\t1075000\t1080000\t1\n+chr4\t1035000\t1040000\tchr4\t1115000\t1120000\t1\n+chr4\t1035000\t1040000\tchr4\t1135000\t1140000\t1\n+chr4\t1035000\t1040000\tchr4\t1170000\t1175000\t1\n+chr4\t1035000\t1040000\tchr4\t1200000\t1205000\t1\n+chr4\t1050000\t1055000\tchr4\t1155000\t1160000\t1\n+chr4\t1055000\t1060000\tchr4\t1100000\t1105000\t1\n+chr4\t1055000\t1060000\tchr4\t1105000\t1110000\t1\n+chr4\t1055000\t1060000\tchr4\t1155000\t1160000\t1\n+chr4\t1060000\t1065000\tchr4\t1060000\t1065000\t2\n+chr4\t1060000\t1065000\tchr4\t1065000\t1070000\t1\n+chr4\t1060000\t1065000\tchr4\t1195000\t1200000\t1\n+chr4\t1060000\t1065000\tchr4\t1210000\t1215000\t1\n+chr4\t1070000\t1075000\tchr4\t1085000\t1090000\t1\n+chr4\t1080000\t1085000\tchr4\t1080000\t1085000\t1\n+chr4\t1080000\t1085000\tchr4\t1095000\t1100000\t1\n+chr4\t1085000\t1090000\tchr4\t1085000\t1090000\t1\n+chr4\t1085000\t1090000\tchr4\t1200000\t1205000\t1\n+chr4\t1090000\t1095000\tchr4\t1180000\t1185000\t1\n+chr4\t1090000\t1095000\tchr4\t1185000\t1190000\t1\n+chr4\t1095000\t1100000\tchr4\t1190000\t1195000\t1\n+chr4\t1100000\t1105000\tchr4\t1100000\t1105000\t1\n+chr4\t1100000\t1105000\tchr4\t1105000\t1110000\t1\n+chr4\t1105000\t1110000\tchr4\t1120000\t1125000\t1\n+chr4\t1105000\t1110000\tchr4\t1130000\t1135000\t1\n+chr4\t1110000\t1115000\tchr4\t1140000\t1145000\t1\n+chr4\t1115000\t1120000\tchr4\t1115000\t1120000\t1\n+chr4\t1125000\t1130000\tchr4\t1130000\t1135000\t1\n+chr4\t1130000\t1135000\tchr4\t1135000\t1140000\t1\n+chr4\t1130000\t1135000\tchr4\t1175000\t1180000\t1\n+chr4\t1135000\t1140000\tchr4\t1135000\t1140000\t1\n+chr4\t1135000\t1140000\tchr4\t1150000\t1155000\t2\n+chr4\t1135000\t1140000\tchr4\t1155000\t1160000\t1\n+chr4\t1135000\t1140000\tchr4\t1180000\t1185000\t1\n+chr4\t1135000\t1140000\tchr4\t1205000\t1210000\t1\n+chr4\t1140000\t1145000\tchr4\t1145000\t1150000\t1\n+chr4\t1140000\t1145000\tchr4\t1165000\t1170000\t1\n+chr4\t1140000\t1145000\tchr4\t1180000\t1185000\t1\n+chr4\t1140000\t1145000\tchr4\t1185000\t1190000\t1\n+chr4\t1145000\t1150000\tchr4\t1160000\t1165000\t2\n+chr4\t1155000\t1160000\tchr4\t1155000\t1160000\t1\n+chr4\t1165000\t1170000\tchr4\t1165000\t1170000\t3\n+chr4\t1170000\t1175000\tchr4\t1185000\t1190000\t1\n+chr4\t1170000\t1175000\tchr4\t1210000\t1215000\t1\n+chr4\t1175000\t1180000\tchr4\t1175000\t1180000\t1\n+chr4\t1175000\t1180000\tchr4\t1190000\t1195000\t1\n+chr4\t1180000\t1185000\tchr4\t1180000\t1185000\t1\n+chr4\t1185000\t1190000\tchr4\t1200000\t1205000\t1\n+chr4\t1185000\t1190000\tchr4\t1250000\t1255000\t1\n+chr4\t1190000\t1195000\tchr4\t1210000\t1215000\t1\n+chr4\t1195000\t1200000\tchr4\t1195000\t1200000\t1\n+chr4\t1200000\t1205000\tchr4\t1205000\t1210000\t1\n+chr4\t1245000\t1250000\tchr4\t1245000\t1250000\t1\n+chr4\t1245000\t1250000\tchr4\t1250000\t1255000\t1\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicConvertFormat/small_test_matrix_chr4.homer
b
Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicConvertFormat/test_matrix.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/test_matrix.bed Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,3114 @@\n+chr1\t0\t1000000\t1\n+chr1\t1000000\t2000000\t2\n+chr1\t2000000\t3000000\t3\n+chr1\t3000000\t4000000\t4\n+chr1\t4000000\t5000000\t5\n+chr1\t5000000\t6000000\t6\n+chr1\t6000000\t7000000\t7\n+chr1\t7000000\t8000000\t8\n+chr1\t8000000\t9000000\t9\n+chr1\t9000000\t10000000\t10\n+chr1\t10000000\t11000000\t11\n+chr1\t11000000\t12000000\t12\n+chr1\t12000000\t13000000\t13\n+chr1\t13000000\t14000000\t14\n+chr1\t14000000\t15000000\t15\n+chr1\t15000000\t16000000\t16\n+chr1\t16000000\t17000000\t17\n+chr1\t17000000\t18000000\t18\n+chr1\t18000000\t19000000\t19\n+chr1\t19000000\t20000000\t20\n+chr1\t20000000\t21000000\t21\n+chr1\t21000000\t22000000\t22\n+chr1\t22000000\t23000000\t23\n+chr1\t23000000\t24000000\t24\n+chr1\t24000000\t25000000\t25\n+chr1\t25000000\t26000000\t26\n+chr1\t26000000\t27000000\t27\n+chr1\t27000000\t28000000\t28\n+chr1\t28000000\t29000000\t29\n+chr1\t29000000\t30000000\t30\n+chr1\t30000000\t31000000\t31\n+chr1\t31000000\t32000000\t32\n+chr1\t32000000\t33000000\t33\n+chr1\t33000000\t34000000\t34\n+chr1\t34000000\t35000000\t35\n+chr1\t35000000\t36000000\t36\n+chr1\t36000000\t37000000\t37\n+chr1\t37000000\t38000000\t38\n+chr1\t38000000\t39000000\t39\n+chr1\t39000000\t40000000\t40\n+chr1\t40000000\t41000000\t41\n+chr1\t41000000\t42000000\t42\n+chr1\t42000000\t43000000\t43\n+chr1\t43000000\t44000000\t44\n+chr1\t44000000\t45000000\t45\n+chr1\t45000000\t46000000\t46\n+chr1\t46000000\t47000000\t47\n+chr1\t47000000\t48000000\t48\n+chr1\t48000000\t49000000\t49\n+chr1\t49000000\t50000000\t50\n+chr1\t50000000\t51000000\t51\n+chr1\t51000000\t52000000\t52\n+chr1\t52000000\t53000000\t53\n+chr1\t53000000\t54000000\t54\n+chr1\t54000000\t55000000\t55\n+chr1\t55000000\t56000000\t56\n+chr1\t56000000\t57000000\t57\n+chr1\t57000000\t58000000\t58\n+chr1\t58000000\t59000000\t59\n+chr1\t59000000\t60000000\t60\n+chr1\t60000000\t61000000\t61\n+chr1\t61000000\t62000000\t62\n+chr1\t62000000\t63000000\t63\n+chr1\t63000000\t64000000\t64\n+chr1\t64000000\t65000000\t65\n+chr1\t65000000\t66000000\t66\n+chr1\t66000000\t67000000\t67\n+chr1\t67000000\t68000000\t68\n+chr1\t68000000\t69000000\t69\n+chr1\t69000000\t70000000\t70\n+chr1\t70000000\t71000000\t71\n+chr1\t71000000\t72000000\t72\n+chr1\t72000000\t73000000\t73\n+chr1\t73000000\t74000000\t74\n+chr1\t74000000\t75000000\t75\n+chr1\t75000000\t76000000\t76\n+chr1\t76000000\t77000000\t77\n+chr1\t77000000\t78000000\t78\n+chr1\t78000000\t79000000\t79\n+chr1\t79000000\t80000000\t80\n+chr1\t80000000\t81000000\t81\n+chr1\t81000000\t82000000\t82\n+chr1\t82000000\t83000000\t83\n+chr1\t83000000\t84000000\t84\n+chr1\t84000000\t85000000\t85\n+chr1\t85000000\t86000000\t86\n+chr1\t86000000\t87000000\t87\n+chr1\t87000000\t88000000\t88\n+chr1\t88000000\t89000000\t89\n+chr1\t89000000\t90000000\t90\n+chr1\t90000000\t91000000\t91\n+chr1\t91000000\t92000000\t92\n+chr1\t92000000\t93000000\t93\n+chr1\t93000000\t94000000\t94\n+chr1\t94000000\t95000000\t95\n+chr1\t95000000\t96000000\t96\n+chr1\t96000000\t97000000\t97\n+chr1\t97000000\t98000000\t98\n+chr1\t98000000\t99000000\t99\n+chr1\t99000000\t100000000\t100\n+chr1\t100000000\t101000000\t101\n+chr1\t101000000\t102000000\t102\n+chr1\t102000000\t103000000\t103\n+chr1\t103000000\t104000000\t104\n+chr1\t104000000\t105000000\t105\n+chr1\t105000000\t106000000\t106\n+chr1\t106000000\t107000000\t107\n+chr1\t107000000\t108000000\t108\n+chr1\t108000000\t109000000\t109\n+chr1\t109000000\t110000000\t110\n+chr1\t110000000\t111000000\t111\n+chr1\t111000000\t112000000\t112\n+chr1\t112000000\t113000000\t113\n+chr1\t113000000\t114000000\t114\n+chr1\t114000000\t115000000\t115\n+chr1\t115000000\t116000000\t116\n+chr1\t116000000\t117000000\t117\n+chr1\t117000000\t118000000\t118\n+chr1\t118000000\t119000000\t119\n+chr1\t119000000\t120000000\t120\n+chr1\t120000000\t121000000\t121\n+chr1\t121000000\t122000000\t122\n+chr1\t122000000\t123000000\t123\n+chr1\t123000000\t124000000\t124\n+chr1\t124000000\t125000000\t125\n+chr1\t125000000\t126000000\t126\n+chr1\t126000000\t127000000\t127\n+chr1\t127000000\t128000000\t128\n+chr1\t128000000\t129000000\t129\n+chr1\t129000000\t130000000\t130\n+chr1\t130000000\t131000000\t131\n+chr1\t131000000\t132000000\t132\n+chr1\t132000000\t133000000\t133\n+chr1\t133000000\t134000000\t134\n+chr1\t134000000\t135000000\t135\n+chr1\t135000000\t136000000\t136\n+chr1\t136000000\t137000000\t137\n+chr1\t137000000\t138000000\t138\n+chr1\t138000000\t139000000\t139\n+chr1\t139000000\t140000000\t140\n+chr1\t140000000\t141000000\t141\n+chr1\t141000000\t142000000\t142\n+chr1\t142000000\t143000000\t143\n+chr1\t143000000\t144000'..b'\t2979\n+chrX\t82000000\t83000000\t2980\n+chrX\t83000000\t84000000\t2981\n+chrX\t84000000\t85000000\t2982\n+chrX\t85000000\t86000000\t2983\n+chrX\t86000000\t87000000\t2984\n+chrX\t87000000\t88000000\t2985\n+chrX\t88000000\t89000000\t2986\n+chrX\t89000000\t90000000\t2987\n+chrX\t90000000\t91000000\t2988\n+chrX\t91000000\t92000000\t2989\n+chrX\t92000000\t93000000\t2990\n+chrX\t93000000\t94000000\t2991\n+chrX\t94000000\t95000000\t2992\n+chrX\t95000000\t96000000\t2993\n+chrX\t96000000\t97000000\t2994\n+chrX\t97000000\t98000000\t2995\n+chrX\t98000000\t99000000\t2996\n+chrX\t99000000\t100000000\t2997\n+chrX\t100000000\t101000000\t2998\n+chrX\t101000000\t102000000\t2999\n+chrX\t102000000\t103000000\t3000\n+chrX\t103000000\t104000000\t3001\n+chrX\t104000000\t105000000\t3002\n+chrX\t105000000\t106000000\t3003\n+chrX\t106000000\t107000000\t3004\n+chrX\t107000000\t108000000\t3005\n+chrX\t108000000\t109000000\t3006\n+chrX\t109000000\t110000000\t3007\n+chrX\t110000000\t111000000\t3008\n+chrX\t111000000\t112000000\t3009\n+chrX\t112000000\t113000000\t3010\n+chrX\t113000000\t114000000\t3011\n+chrX\t114000000\t115000000\t3012\n+chrX\t115000000\t116000000\t3013\n+chrX\t116000000\t117000000\t3014\n+chrX\t117000000\t118000000\t3015\n+chrX\t118000000\t119000000\t3016\n+chrX\t119000000\t120000000\t3017\n+chrX\t120000000\t121000000\t3018\n+chrX\t121000000\t122000000\t3019\n+chrX\t122000000\t123000000\t3020\n+chrX\t123000000\t124000000\t3021\n+chrX\t124000000\t125000000\t3022\n+chrX\t125000000\t126000000\t3023\n+chrX\t126000000\t127000000\t3024\n+chrX\t127000000\t128000000\t3025\n+chrX\t128000000\t129000000\t3026\n+chrX\t129000000\t130000000\t3027\n+chrX\t130000000\t131000000\t3028\n+chrX\t131000000\t132000000\t3029\n+chrX\t132000000\t133000000\t3030\n+chrX\t133000000\t134000000\t3031\n+chrX\t134000000\t135000000\t3032\n+chrX\t135000000\t136000000\t3033\n+chrX\t136000000\t137000000\t3034\n+chrX\t137000000\t138000000\t3035\n+chrX\t138000000\t139000000\t3036\n+chrX\t139000000\t140000000\t3037\n+chrX\t140000000\t141000000\t3038\n+chrX\t141000000\t142000000\t3039\n+chrX\t142000000\t143000000\t3040\n+chrX\t143000000\t144000000\t3041\n+chrX\t144000000\t145000000\t3042\n+chrX\t145000000\t146000000\t3043\n+chrX\t146000000\t147000000\t3044\n+chrX\t147000000\t148000000\t3045\n+chrX\t148000000\t149000000\t3046\n+chrX\t149000000\t150000000\t3047\n+chrX\t150000000\t151000000\t3048\n+chrX\t151000000\t152000000\t3049\n+chrX\t152000000\t153000000\t3050\n+chrX\t153000000\t154000000\t3051\n+chrX\t154000000\t155000000\t3052\n+chrX\t155000000\t155270560\t3053\n+chrY\t0\t1000000\t3054\n+chrY\t1000000\t2000000\t3055\n+chrY\t2000000\t3000000\t3056\n+chrY\t3000000\t4000000\t3057\n+chrY\t4000000\t5000000\t3058\n+chrY\t5000000\t6000000\t3059\n+chrY\t6000000\t7000000\t3060\n+chrY\t7000000\t8000000\t3061\n+chrY\t8000000\t9000000\t3062\n+chrY\t9000000\t10000000\t3063\n+chrY\t10000000\t11000000\t3064\n+chrY\t11000000\t12000000\t3065\n+chrY\t12000000\t13000000\t3066\n+chrY\t13000000\t14000000\t3067\n+chrY\t14000000\t15000000\t3068\n+chrY\t15000000\t16000000\t3069\n+chrY\t16000000\t17000000\t3070\n+chrY\t17000000\t18000000\t3071\n+chrY\t18000000\t19000000\t3072\n+chrY\t19000000\t20000000\t3073\n+chrY\t20000000\t21000000\t3074\n+chrY\t21000000\t22000000\t3075\n+chrY\t22000000\t23000000\t3076\n+chrY\t23000000\t24000000\t3077\n+chrY\t24000000\t25000000\t3078\n+chrY\t25000000\t26000000\t3079\n+chrY\t26000000\t27000000\t3080\n+chrY\t27000000\t28000000\t3081\n+chrY\t28000000\t29000000\t3082\n+chrY\t29000000\t30000000\t3083\n+chrY\t30000000\t31000000\t3084\n+chrY\t31000000\t32000000\t3085\n+chrY\t32000000\t33000000\t3086\n+chrY\t33000000\t34000000\t3087\n+chrY\t34000000\t35000000\t3088\n+chrY\t35000000\t36000000\t3089\n+chrY\t36000000\t37000000\t3090\n+chrY\t37000000\t38000000\t3091\n+chrY\t38000000\t39000000\t3092\n+chrY\t39000000\t40000000\t3093\n+chrY\t40000000\t41000000\t3094\n+chrY\t41000000\t42000000\t3095\n+chrY\t42000000\t43000000\t3096\n+chrY\t43000000\t44000000\t3097\n+chrY\t44000000\t45000000\t3098\n+chrY\t45000000\t46000000\t3099\n+chrY\t46000000\t47000000\t3100\n+chrY\t47000000\t48000000\t3101\n+chrY\t48000000\t49000000\t3102\n+chrY\t49000000\t50000000\t3103\n+chrY\t50000000\t51000000\t3104\n+chrY\t51000000\t52000000\t3105\n+chrY\t52000000\t53000000\t3106\n+chrY\t53000000\t54000000\t3107\n+chrY\t54000000\t55000000\t3108\n+chrY\t55000000\t56000000\t3109\n+chrY\t56000000\t57000000\t3110\n+chrY\t57000000\t58000000\t3111\n+chrY\t58000000\t59000000\t3112\n+chrY\t59000000\t59373566\t3113\n+chrM\t0\t16571\t3114\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCorrectMatrix/diagnostic_plot.png
b
Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5
b
Binary file test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCorrelate_heatmap_result1.png
b
Binary file test-data/hicCorrelate_heatmap_result1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicCorrelate_scatter_result1.png
b
Binary file test-data/hicCorrelate_scatter_result1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicFindRestrictionSites/reference_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/reference_genome.fasta Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,2 @@
+>chr1
+CTACGGTACGAACGTACGGTACGcgtaCGNAGTCATG
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicFindRestrictionSites/restriction_sites.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/restriction_sites.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,4 @@
+chr1 5 9 . 0 +
+chr1 13 17 . 0 +
+chr1 18 22 . 0 +
+chr1 24 28 . 0 +
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicInfo/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.3
+File: matrix_name.h5
+Size: 33,754
+Bin_length: 5000
+Sum of matrix: 35778.0
+Chromosomes: chr2L, chr2LHet, chr2R, chr2RHet, chr3L, chr3LHet, chr3R, chr3RHet, chr4, chrM, chrUextra, chrU, chrX, chrXHet, chrYHet
+Non-zero elements: 69,213
+Minimum (non zero): 1
+Maximum: 8
+NaN bins: 0
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo_output.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,10 @@
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.1
+File: matrix_name.h5
+Size: 3,383
+Bin_length: 50000
+Sum of matrix: 32798.5
+Chromosomes: chr2RHet, chr3RHet, chr2LHet, chr4, chrYHet, chr3L, chr2L, chrU, chrX, chrXHet, chr2R, chr3R, chrUextra, chrM, chr3LHet
+Non-zero elements: 45,981
+Minimum (non zero): 1
+Maximum: 68
+NaN bins: 664
\ No newline at end of file
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicMergeLoops/gm12878_10kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_10kb.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,1028 @@\n+1\t10000\t20000\t1\t250000\t260000\t0.001\n+1\t140000\t150000\t1\t680000\t690000\t0.001\n+1\t540000\t550000\t1\t640000\t650000\t0.001\n+1\t630000\t640000\t1\t1140000\t1150000\t0.001\n+1\t1050000\t1060000\t1\t1180000\t1190000\t0.001\n+1\t1310000\t1320000\t1\t1410000\t1420000\t0.001\n+1\t1710000\t1720000\t1\t1830000\t1840000\t0.001\n+1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407135\n+1\t2120000\t2130000\t1\t2310000\t2320000\t0.001\n+1\t2110000\t2120000\t1\t2710000\t2720000\t0.001\n+1\t2080000\t2090000\t1\t3330000\t3340000\t0.001\n+1\t2130000\t2140000\t1\t3570000\t3580000\t0.001\n+1\t2120000\t2130000\t1\t2480000\t2490000\t0.001\n+1\t2480000\t2490000\t1\t3570000\t3580000\t0.001\n+1\t2340000\t2350000\t1\t3340000\t3350000\t0.001\n+1\t2340000\t2350000\t1\t2480000\t2490000\t0.001\n+1\t2590000\t2600000\t1\t3300000\t3310000\t0.001\n+1\t2580000\t2590000\t1\t2680000\t2690000\t0.001\n+1\t2600000\t2610000\t1\t3170000\t3180000\t0.001\n+1\t2850000\t2860000\t1\t4400000\t4410000\t0.001\n+1\t2860000\t2870000\t1\t4770000\t4780000\t0.001\n+1\t2850000\t2860000\t1\t4160000\t4170000\t0.001\n+1\t3070000\t3080000\t1\t4190000\t4200000\t0.001\n+1\t3110000\t3120000\t1\t4480000\t4490000\t0.001\n+1\t3240000\t3250000\t1\t4220000\t4230000\t0.001\n+1\t3290000\t3300000\t1\t4380000\t4390000\t0.001\n+1\t3400000\t3410000\t1\t3530000\t3540000\t0.001\n+1\t3540000\t3550000\t1\t3640000\t3650000\t0.001\n+1\t3820000\t3830000\t1\t5510000\t5520000\t0.001\n+1\t3820000\t3830000\t1\t4880000\t4890000\t0.001\n+1\t3820000\t3830000\t1\t5800000\t5810000\t0.001\n+1\t3830000\t3840000\t1\t4710000\t4720000\t0.001\n+1\t3840000\t3850000\t1\t3990000\t4000000\t0.001\n+1\t3840000\t3850000\t1\t4430000\t4440000\t0.001\n+1\t4190000\t4200000\t1\t5430000\t5440000\t0.001\n+1\t4010000\t4020000\t1\t5790000\t5800000\t0.001\n+1\t4150000\t4160000\t1\t5660000\t5670000\t0.001\n+1\t4710000\t4720000\t1\t4880000\t4890000\t0.001\n+1\t4280000\t4290000\t1\t5250000\t5260000\t0.001\n+1\t5570000\t5580000\t1\t5970000\t5980000\t0.001\n+1\t6770000\t6780000\t1\t7700000\t7710000\t0.001\n+1\t6540000\t6550000\t1\t6700000\t6710000\t0.001\n+1\t6530000\t6540000\t1\t7270000\t7280000\t0.001\n+1\t6780000\t6790000\t1\t7130000\t7140000\t0.001\n+1\t6770000\t6780000\t1\t7270000\t7280000\t0.001\n+1\t6850000\t6860000\t1\t6950000\t6960000\t0.001\n+1\t7100000\t7110000\t1\t7700000\t7710000\t0.001\n+1\t7450000\t7460000\t1\t7550000\t7560000\t0.001\n+1\t7860000\t7870000\t1\t7960000\t7970000\t0.001\n+1\t8080000\t8090000\t1\t8370000\t8380000\t0.001\n+1\t8050000\t8060000\t1\t8800000\t8810000\t0.001\n+1\t8140000\t8150000\t1\t8240000\t8250000\t0.001\n+1\t8620000\t8630000\t1\t8730000\t8740000\t0.001\n+1\t8480000\t8490000\t1\t8580000\t8590000\t0.001\n+1\t8800000\t8810000\t1\t8900000\t8910000\t0.001\n+1\t8960000\t8970000\t1\t9060000\t9070000\t0.001\n+1\t9010000\t9020000\t1\t9520000\t9530000\t0.001\n+1\t9340000\t9350000\t1\t9510000\t9520000\t0.001\n+1\t9650000\t9660000\t1\t10460000\t10470000\t0.001\n+1\t9680000\t9690000\t1\t9780000\t9790000\t0.001\n+1\t9830000\t9840000\t1\t9930000\t9940000\t0.001\n+1\t10270000\t10280000\t1\t10390000\t10400000\t0.001\n+1\t10560000\t10570000\t1\t11700000\t11710000\t0.001\n+1\t10560000\t10570000\t1\t10920000\t10930000\t0.001\n+1\t10580000\t10590000\t1\t10680000\t10690000\t0.001\n+1\t11090000\t11100000\t1\t11700000\t11710000\t0.001\n+1\t11170000\t11180000\t1\t11270000\t11280000\t0.001\n+1\t11390000\t11400000\t1\t11700000\t11710000\t0.001\n+1\t12170000\t12180000\t1\t12270000\t12280000\t0.001\n+1\t12370000\t12380000\t1\t12670000\t12680000\t0.001\n+1\t12400000\t12410000\t1\t13470000\t13480000\t0.001\n+1\t12600000\t12610000\t1\t13160000\t13170000\t0.001\n+1\t13110000\t13120000\t1\t13630000\t13640000\t0.001\n+1\t13010000\t13020000\t1\t13120000\t13130000\t0.001\n+1\t13030000\t13040000\t1\t13320000\t13330000\t0.001\n+1\t12960000\t12970000\t1\t14300000\t14310000\t0.001\n+1\t13160000\t13170000\t1\t14520000\t14530000\t0.001\n+1\t13320000\t13330000\t1\t13440000\t13450000\t0.001\n+1\t13350000\t13360000\t1\t13630000\t13640000\t0.00899288810192917\n+1\t13500000\t13510000\t1\t13720000\t13730000\t0.001\n+1\t13690000\t13700000\t1\t15390000\t15400000\t0.001\n+1\t13990000\t14000000\t1\t14130000\t14140000\t0.001\n+1\t13990000\t14000000\t1\t14280000\t14290000\t0.001\n+1\t14280000\t14290000\t1\t15370000\t15380000\t0.001\n+1\t14150000\t14160000\t1\t14280000\t14290000\t0.001\n+1\t14420000\t14430000\t1\t15620000\t15630000\t0.001\n+1\t14430000\t14440000\t1\t14890000\t14900000\t0.001\n+1\t14430000\t14440000\t1\t15370000\t15380000\t0.001\n+1\t14940000\t14950000\t1\t15050000\t15060000\t0.001\n+1\t14720000\t14730000\t1\t15'..b'0.001\n+1\t229860000\t229870000\t1\t229970000\t229980000\t0.001\n+1\t230240000\t230250000\t1\t230340000\t230350000\t0.001\n+1\t230770000\t230780000\t1\t231740000\t231750000\t0.033738281836102446\n+1\t231050000\t231060000\t1\t231340000\t231350000\t0.001\n+1\t231060000\t231070000\t1\t231730000\t231740000\t0.001\n+1\t231490000\t231500000\t1\t231720000\t231730000\t0.001\n+1\t231990000\t232000000\t1\t233140000\t233150000\t0.001\n+1\t232000000\t232010000\t1\t232760000\t232770000\t0.001\n+1\t232000000\t232010000\t1\t233370000\t233380000\t0.001\n+1\t232770000\t232780000\t1\t233370000\t233380000\t0.001\n+1\t232770000\t232780000\t1\t233160000\t233170000\t0.001\n+1\t233480000\t233490000\t1\t234460000\t234470000\t0.001\n+1\t233730000\t233740000\t1\t234380000\t234390000\t0.001\n+1\t233530000\t233540000\t1\t234200000\t234210000\t0.001\n+1\t233570000\t233580000\t1\t233920000\t233930000\t0.001\n+1\t233620000\t233630000\t1\t233720000\t233730000\t0.001\n+1\t234340000\t234350000\t1\t234440000\t234450000\t0.001\n+1\t234610000\t234620000\t1\t235580000\t235590000\t0.001\n+1\t234630000\t234640000\t1\t235240000\t235250000\t0.001\n+1\t234630000\t234640000\t1\t235140000\t235150000\t0.001\n+1\t234630000\t234640000\t1\t234730000\t234740000\t0.001\n+1\t234740000\t234750000\t1\t234860000\t234870000\t0.001\n+1\t234860000\t234870000\t1\t234970000\t234980000\t0.001\n+1\t235140000\t235150000\t1\t235240000\t235250000\t0.001\n+1\t235410000\t235420000\t1\t235570000\t235580000\t0.001\n+1\t235670000\t235680000\t1\t235940000\t235950000\t0.001\n+1\t235670000\t235680000\t1\t236130000\t236140000\t0.001\n+1\t236020000\t236030000\t1\t236130000\t236140000\t0.001\n+1\t236270000\t236280000\t1\t236650000\t236660000\t0.001\n+1\t236320000\t236330000\t1\t236440000\t236450000\t0.001\n+1\t236260000\t236270000\t1\t237030000\t237040000\t0.001\n+1\t236770000\t236780000\t1\t237720000\t237730000\t0.001\n+1\t236770000\t236780000\t1\t237540000\t237550000\t0.001\n+1\t236920000\t236930000\t1\t237720000\t237730000\t0.001\n+1\t236910000\t236920000\t1\t237540000\t237550000\t0.001\n+1\t237080000\t237090000\t1\t237730000\t237740000\t0.001\n+1\t238010000\t238020000\t1\t239100000\t239110000\t0.001\n+1\t238400000\t238410000\t1\t240050000\t240060000\t0.001\n+1\t238610000\t238620000\t1\t240070000\t240080000\t0.001\n+1\t239570000\t239580000\t1\t240050000\t240060000\t0.001\n+1\t240890000\t240900000\t1\t241640000\t241650000\t0.001\n+1\t241050000\t241060000\t1\t241650000\t241660000\t0.001\n+1\t241770000\t241780000\t1\t242000000\t242010000\t0.001\n+1\t241690000\t241700000\t1\t241790000\t241800000\t0.001\n+1\t242180000\t242190000\t1\t243200000\t243210000\t0.001\n+1\t242630000\t242640000\t1\t243490000\t243500000\t0.001\n+1\t242630000\t242640000\t1\t243180000\t243190000\t0.001\n+1\t242810000\t242820000\t1\t243490000\t243500000\t0.001\n+1\t243370000\t243380000\t1\t243470000\t243480000\t0.001\n+1\t243220000\t243230000\t1\t244120000\t244130000\t0.001\n+1\t243500000\t243510000\t1\t244430000\t244440000\t0.001\n+1\t243510000\t243520000\t1\t243910000\t243920000\t0.001\n+1\t243870000\t243880000\t1\t244430000\t244440000\t0.001\n+1\t244160000\t244170000\t1\t244270000\t244280000\t0.001\n+1\t244760000\t244770000\t1\t245200000\t245210000\t0.001\n+1\t244760000\t244770000\t1\t244960000\t244970000\t0.001\n+1\t245310000\t245320000\t1\t246160000\t246170000\t0.001\n+1\t245310000\t245320000\t1\t246860000\t246870000\t0.001\n+1\t245310000\t245320000\t1\t246610000\t246620000\t0.001\n+1\t245310000\t245320000\t1\t246440000\t246450000\t0.001\n+1\t245400000\t245410000\t1\t245500000\t245510000\t0.001\n+1\t245680000\t245690000\t1\t246620000\t246630000\t0.001\n+1\t245820000\t245830000\t1\t246600000\t246610000\t0.001\n+1\t246170000\t246180000\t1\t246610000\t246620000\t0.001\n+1\t246050000\t246060000\t1\t246160000\t246170000\t0.001\n+1\t246490000\t246500000\t1\t246590000\t246600000\t0.001\n+1\t246170000\t246180000\t1\t246880000\t246890000\t0.001\n+1\t246660000\t246670000\t1\t246860000\t246870000\t0.001\n+1\t247190000\t247200000\t1\t247300000\t247310000\t0.001\n+1\t247370000\t247380000\t1\t247490000\t247500000\t0.001\n+1\t247550000\t247560000\t1\t247650000\t247660000\t0.001\n+1\t247840000\t247850000\t1\t249100000\t249110000\t0.001\n+1\t248080000\t248090000\t1\t248240000\t248250000\t0.001\n+1\t248090000\t248100000\t1\t249100000\t249110000\t0.001\n+1\t248600000\t248610000\t1\t248810000\t248820000\t0.001\n+1\t248400000\t248410000\t1\t249100000\t249110000\t0.001\n+1\t248560000\t248570000\t1\t249100000\t249110000\t0.001\n+1\t248900000\t248910000\t1\t249070000\t249080000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicMergeLoops/gm12878_25kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_25kb.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,402 @@\n+1\t1050000\t1075000\t1\t1175000\t1200000\t0.001\n+1\t2325000\t2350000\t1\t3325000\t3350000\t0.001\n+1\t2125000\t2150000\t1\t2300000\t2325000\t0.001\n+1\t2875000\t2900000\t1\t4350000\t4375000\t0.001\n+1\t3525000\t3550000\t1\t3625000\t3650000\t0.001\n+1\t4775000\t4800000\t1\t4875000\t4900000\t0.001\n+1\t4275000\t4300000\t1\t4375000\t4400000\t0.001\n+1\t5100000\t5125000\t1\t5200000\t5225000\t0.001\n+1\t5675000\t5700000\t1\t5775000\t5800000\t0.001\n+1\t5875000\t5900000\t1\t7200000\t7225000\t0.001\n+1\t6300000\t6325000\t1\t6400000\t6425000\t0.001\n+1\t6850000\t6875000\t1\t6950000\t6975000\t0.001\n+1\t7400000\t7425000\t1\t7500000\t7525000\t0.001\n+1\t7850000\t7875000\t1\t7950000\t7975000\t0.001\n+1\t8075000\t8100000\t1\t8350000\t8375000\t0.001\n+1\t8625000\t8650000\t1\t8725000\t8750000\t0.001\n+1\t9325000\t9350000\t1\t9525000\t9550000\t0.001\n+1\t9825000\t9850000\t1\t9925000\t9950000\t0.001\n+1\t10275000\t10300000\t1\t10375000\t10400000\t0.001\n+1\t12175000\t12200000\t1\t12275000\t12300000\t0.001\n+1\t12350000\t12375000\t1\t12675000\t12700000\t0.001\n+1\t12975000\t13000000\t1\t13375000\t13400000\t0.001\n+1\t13100000\t13125000\t1\t14300000\t14325000\t0.001\n+1\t13550000\t13575000\t1\t14325000\t14350000\t0.001\n+1\t13475000\t13500000\t1\t13700000\t13725000\t0.001\n+1\t13975000\t14000000\t1\t14125000\t14150000\t0.001\n+1\t14425000\t14450000\t1\t15350000\t15375000\t0.001\n+1\t15475000\t15500000\t1\t15575000\t15600000\t0.001\n+1\t16125000\t16150000\t1\t16225000\t16250000\t0.001\n+1\t16975000\t17000000\t1\t17075000\t17100000\t0.001\n+1\t17450000\t17475000\t1\t17550000\t17575000\t0.001\n+1\t17825000\t17850000\t1\t17925000\t17950000\t0.001\n+1\t19800000\t19825000\t1\t19900000\t19925000\t0.001\n+1\t18925000\t18950000\t1\t19125000\t19150000\t0.001\n+1\t19225000\t19250000\t1\t19400000\t19425000\t0.001\n+1\t20225000\t20250000\t1\t20475000\t20500000\t0.001\n+1\t20525000\t20550000\t1\t20800000\t20825000\t0.001\n+1\t21100000\t21125000\t1\t22350000\t22375000\t0.001\n+1\t21575000\t21600000\t1\t21675000\t21700000\t0.0010553575253769208\n+1\t22150000\t22175000\t1\t22250000\t22275000\t0.001\n+1\t22450000\t22475000\t1\t22600000\t22625000\t0.001\n+1\t22725000\t22750000\t1\t22950000\t22975000\t0.001\n+1\t23025000\t23050000\t1\t23200000\t23225000\t0.001\n+1\t23400000\t23425000\t1\t23500000\t23525000\t0.001\n+1\t23850000\t23875000\t1\t23950000\t23975000\t0.001\n+1\t24125000\t24150000\t1\t24225000\t24250000\t0.001\n+1\t24325000\t24350000\t1\t26075000\t26100000\t0.001\n+1\t25000000\t25025000\t1\t25150000\t25175000\t0.001\n+1\t24525000\t24550000\t1\t24700000\t24725000\t0.001\n+1\t25925000\t25950000\t1\t26100000\t26125000\t0.001\n+1\t26575000\t26600000\t1\t26675000\t26700000\t0.001\n+1\t26925000\t26950000\t1\t27100000\t27125000\t0.001\n+1\t27425000\t27450000\t1\t27600000\t27625000\t0.001\n+1\t28825000\t28850000\t1\t28925000\t28950000\t0.001\n+1\t29200000\t29225000\t1\t29350000\t29375000\t0.001\n+1\t29550000\t29575000\t1\t31175000\t31200000\t0.001\n+1\t30425000\t30450000\t1\t30525000\t30550000\t0.001\n+1\t31250000\t31275000\t1\t31375000\t31400000\t0.001\n+1\t31900000\t31925000\t1\t32000000\t32025000\t0.001\n+1\t32675000\t32700000\t1\t32775000\t32800000\t0.001\n+1\t32975000\t33000000\t1\t33075000\t33100000\t0.001\n+1\t33400000\t33425000\t1\t33500000\t33525000\t0.001\n+1\t33825000\t33850000\t1\t33925000\t33950000\t0.001\n+1\t34100000\t34125000\t1\t35200000\t35225000\t0.001\n+1\t34300000\t34325000\t1\t34400000\t34425000\t0.001\n+1\t34925000\t34950000\t1\t35050000\t35075000\t0.001\n+1\t35650000\t35675000\t1\t35750000\t35775000\t0.001\n+1\t36775000\t36800000\t1\t36875000\t36900000\t0.001\n+1\t37325000\t37350000\t1\t37425000\t37450000\t0.001\n+1\t37675000\t37700000\t1\t37775000\t37800000\t0.001\n+1\t38050000\t38075000\t1\t38150000\t38175000\t0.001\n+1\t38325000\t38350000\t1\t38425000\t38450000\t0.001\n+1\t39550000\t39575000\t1\t39650000\t39675000\t0.0012254650005710432\n+1\t40375000\t40400000\t1\t40475000\t40500000\t0.001\n+1\t40600000\t40625000\t1\t40800000\t40825000\t0.001\n+1\t42100000\t42125000\t1\t42200000\t42225000\t0.001\n+1\t41775000\t41800000\t1\t41875000\t41900000\t0.001\n+1\t43025000\t43050000\t1\t43200000\t43225000\t0.001\n+1\t43375000\t43400000\t1\t43525000\t43550000\t0.001\n+1\t43700000\t43725000\t1\t43800000\t43825000\t0.001\n+1\t44225000\t44250000\t1\t44375000\t44400000\t0.001\n+1\t44825000\t44850000\t1\t45050000\t45075000\t0.001\n+1\t45475000\t45500000\t1\t45750000\t45775000\t0.001\n+1\t45800000\t45825000\t1\t45950000\t45975000\t0.001\n+1\t46150000\t46175000\t1\t46250000\t46275000\t0.001\n+1\t46500000\t46525000\t1\t466'..b'.001\n+1\t200575000\t200600000\t1\t200750000\t200775000\t0.001\n+1\t201525000\t201550000\t1\t201650000\t201675000\t0.001\n+1\t202450000\t202475000\t1\t202550000\t202575000\t0.001\n+1\t203000000\t203025000\t1\t203175000\t203200000\t0.001\n+1\t203100000\t203125000\t1\t204800000\t204825000\t0.001\n+1\t203300000\t203325000\t1\t203400000\t203425000\t0.001\n+1\t203825000\t203850000\t1\t204075000\t204100000\t0.001\n+1\t204125000\t204150000\t1\t204325000\t204350000\t0.001\n+1\t205350000\t205375000\t1\t205450000\t205475000\t0.001\n+1\t205875000\t205900000\t1\t206225000\t206250000\t0.001\n+1\t206150000\t206175000\t1\t206600000\t206625000\t0.001\n+1\t206125000\t206150000\t1\t207700000\t207725000\t0.001\n+1\t206650000\t206675000\t1\t206750000\t206775000\t0.001\n+1\t207250000\t207275000\t1\t207650000\t207675000\t0.001\n+1\t209250000\t209275000\t1\t209350000\t209375000\t0.001\n+1\t208050000\t208075000\t1\t208150000\t208175000\t0.001\n+1\t209750000\t209775000\t1\t209850000\t209875000\t0.001\n+1\t210300000\t210325000\t1\t210475000\t210500000\t0.001\n+1\t212000000\t212025000\t1\t212100000\t212125000\t0.001\n+1\t212225000\t212250000\t1\t212525000\t212550000\t0.001\n+1\t214500000\t214525000\t1\t215675000\t215700000\t0.001\n+1\t214975000\t215000000\t1\t215675000\t215700000\t0.001\n+1\t215100000\t215125000\t1\t215200000\t215225000\t0.001\n+1\t216475000\t216500000\t1\t217900000\t217925000\t0.001\n+1\t216475000\t216500000\t1\t218325000\t218350000\t0.001\n+1\t217650000\t217675000\t1\t217775000\t217800000\t0.001\n+1\t218500000\t218525000\t1\t219725000\t219750000\t0.001\n+1\t219250000\t219275000\t1\t219350000\t219375000\t0.001\n+1\t220175000\t220200000\t1\t220275000\t220300000\t0.001\n+1\t221000000\t221025000\t1\t222350000\t222375000\t0.001\n+1\t221225000\t221250000\t1\t221325000\t221350000\t0.001\n+1\t221625000\t221650000\t1\t223250000\t223275000\t0.001\n+1\t222650000\t222675000\t1\t224125000\t224150000\t0.001\n+1\t222950000\t222975000\t1\t223250000\t223275000\t0.001\n+1\t223700000\t223725000\t1\t223800000\t223825000\t0.001\n+1\t224000000\t224025000\t1\t224100000\t224125000\t0.001\n+1\t224300000\t224325000\t1\t224500000\t224525000\t0.001\n+1\t224875000\t224900000\t1\t225025000\t225050000\t0.001\n+1\t226400000\t226425000\t1\t226500000\t226525000\t0.001\n+1\t226700000\t226725000\t1\t228075000\t228100000\t0.001\n+1\t226800000\t226825000\t1\t227000000\t227025000\t0.001\n+1\t227750000\t227775000\t1\t227850000\t227875000\t0.001\n+1\t227825000\t227850000\t1\t228750000\t228775000\t0.001\n+1\t228575000\t228600000\t1\t228675000\t228700000\t0.001\n+1\t228800000\t228825000\t1\t229350000\t229375000\t0.001\n+1\t228750000\t228775000\t1\t230650000\t230675000\t0.001\n+1\t229375000\t229400000\t1\t230425000\t230450000\t0.001\n+1\t229375000\t229400000\t1\t229600000\t229625000\t0.001\n+1\t229775000\t229800000\t1\t230425000\t230450000\t0.001\n+1\t230225000\t230250000\t1\t230325000\t230350000\t0.001\n+1\t231050000\t231075000\t1\t231150000\t231175000\t0.0017961887465136447\n+1\t231475000\t231500000\t1\t231725000\t231750000\t0.001\n+1\t233525000\t233550000\t1\t234200000\t234225000\t0.001\n+1\t232950000\t232975000\t1\t233050000\t233075000\t0.001\n+1\t233550000\t233575000\t1\t233925000\t233950000\t0.001\n+1\t234325000\t234350000\t1\t234425000\t234450000\t0.001\n+1\t235400000\t235425000\t1\t235575000\t235600000\t0.001\n+1\t235675000\t235700000\t1\t235925000\t235950000\t0.001\n+1\t236000000\t236025000\t1\t236100000\t236125000\t0.001\n+1\t236925000\t236950000\t1\t237025000\t237050000\t0.001\n+1\t238000000\t238025000\t1\t239100000\t239125000\t0.001\n+1\t238025000\t238050000\t1\t240025000\t240050000\t0.001\n+1\t238225000\t238250000\t1\t238325000\t238350000\t0.001\n+1\t238400000\t238425000\t1\t240050000\t240075000\t0.001\n+1\t238825000\t238850000\t1\t238925000\t238950000\t0.001\n+1\t241325000\t241350000\t1\t241425000\t241450000\t0.001\n+1\t242175000\t242200000\t1\t243175000\t243200000\t0.001\n+1\t242925000\t242950000\t1\t243025000\t243050000\t0.001\n+1\t243500000\t243525000\t1\t244425000\t244450000\t0.001\n+1\t243350000\t243375000\t1\t243450000\t243475000\t0.001\n+1\t243725000\t243750000\t1\t243825000\t243850000\t0.001\n+1\t245300000\t245325000\t1\t246600000\t246625000\t0.001\n+1\t245300000\t245325000\t1\t246150000\t246175000\t0.001\n+1\t246050000\t246075000\t1\t246150000\t246175000\t0.001\n+1\t246650000\t246675000\t1\t246850000\t246875000\t0.001\n+1\t247200000\t247225000\t1\t247300000\t247325000\t0.001\n+1\t248625000\t248650000\t1\t248725000\t248750000\t0.001\n+1\t248550000\t248575000\t1\t249125000\t249150000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicMergeLoops/gm12878_5kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_5kb.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,323 @@\n+1\t80000\t85000\t1\t555000\t560000\t0.001\n+1\t135000\t140000\t1\t660000\t665000\t0.001\n+1\t605000\t610000\t1\t830000\t835000\t0.001\n+1\t2120000\t2125000\t1\t2320000\t2325000\t0.001\n+1\t2345000\t2350000\t1\t2700000\t2705000\t0.001\n+1\t3845000\t3850000\t1\t4110000\t4115000\t0.001\n+1\t6780000\t6785000\t1\t7130000\t7135000\t0.001\n+1\t8085000\t8090000\t1\t8375000\t8380000\t0.001\n+1\t8620000\t8625000\t1\t8900000\t8905000\t0.001\n+1\t9345000\t9350000\t1\t9550000\t9555000\t0.001\n+1\t9935000\t9940000\t1\t10485000\t10490000\t0.001\n+1\t10555000\t10560000\t1\t10925000\t10930000\t0.001\n+1\t10570000\t10575000\t1\t11000000\t11005000\t0.001\n+1\t11095000\t11100000\t1\t11700000\t11705000\t0.001\n+1\t11305000\t11310000\t1\t11700000\t11705000\t0.001\n+1\t11395000\t11400000\t1\t11700000\t11705000\t0.001\n+1\t12370000\t12375000\t1\t12675000\t12680000\t0.001\n+1\t12845000\t12850000\t1\t13450000\t13455000\t0.001\n+1\t12950000\t12955000\t1\t13630000\t13635000\t0.001\n+1\t13035000\t13040000\t1\t13325000\t13330000\t0.001\n+1\t12905000\t12910000\t1\t13180000\t13185000\t0.001\n+1\t13020000\t13025000\t1\t13485000\t13490000\t0.001\n+1\t13130000\t13135000\t1\t13335000\t13340000\t0.001\n+1\t13125000\t13130000\t1\t13505000\t13510000\t0.001\n+1\t13350000\t13355000\t1\t13630000\t13635000\t0.001\n+1\t13335000\t13340000\t1\t13540000\t13545000\t0.001\n+1\t13505000\t13510000\t1\t13725000\t13730000\t0.001\n+1\t16115000\t16120000\t1\t16380000\t16385000\t0.001\n+1\t16115000\t16120000\t1\t16320000\t16325000\t0.001\n+1\t16835000\t16840000\t1\t17065000\t17070000\t0.001\n+1\t16860000\t16865000\t1\t17195000\t17200000\t0.001\n+1\t16950000\t16955000\t1\t17270000\t17275000\t0.001\n+1\t20240000\t20245000\t1\t20475000\t20480000\t0.001\n+1\t20540000\t20545000\t1\t20820000\t20825000\t0.001\n+1\t21020000\t21025000\t1\t21520000\t21525000\t0.001\n+1\t21310000\t21315000\t1\t21520000\t21525000\t0.001\n+1\t22020000\t22025000\t1\t22285000\t22290000\t0.001\n+1\t22460000\t22465000\t1\t22960000\t22965000\t0.001\n+1\t23000000\t23005000\t1\t23255000\t23260000\t0.001\n+1\t23300000\t23305000\t1\t23510000\t23515000\t0.001\n+1\t24520000\t24525000\t1\t24720000\t24725000\t0.001\n+1\t24525000\t24530000\t1\t24960000\t24965000\t0.001\n+1\t25175000\t25180000\t1\t25530000\t25535000\t0.001\n+1\t25170000\t25175000\t1\t25425000\t25430000\t0.001\n+1\t25725000\t25730000\t1\t26130000\t26135000\t0.001\n+1\t25870000\t25875000\t1\t26135000\t26140000\t0.001\n+1\t25935000\t25940000\t1\t26135000\t26140000\t0.001\n+1\t26920000\t26925000\t1\t27120000\t27125000\t0.001\n+1\t27370000\t27375000\t1\t27610000\t27615000\t0.001\n+1\t27715000\t27720000\t1\t27930000\t27935000\t0.001\n+1\t29205000\t29210000\t1\t29525000\t29530000\t0.001\n+1\t33340000\t33345000\t1\t33550000\t33555000\t0.001\n+1\t36030000\t36035000\t1\t36240000\t36245000\t0.001\n+1\t38485000\t38490000\t1\t39300000\t39305000\t0.001\n+1\t39975000\t39980000\t1\t40235000\t40240000\t0.001\n+1\t40545000\t40550000\t1\t40800000\t40805000\t0.001\n+1\t41075000\t41080000\t1\t41310000\t41315000\t0.001\n+1\t42040000\t42045000\t1\t42635000\t42640000\t0.001\n+1\t43240000\t43245000\t1\t43535000\t43540000\t0.001\n+1\t43680000\t43685000\t1\t43880000\t43885000\t0.001\n+1\t43990000\t43995000\t1\t44400000\t44405000\t0.001\n+1\t43995000\t44000000\t1\t44510000\t44515000\t0.001\n+1\t45295000\t45300000\t1\t45765000\t45770000\t0.001\n+1\t45480000\t45485000\t1\t45765000\t45770000\t0.001\n+1\t45475000\t45480000\t1\t45960000\t45965000\t0.001\n+1\t45825000\t45830000\t1\t46035000\t46040000\t0.001\n+1\t47340000\t47345000\t1\t47555000\t47560000\t0.001\n+1\t47895000\t47900000\t1\t48175000\t48180000\t0.001\n+1\t50830000\t50835000\t1\t51165000\t51170000\t0.001\n+1\t51240000\t51245000\t1\t51650000\t51655000\t0.001\n+1\t51335000\t51340000\t1\t51655000\t51660000\t0.001\n+1\t54585000\t54590000\t1\t54955000\t54960000\t0.001\n+1\t59200000\t59205000\t1\t60160000\t60165000\t0.001\n+1\t59240000\t59245000\t1\t59750000\t59755000\t0.001\n+1\t62640000\t62645000\t1\t62870000\t62875000\t0.001\n+1\t62970000\t62975000\t1\t63210000\t63215000\t0.001\n+1\t64085000\t64090000\t1\t64705000\t64710000\t0.001\n+1\t64155000\t64160000\t1\t64600000\t64605000\t0.001\n+1\t65530000\t65535000\t1\t66155000\t66160000\t0.001\n+1\t65700000\t65705000\t1\t66150000\t66155000\t0.001\n+1\t66425000\t66430000\t1\t66910000\t66915000\t0.001\n+1\t66425000\t66430000\t1\t66705000\t66710000\t0.001\n+1\t66710000\t66715000\t1\t66910000\t66915000\t0.001\n+1\t67695000\t67700000\t1\t67965000\t67970000\t0.001\n+1\t68025000\t68030000\t1\t68225000\t68230000\t0.001\n+1\t68590000\t68595000\t1\t68805000\t68810000\t0'..b'5000\t182760000\t0.001\n+1\t182930000\t182935000\t1\t183190000\t183195000\t0.001\n+1\t183625000\t183630000\t1\t183880000\t183885000\t0.001\n+1\t184770000\t184775000\t1\t184970000\t184975000\t0.001\n+1\t185780000\t185785000\t1\t186180000\t186185000\t0.001\n+1\t186450000\t186455000\t1\t186950000\t186955000\t0.001\n+1\t186575000\t186580000\t1\t186955000\t186960000\t0.001\n+1\t192440000\t192445000\t1\t192985000\t192990000\t0.001\n+1\t192775000\t192780000\t1\t192985000\t192990000\t0.001\n+1\t196115000\t196120000\t1\t196625000\t196630000\t0.001\n+1\t197490000\t197495000\t1\t197890000\t197895000\t0.001\n+1\t198055000\t198060000\t1\t198325000\t198330000\t0.001\n+1\t198740000\t198745000\t1\t199210000\t199215000\t0.001\n+1\t198740000\t198745000\t1\t199430000\t199435000\t0.001\n+1\t198905000\t198910000\t1\t199210000\t199215000\t0.001\n+1\t199650000\t199655000\t1\t200470000\t200475000\t0.001\n+1\t200110000\t200115000\t1\t200460000\t200465000\t0.001\n+1\t200250000\t200255000\t1\t200455000\t200460000\t0.001\n+1\t200590000\t200595000\t1\t200800000\t200805000\t0.001\n+1\t201525000\t201530000\t1\t201760000\t201765000\t0.001\n+1\t203470000\t203475000\t1\t203670000\t203675000\t0.001\n+1\t203830000\t203835000\t1\t204095000\t204100000\t0.001\n+1\t204130000\t204135000\t1\t204330000\t204335000\t0.001\n+1\t204535000\t204540000\t1\t204775000\t204780000\t0.001\n+1\t205760000\t205765000\t1\t206230000\t206235000\t0.001\n+1\t205890000\t205895000\t1\t206230000\t206235000\t0.001\n+1\t205895000\t205900000\t1\t206330000\t206335000\t0.001\n+1\t206090000\t206095000\t1\t206535000\t206540000\t0.001\n+1\t206905000\t206910000\t1\t207155000\t207160000\t0.001\n+1\t207255000\t207260000\t1\t207580000\t207585000\t0.001\n+1\t207380000\t207385000\t1\t207705000\t207710000\t0.001\n+1\t210030000\t210035000\t1\t210480000\t210485000\t0.001\n+1\t210580000\t210585000\t1\t211305000\t211310000\t0.001\n+1\t210755000\t210760000\t1\t211305000\t211310000\t0.001\n+1\t211850000\t211855000\t1\t212200000\t212205000\t0.001\n+1\t212240000\t212245000\t1\t212465000\t212470000\t0.001\n+1\t212235000\t212240000\t1\t212625000\t212630000\t0.001\n+1\t212650000\t212655000\t1\t212955000\t212960000\t0.001\n+1\t212835000\t212840000\t1\t213165000\t213170000\t0.001\n+1\t212970000\t212975000\t1\t213170000\t213175000\t0.001\n+1\t221040000\t221045000\t1\t221610000\t221615000\t0.001\n+1\t221045000\t221050000\t1\t221375000\t221380000\t0.001\n+1\t221650000\t221655000\t1\t222340000\t222345000\t0.001\n+1\t224300000\t224305000\t1\t224520000\t224525000\t0.001\n+1\t224700000\t224705000\t1\t225040000\t225045000\t0.001\n+1\t224700000\t224705000\t1\t225110000\t225115000\t0.001\n+1\t224825000\t224830000\t1\t225040000\t225045000\t0.001\n+1\t225660000\t225665000\t1\t226095000\t226100000\t0.001\n+1\t225660000\t225665000\t1\t226160000\t226165000\t0.001\n+1\t225660000\t225665000\t1\t225955000\t225960000\t0.001\n+1\t226815000\t226820000\t1\t227015000\t227020000\t0.001\n+1\t227665000\t227670000\t1\t228140000\t228145000\t0.001\n+1\t228800000\t228805000\t1\t229360000\t229365000\t0.001\n+1\t229390000\t229395000\t1\t229615000\t229620000\t0.001\n+1\t231490000\t231495000\t1\t231725000\t231730000\t0.001\n+1\t232765000\t232770000\t1\t233375000\t233380000\t0.001\n+1\t233530000\t233535000\t1\t234200000\t234205000\t0.001\n+1\t233575000\t233580000\t1\t233925000\t233930000\t0.001\n+1\t234635000\t234640000\t1\t235245000\t235250000\t0.001\n+1\t234630000\t234635000\t1\t235145000\t235150000\t0.001\n+1\t234635000\t234640000\t1\t234975000\t234980000\t0.001\n+1\t234740000\t234745000\t1\t235105000\t235110000\t0.001\n+1\t235015000\t235020000\t1\t235245000\t235250000\t0.001\n+1\t235265000\t235270000\t1\t235575000\t235580000\t0.001\n+1\t235675000\t235680000\t1\t235945000\t235950000\t0.001\n+1\t235675000\t235680000\t1\t236135000\t236140000\t0.001\n+1\t236265000\t236270000\t1\t236650000\t236655000\t0.001\n+1\t241690000\t241695000\t1\t242005000\t242010000\t0.001\n+1\t242635000\t242640000\t1\t243175000\t243180000\t0.001\n+1\t243215000\t243220000\t1\t243485000\t243490000\t0.001\n+1\t243505000\t243510000\t1\t244435000\t244440000\t0.001\n+1\t244765000\t244770000\t1\t244965000\t244970000\t0.001\n+1\t244765000\t244770000\t1\t245205000\t245210000\t0.001\n+1\t244960000\t244965000\t1\t245205000\t245210000\t0.001\n+1\t245315000\t245320000\t1\t246165000\t246170000\t0.001\n+1\t246175000\t246180000\t1\t246610000\t246615000\t0.001\n+1\t246660000\t246665000\t1\t246860000\t246865000\t0.001\n+1\t248565000\t248570000\t1\t249100000\t249105000\t0.001\n+1\t248595000\t248600000\t1\t248820000\t248825000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicMergeLoops/gm12878_all.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,1256 @@\n+1\t10000\t20000\t1\t250000\t260000\t0.001\n+1\t80000\t85000\t1\t555000\t560000\t0.001\n+1\t140000\t150000\t1\t680000\t690000\t0.001\n+1\t540000\t550000\t1\t640000\t650000\t0.001\n+1\t605000\t610000\t1\t830000\t835000\t0.001\n+1\t630000\t640000\t1\t1140000\t1150000\t0.001\n+1\t1050000\t1075000\t1\t1175000\t1200000\t0.001\n+1\t1310000\t1320000\t1\t1410000\t1420000\t0.001\n+1\t1710000\t1720000\t1\t1830000\t1840000\t0.001\n+1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407133\n+1\t2080000\t2090000\t1\t3330000\t3340000\t0.001\n+1\t2110000\t2120000\t1\t2710000\t2720000\t0.001\n+1\t2120000\t2130000\t1\t2480000\t2490000\t0.001\n+1\t2125000\t2150000\t1\t2300000\t2325000\t0.001\n+1\t2130000\t2140000\t1\t3570000\t3580000\t0.001\n+1\t2325000\t2350000\t1\t3325000\t3350000\t0.001\n+1\t2340000\t2350000\t1\t2480000\t2490000\t0.001\n+1\t2345000\t2350000\t1\t2700000\t2705000\t0.001\n+1\t2480000\t2490000\t1\t3570000\t3580000\t0.001\n+1\t2580000\t2590000\t1\t2680000\t2690000\t0.001\n+1\t2590000\t2600000\t1\t3300000\t3310000\t0.001\n+1\t2600000\t2610000\t1\t3170000\t3180000\t0.001\n+1\t2850000\t2860000\t1\t4400000\t4410000\t0.001\n+1\t2850000\t2860000\t1\t4160000\t4170000\t0.001\n+1\t2860000\t2870000\t1\t4770000\t4780000\t0.001\n+1\t2875000\t2900000\t1\t4350000\t4375000\t0.001\n+1\t3070000\t3080000\t1\t4190000\t4200000\t0.001\n+1\t3110000\t3120000\t1\t4480000\t4490000\t0.001\n+1\t3240000\t3250000\t1\t4220000\t4230000\t0.001\n+1\t3290000\t3300000\t1\t4380000\t4390000\t0.001\n+1\t3400000\t3410000\t1\t3530000\t3540000\t0.001\n+1\t3525000\t3550000\t1\t3625000\t3650000\t0.001\n+1\t3820000\t3830000\t1\t5510000\t5520000\t0.001\n+1\t3820000\t3830000\t1\t4880000\t4890000\t0.001\n+1\t3820000\t3830000\t1\t5800000\t5810000\t0.001\n+1\t3830000\t3840000\t1\t4710000\t4720000\t0.001\n+1\t3840000\t3850000\t1\t3990000\t4000000\t0.001\n+1\t3840000\t3850000\t1\t4430000\t4440000\t0.001\n+1\t3845000\t3850000\t1\t4110000\t4115000\t0.001\n+1\t4010000\t4020000\t1\t5790000\t5800000\t0.001\n+1\t4150000\t4160000\t1\t5660000\t5670000\t0.001\n+1\t4190000\t4200000\t1\t5430000\t5440000\t0.001\n+1\t4275000\t4300000\t1\t4375000\t4400000\t0.001\n+1\t4280000\t4290000\t1\t5250000\t5260000\t0.001\n+1\t4710000\t4720000\t1\t4880000\t4890000\t0.001\n+1\t4775000\t4800000\t1\t4875000\t4900000\t0.001\n+1\t5100000\t5125000\t1\t5200000\t5225000\t0.001\n+1\t5570000\t5580000\t1\t5970000\t5980000\t0.001\n+1\t5675000\t5700000\t1\t5775000\t5800000\t0.001\n+1\t5875000\t5900000\t1\t7200000\t7225000\t0.001\n+1\t6300000\t6325000\t1\t6400000\t6425000\t0.001\n+1\t6530000\t6540000\t1\t7270000\t7280000\t0.001\n+1\t6540000\t6550000\t1\t6700000\t6710000\t0.001\n+1\t6770000\t6780000\t1\t7270000\t7280000\t0.001\n+1\t6770000\t6780000\t1\t7700000\t7710000\t0.001\n+1\t6780000\t6790000\t1\t7130000\t7140000\t0.001\n+1\t6850000\t6875000\t1\t6950000\t6975000\t0.001\n+1\t7100000\t7110000\t1\t7700000\t7710000\t0.001\n+1\t7400000\t7425000\t1\t7500000\t7525000\t0.001\n+1\t7450000\t7460000\t1\t7550000\t7560000\t0.001\n+1\t7850000\t7875000\t1\t7950000\t7975000\t0.001\n+1\t8050000\t8060000\t1\t8800000\t8810000\t0.001\n+1\t8075000\t8100000\t1\t8350000\t8375000\t0.001\n+1\t8140000\t8150000\t1\t8240000\t8250000\t0.001\n+1\t8480000\t8490000\t1\t8580000\t8590000\t0.001\n+1\t8620000\t8625000\t1\t8900000\t8905000\t0.001\n+1\t8625000\t8650000\t1\t8725000\t8750000\t0.001\n+1\t8800000\t8810000\t1\t8900000\t8910000\t0.001\n+1\t8960000\t8970000\t1\t9060000\t9070000\t0.001\n+1\t9010000\t9020000\t1\t9520000\t9530000\t0.001\n+1\t9325000\t9350000\t1\t9525000\t9550000\t0.001\n+1\t9650000\t9660000\t1\t10460000\t10470000\t0.001\n+1\t9680000\t9690000\t1\t9780000\t9790000\t0.001\n+1\t9825000\t9850000\t1\t9925000\t9950000\t0.001\n+1\t9935000\t9940000\t1\t10485000\t10490000\t0.001\n+1\t10275000\t10300000\t1\t10375000\t10400000\t0.001\n+1\t10560000\t10570000\t1\t10920000\t10930000\t0.001\n+1\t10560000\t10570000\t1\t11700000\t11710000\t0.001\n+1\t10570000\t10575000\t1\t11000000\t11005000\t0.001\n+1\t10580000\t10590000\t1\t10680000\t10690000\t0.001\n+1\t11090000\t11100000\t1\t11700000\t11710000\t0.001\n+1\t11170000\t11180000\t1\t11270000\t11280000\t0.001\n+1\t11305000\t11310000\t1\t11700000\t11705000\t0.001\n+1\t11390000\t11400000\t1\t11700000\t11710000\t0.001\n+1\t12175000\t12200000\t1\t12275000\t12300000\t0.001\n+1\t12350000\t12375000\t1\t12675000\t12700000\t0.001\n+1\t12400000\t12410000\t1\t13470000\t13480000\t0.001\n+1\t12600000\t12610000\t1\t13160000\t13170000\t0.001\n+1\t12845000\t12850000\t1\t13450000\t13455000\t0.001\n+1\t12905000\t12910000\t1\t13180000\t13185000\t0.001\n+1\t12950000\t12955000\t1\t13630000\t13635000\t0.001\n+1\t129600'..b'0000\t233730000\t0.001\n+1\t233730000\t233740000\t1\t234380000\t234390000\t0.001\n+1\t234325000\t234350000\t1\t234425000\t234450000\t0.001\n+1\t234610000\t234620000\t1\t235580000\t235590000\t0.001\n+1\t234630000\t234640000\t1\t235140000\t235150000\t0.001\n+1\t234630000\t234640000\t1\t234730000\t234740000\t0.001\n+1\t234630000\t234640000\t1\t235240000\t235250000\t0.001\n+1\t234635000\t234640000\t1\t234975000\t234980000\t0.001\n+1\t234740000\t234750000\t1\t234860000\t234870000\t0.001\n+1\t234740000\t234745000\t1\t235105000\t235110000\t0.001\n+1\t234860000\t234870000\t1\t234970000\t234980000\t0.001\n+1\t235015000\t235020000\t1\t235245000\t235250000\t0.001\n+1\t235140000\t235150000\t1\t235240000\t235250000\t0.001\n+1\t235265000\t235270000\t1\t235575000\t235580000\t0.001\n+1\t235400000\t235425000\t1\t235575000\t235600000\t0.001\n+1\t235670000\t235680000\t1\t236130000\t236140000\t0.001\n+1\t235675000\t235700000\t1\t235925000\t235950000\t0.001\n+1\t236000000\t236025000\t1\t236100000\t236125000\t0.001\n+1\t236260000\t236270000\t1\t237030000\t237040000\t0.001\n+1\t236270000\t236280000\t1\t236650000\t236660000\t0.001\n+1\t236320000\t236330000\t1\t236440000\t236450000\t0.001\n+1\t236770000\t236780000\t1\t237540000\t237550000\t0.001\n+1\t236770000\t236780000\t1\t237720000\t237730000\t0.001\n+1\t236910000\t236920000\t1\t237540000\t237550000\t0.001\n+1\t236920000\t236930000\t1\t237720000\t237730000\t0.001\n+1\t236925000\t236950000\t1\t237025000\t237050000\t0.001\n+1\t237080000\t237090000\t1\t237730000\t237740000\t0.001\n+1\t238000000\t238025000\t1\t239100000\t239125000\t0.001\n+1\t238025000\t238050000\t1\t240025000\t240050000\t0.001\n+1\t238225000\t238250000\t1\t238325000\t238350000\t0.001\n+1\t238400000\t238425000\t1\t240050000\t240075000\t0.001\n+1\t238610000\t238620000\t1\t240070000\t240080000\t0.001\n+1\t238825000\t238850000\t1\t238925000\t238950000\t0.001\n+1\t239570000\t239580000\t1\t240050000\t240060000\t0.001\n+1\t240890000\t240900000\t1\t241640000\t241650000\t0.001\n+1\t241050000\t241060000\t1\t241650000\t241660000\t0.001\n+1\t241325000\t241350000\t1\t241425000\t241450000\t0.001\n+1\t241690000\t241695000\t1\t242005000\t242010000\t0.001\n+1\t241690000\t241700000\t1\t241790000\t241800000\t0.001\n+1\t241770000\t241780000\t1\t242000000\t242010000\t0.001\n+1\t242175000\t242200000\t1\t243175000\t243200000\t0.001\n+1\t242630000\t242640000\t1\t243180000\t243190000\t0.001\n+1\t242630000\t242640000\t1\t243490000\t243500000\t0.001\n+1\t242810000\t242820000\t1\t243490000\t243500000\t0.001\n+1\t242925000\t242950000\t1\t243025000\t243050000\t0.001\n+1\t243215000\t243220000\t1\t243485000\t243490000\t0.001\n+1\t243220000\t243230000\t1\t244120000\t244130000\t0.001\n+1\t243350000\t243375000\t1\t243450000\t243475000\t0.001\n+1\t243500000\t243525000\t1\t244425000\t244450000\t0.001\n+1\t243510000\t243520000\t1\t243910000\t243920000\t0.001\n+1\t243725000\t243750000\t1\t243825000\t243850000\t0.001\n+1\t243870000\t243880000\t1\t244430000\t244440000\t0.001\n+1\t244160000\t244170000\t1\t244270000\t244280000\t0.001\n+1\t244760000\t244770000\t1\t244960000\t244970000\t0.001\n+1\t244760000\t244770000\t1\t245200000\t245210000\t0.001\n+1\t244960000\t244965000\t1\t245205000\t245210000\t0.001\n+1\t245300000\t245325000\t1\t246600000\t246625000\t0.001\n+1\t245300000\t245325000\t1\t246150000\t246175000\t0.001\n+1\t245310000\t245320000\t1\t246860000\t246870000\t0.001\n+1\t245310000\t245320000\t1\t246440000\t246450000\t0.001\n+1\t245400000\t245410000\t1\t245500000\t245510000\t0.001\n+1\t245680000\t245690000\t1\t246620000\t246630000\t0.001\n+1\t245820000\t245830000\t1\t246600000\t246610000\t0.001\n+1\t246050000\t246075000\t1\t246150000\t246175000\t0.001\n+1\t246170000\t246180000\t1\t246880000\t246890000\t0.001\n+1\t246170000\t246180000\t1\t246610000\t246620000\t0.001\n+1\t246490000\t246500000\t1\t246590000\t246600000\t0.001\n+1\t246650000\t246675000\t1\t246850000\t246875000\t0.001\n+1\t247200000\t247225000\t1\t247300000\t247325000\t0.001\n+1\t247370000\t247380000\t1\t247490000\t247500000\t0.001\n+1\t247550000\t247560000\t1\t247650000\t247660000\t0.001\n+1\t247840000\t247850000\t1\t249100000\t249110000\t0.001\n+1\t248080000\t248090000\t1\t248240000\t248250000\t0.001\n+1\t248090000\t248100000\t1\t249100000\t249110000\t0.001\n+1\t248400000\t248410000\t1\t249100000\t249110000\t0.001\n+1\t248550000\t248575000\t1\t249125000\t249150000\t0.001\n+1\t248600000\t248610000\t1\t248810000\t248820000\t0.001\n+1\t248625000\t248650000\t1\t248725000\t248750000\t0.001\n+1\t248900000\t248910000\t1\t249070000\t249080000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca1_test1.bw
b
Binary file test-data/hicPCA/pca1_test1.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca1_test2.bw
b
Binary file test-data/hicPCA/pca1_test2.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca1_test3.bw
b
Binary file test-data/hicPCA/pca1_test3.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca2_test1.bw
b
Binary file test-data/hicPCA/pca2_test1.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca2_test2.bw
b
Binary file test-data/hicPCA/pca2_test2.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPCA/pca2_test3.bw
b
Binary file test-data/hicPCA/pca2_test3.bw has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotAverageRegions/defaults.png
b
Binary file test-data/hicPlotAverageRegions/defaults.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotAverageRegions/defaults_log.png
b
Binary file test-data/hicPlotAverageRegions/defaults_log.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotAverageRegions/defaults_log1p.png
b
Binary file test-data/hicPlotAverageRegions/defaults_log1p.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png
b
Binary file test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotDistVsCounts_result1.png
b
Binary file test-data/hicPlotDistVsCounts_result1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotDistVsCounts_result2.png
b
Binary file test-data/hicPlotDistVsCounts_result2.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotMatrix/plot1.png
b
Binary file test-data/hicPlotMatrix/plot1.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotMatrix/plot2.pdf
b
Binary file test-data/hicPlotMatrix/plot2.pdf has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotMatrix/plot3_pca.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,2781 @@\n+<?xml version="1.0" encoding="utf-8" standalone="no"?>\n+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"\n+  "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n+<!-- Created with matplotlib (https://matplotlib.org/) -->\n+<svg height="612pt" version="1.1" viewBox="0 0 576 612" width="576pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n+ <defs>\n+  <style type="text/css">\n+*{stroke-linecap:butt;stroke-linejoin:round;}\n+  </style>\n+ </defs>\n+ <g id="figure_1">\n+  <g id="patch_1">\n+   <path d="M 0 612 \n+L 576 612 \n+L 576 0 \n+L 0 0 \n+z\n+" style="fill:#ffffff;"/>\n+  </g>\n+  <g id="axes_1">\n+   <g id="patch_2">\n+    <path d="M 72 499.310295 \n+L 494.446829 499.310295 \n+L 494.446829 73.44 \n+L 72 73.44 \n+z\n+" style="fill:#ffffff;"/>\n+   </g>\n+   <image height="424.8" id="image363da65b7f" transform="scale(1 -1)translate(0 -424.8)" width="424.8" x="72" xlink:href="data:image/png;base64,\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" y="-72"/>\n+   <g id="matplotlib.axis_1">\n+    <g id="xtick_1">\n+     <g id="line2d_1">\n+      <defs>\n+       <path d="M 0 0 \n+L 0 -3.5 \n+" id="m8cdc9e5860" style="stroke:#000000;stroke-width:0.8;"/>\n+      </defs>\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="72" xlink:href="#m8cdc9e5860" y="73.44"/>\n+      </g>\n+     </g>\n+     <g id="text_1">\n+      <!-- 3.00  -->\n+      <defs>\n+       <path d="M 40.578125 39.3125 \n+Q 47.65625 37.796875 51.625 33 \n+Q 55.609375 28.21875 55.609375 21.1875 \n+Q 55.609375 10.40625 48.1875 4.484375 \n+Q 40.765625 -1.421875 27.09375 -1.421875 \n+Q 22.515625 -1.421875 17.65625 -0.515625 \n+Q 12.796875 0.390625 7.625 2.203125 \n+L 7.625 11.71875 \n+Q 11.71875 9.328125 16.59375 8.109375 \n+Q 21.484375 6.890625 26.8125 6.890625 \n+Q 36.078125 6.890625 40.9375 10.546875 \n+Q 45.796875 14.203125 45.796875 21.1875 \n+Q 45.796875 27.640625 41.28125 31.265625 \n+Q 36.765625 34.90625 28.71875 34.90625 \n+L 20.21875 34.90625 \n+L 20.21875 43.015625 \n+L 29.109375 43.015625 \n+Q 36.375 43.015625 40.234375 45.921875 \n+Q 44.09375 48.828125 44.09375 54.296875 \n+Q 44.09375 59.90625 40.109375 62.90625 \n+Q 36.140625 65.921875 28.71875 65.921875 \n+Q 24.65625 65.921875 20.015625 65.03125 \n+Q 15.375 64.15625 9.8125 62.3125 \n+L 9.8125 71.09375 \n+Q 15.4375 72.65625 20.34375 73.4375 \n+Q 25.25 74.21875 29.59375 74.21875 \n+Q 40.828125 74.21875 47.359375 69.109375 \n+Q 53.90625 64.015625 53.90625 55.328125 \n+Q 53.90625 49.265625 50.4375 45.09375 \n+Q 46.96875 40.921875 40.578125 39.3125 \n+z\n+" id="DejaVuSans-51"/>\n+       <path d="M 10.6875 12.40625 \n+L 21 12.40625 \n+L 21 0 \n+L 10.6875 0 \n+z\n+" id="DejaVuSans-46"/>\n+       <path d="M 31.78125 66.40625 \n+Q 24.171875 66.40625 20.328125 58.90625 \n+Q 16.5 51.421875 16.5 36.375 \n+Q 16.5 21.390625 20.328125 13.890625 \n+Q 24.171875 6.390625 31.78125 6.390625 \n+Q 39.453125 6.390625 43.28125 13.890625 \n+Q 47.125 21.390625 47.125 36.375 \n+Q 47.125 51.421875 43.28125 58.90625 \n+Q 39.453125 66.40625 31.78125 66.40625 \n+z\n+M 31.78125 74.21875 \n+Q 44.046875 74.21875 50.515625 64.515625 \n+Q 56.984375 54.828125 56.984375 36.375 \n+Q 56.984375 17.96875 50.515625 8.265625 \n+Q 44.046875 -1.421875 31.78125 -1.421875 \n+Q 19.53125 -1.421875 13.0625 8.265625 \n+Q 6.59375 17.96875 6.59375 36.375 \n+Q 6.59375 54.828125 13.0625 64.515625 \n+Q 19.53125 74.21875 31.78125 74.21875 \n+z\n+" id="DejaVuSans-48"/>\n+       <path id="DejaVuSans-32"/>\n+      </defs>\n+      <g transform="translate(66.131889 65.215023)rotate(-45)scale(0.0833 -0.0833)">\n+       <use '..b'oke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="339.608935"/>\n+      </g>\n+     </g>\n+     <g id="text_18">\n+      <!-- 0.75 -->\n+      <defs>\n+       <path d="M 8.203125 72.90625 \n+L 55.078125 72.90625 \n+L 55.078125 68.703125 \n+L 28.609375 0 \n+L 18.3125 0 \n+L 43.21875 64.59375 \n+L 8.203125 64.59375 \n+z\n+" id="DejaVuSans-55"/>\n+      </defs>\n+      <g transform="translate(525.4 343.408153)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-48"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-55"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-53"/>\n+      </g>\n+     </g>\n+    </g>\n+    <g id="ytick_12">\n+     <g id="line2d_17">\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="286.375148"/>\n+      </g>\n+     </g>\n+     <g id="text_19">\n+      <!-- 1.00 -->\n+      <g transform="translate(525.4 290.174366)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-49"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-48"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-48"/>\n+      </g>\n+     </g>\n+    </g>\n+    <g id="ytick_13">\n+     <g id="line2d_18">\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="233.141361"/>\n+      </g>\n+     </g>\n+     <g id="text_20">\n+      <!-- 1.25 -->\n+      <g transform="translate(525.4 236.940579)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-49"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-50"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-53"/>\n+      </g>\n+     </g>\n+    </g>\n+    <g id="ytick_14">\n+     <g id="line2d_19">\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="179.907574"/>\n+      </g>\n+     </g>\n+     <g id="text_21">\n+      <!-- 1.50 -->\n+      <g transform="translate(525.4 183.706793)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-49"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-53"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-48"/>\n+      </g>\n+     </g>\n+    </g>\n+    <g id="ytick_15">\n+     <g id="line2d_20">\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="126.673787"/>\n+      </g>\n+     </g>\n+     <g id="text_22">\n+      <!-- 1.75 -->\n+      <g transform="translate(525.4 130.473006)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-49"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-55"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-53"/>\n+      </g>\n+     </g>\n+    </g>\n+    <g id="ytick_16">\n+     <g id="line2d_21">\n+      <g>\n+       <use style="stroke:#000000;stroke-width:0.8;" x="518.4" xlink:href="#m64fa8b7061" y="73.44"/>\n+      </g>\n+     </g>\n+     <g id="text_23">\n+      <!-- 2.00 -->\n+      <g transform="translate(525.4 77.239219)scale(0.1 -0.1)">\n+       <use xlink:href="#DejaVuSans-50"/>\n+       <use x="63.623047" xlink:href="#DejaVuSans-46"/>\n+       <use x="95.410156" xlink:href="#DejaVuSans-48"/>\n+       <use x="159.033203" xlink:href="#DejaVuSans-48"/>\n+      </g>\n+     </g>\n+    </g>\n+   </g>\n+   <g id="patch_8">\n+    <path d="M 505.334634 499.310295 \n+L 505.334634 497.646739 \n+L 505.334634 75.103556 \n+L 505.334634 73.44 \n+L 518.4 73.44 \n+L 518.4 75.103556 \n+L 518.4 497.646739 \n+L 518.4 499.310295 \n+z\n+" style="fill:none;stroke:#000000;stroke-linejoin:miter;stroke-width:0.8;"/>\n+   </g>\n+  </g>\n+ </g>\n+ <defs>\n+  <clipPath id="pbab51a357b">\n+   <rect height="33.876046" width="422.446829" x="72" y="510.803954"/>\n+  </clipPath>\n+  <clipPath id="pf05c0f3022">\n+   <rect height="425.870295" width="13.065366" x="505.334634" y="73.44"/>\n+  </clipPath>\n+ </defs>\n+</svg>\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotSVL/p_values.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,4 @@
+# Created with HiCExplorer's hicPlotSVL 3.3
+# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
+# Short range contacts: <= 2000000
+0_small_test_matrix.h5 1_small_test_matrix.h5 1.0
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotSVL/plot.png
b
Binary file test-data/hicPlotSVL/plot.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicPlotSVL/ratios.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,8 @@
+# Created with HiCExplorer's hicPlotSVL 3.3
+# Short range vs long range contacts per chromosome: raw data
+# Short range contacts: <= 2000000
+# 0_small_test_matrix.h5 1_small_test_matrix.h5
+# Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000
+chr2L 4.7639676113360325 11767 2470 4.7639676113360325 11767 2470
+chr3L 4.8960869565217395 11261 2300 4.8960869565217395 11261 2300
+chr4
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicQuickQC/QC.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicQuickQC/QC.log Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,29 @@
+
+File /tmp/tmpp4d6khlj.h5
+Sequenced reads 983
+Min rest. site distance 300
+Max library insert size 1000
+
+# count (percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality 300 (30.52)
+Hi-C contacts 215 (21.87)
+One mate unmapped 506 (51.48)
+One mate not unique 13 (1.32)
+Low mapping quality 164 (16.68)
+
+# count (percentage w.r.t. mappable, unique and high quality pairs)
+dangling end 0 (0.00)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 85 (28.33)
+self circle 0 (0.00)
+duplicated pairs 0 (0.00)
+
+# count (percentage w.r.t. total valid pairs used)
+inter chromosomal 24 (11.16)
+Intra short range (< 20kb) 61 (28.37)
+Intra long range (>= 20kb) 130 (60.47)
+Read pair type: inward pairs 42 (19.53)
+Read pair type: outward pairs 66 (30.70)
+Read pair type: left pairs 48 (22.33)
+Read pair type: right pairs 35 (16.28)
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicTransform/obs_exp_norm.h5
b
Binary file test-data/hicTransform/obs_exp_norm.h5 has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,5903 @@\n+chr1\t237570\t237942\tregion_12575\t0\t+\n+chr1\t521398\t521603\tregion_25163\t0\t+\n+chr1\t569733\t570121\tregion_46504\t0\t+\n+chr1\t713987\t714365\tregion_26941\t0\t+\n+chr1\t793341\t793542\tregion_27446\t0\t+\n+chr1\t805168\t805444\tregion_19499\t0\t+\n+chr1\t839991\t840329\tregion_22280\t0\t+\n+chr1\t856451\t856737\tregion_30261\t0\t+\n+chr1\t873533\t873837\tregion_17595\t0\t+\n+chr1\t886876\t886983\tregion_38607\t0\t+\n+chr1\t894384\t894749\tregion_40963\t0\t+\n+chr1\t902196\t902278\tregion_44335\t0\t+\n+chr1\t911452\t911761\tregion_22213\t0\t+\n+chr1\t919428\t919915\tregion_8832\t0\t+\n+chr1\t937221\t937593\tregion_24230\t0\t+\n+chr1\t950754\t951010\tregion_41625\t0\t+\n+chr1\t954667\t954954\tregion_38802\t0\t+\n+chr1\t966672\t966902\tregion_32413\t0\t+\n+chr1\t967907\t968787\tregion_6526\t0\t+\n+chr1\t974207\t974385\tregion_54361\t0\t+\n+chr1\t986145\t986296\tregion_39601\t0\t+\n+chr1\t995276\t995316\tregion_40603\t0\t+\n+chr1\t998959\t999690\tregion_4557\t0\t+\n+chr1\t1057373\t1058080\tregion_1150\t0\t+\n+chr1\t1107295\t1107492\tregion_56364\t0\t+\n+chr1\t1136912\t1137112\tregion_32099\t0\t+\n+chr1\t1142067\t1142321\tregion_47363\t0\t+\n+chr1\t1150565\t1150702\tregion_48790\t0\t+\n+chr1\t1166119\t1167029\tregion_20466\t0\t+\n+chr1\t1185813\t1185948\tregion_46195\t0\t+\n+chr1\t1209638\t1209733\tregion_46943\t0\t+\n+chr1\t1225554\t1225897\tregion_15808\t0\t+\n+chr1\t1227202\t1227595\tregion_9258\t0\t+\n+chr1\t1235596\t1235647\tregion_63971\t0\t+\n+chr1\t1237388\t1237537\tregion_46196\t0\t+\n+chr1\t1240639\t1240973\tregion_25237\t0\t+\n+chr1\t1241553\t1241762\tregion_49888\t0\t+\n+chr1\t1280026\t1280363\tregion_23642\t0\t+\n+chr1\t1285132\t1285399\tregion_37107\t0\t+\n+chr1\t1307416\t1307838\tregion_9704\t0\t+\n+chr1\t1337352\t1337707\tregion_31138\t0\t+\n+chr1\t1342404\t1343433\tregion_33544\t0\t+\n+chr1\t1353536\t1353613\tregion_63972\t0\t+\n+chr1\t1357843\t1357908\tregion_42858\t0\t+\n+chr1\t1373108\t1373115\tregion_51599\t0\t+\n+chr1\t1373360\t1373684\tregion_59786\t0\t+\n+chr1\t1376267\t1376650\tregion_8613\t0\t+\n+chr1\t1377059\t1377207\tregion_60172\t0\t+\n+chr1\t1440290\t1440574\tregion_54889\t0\t+\n+chr1\t1440903\t1441103\tregion_54362\t0\t+\n+chr1\t1533139\t1533314\tregion_36733\t0\t+\n+chr1\t1550435\t1551064\tregion_24937\t0\t+\n+chr1\t1603367\t1603368\tregion_51600\t0\t+\n+chr1\t1609148\t1609971\tregion_19006\t0\t+\n+chr1\t1610356\t1610731\tregion_23382\t0\t+\n+chr1\t1655649\t1655942\tregion_64571\t0\t+\n+chr1\t1695880\t1695931\tregion_63973\t0\t+\n+chr1\t1706905\t1707425\tregion_43220\t0\t+\n+chr1\t1710284\t1710876\tregion_52504\t0\t+\n+chr1\t1711690\t1712378\tregion_22288\t0\t+\n+chr1\t1720502\t1720834\tregion_24938\t0\t+\n+chr1\t1727941\t1728197\tregion_41626\t0\t+\n+chr1\t1731197\t1731492\tregion_34098\t0\t+\n+chr1\t1747185\t1747294\tregion_54999\t0\t+\n+chr1\t1759923\t1760320\tregion_51944\t0\t+\n+chr1\t1780635\t1780740\tregion_61000\t0\t+\n+chr1\t1787180\t1787358\tregion_60173\t0\t+\n+chr1\t1788773\t1788946\tregion_62664\t0\t+\n+chr1\t1796255\t1796272\tregion_51601\t0\t+\n+chr1\t1800896\t1801096\tregion_54363\t0\t+\n+chr1\t1821511\t1821701\tregion_62665\t0\t+\n+chr1\t1823085\t1823298\tregion_36628\t0\t+\n+chr1\t1830698\t1830975\tregion_30262\t0\t+\n+chr1\t1837622\t1838087\tregion_3552\t0\t+\n+chr1\t1840194\t1840670\tregion_21907\t0\t+\n+chr1\t1875462\t1875751\tregion_29889\t0\t+\n+chr1\t1891507\t1891815\tregion_20679\t0\t+\n+chr1\t1976270\t1976560\tregion_44421\t0\t+\n+chr1\t1977929\t1978246\tregion_31789\t0\t+\n+chr1\t2023099\t2023367\tregion_31689\t0\t+\n+chr1\t2052851\t2053379\tregion_25905\t0\t+\n+chr1\t2064623\t2064648\tregion_51602\t0\t+\n+chr1\t2071213\t2071698\tregion_19333\t0\t+\n+chr1\t2105723\t2106103\tregion_12038\t0\t+\n+chr1\t2126534\t2127060\tregion_3195\t0\t+\n+chr1\t2136854\t2137024\tregion_48791\t0\t+\n+chr1\t2144140\t2144455\tregion_28434\t0\t+\n+chr1\t2158823\t2158983\tregion_48792\t0\t+\n+chr1\t2160620\t2160932\tregion_31563\t0\t+\n+chr1\t2165794\t2166091\tregion_37039\t0\t+\n+chr1\t2186945\t2186985\tregion_51603\t0\t+\n+chr1\t2221916\t2222834\tregion_53663\t0\t+\n+chr1\t2231770\t2232780\tregion_29107\t0\t+\n+chr1\t2243029\t2243249\tregion_37978\t0\t+\n+chr1\t2246712\t2246943\tregion_28716\t0\t+\n+chr1\t2313032\t2313595\tregion_2106\t0\t+\n+chr1\t2314096\t2314296\tregion_37587\t0\t+\n+chr1\t2322725\t2322950\tregion_59691\t0\t+\n+chr1\t2343703\t2343772\tregion_51604\t0\t+\n+chr1\t2344272\t2344443\tregion_50817\t0\t+\n+chr1\t2345786\t2346255\tregion_2257\t0\t+\n+chr1\t2347202\t2347415\tregion_35494\t0\t+\n+chr1\t2361572\t2361772\tregion_58664\t0\t+\n+chr1\t2375388\t237555'..b'4\tregion_31355\t0\t+\n+chr1\t244766729\t244767134\tregion_14942\t0\t+\n+chr1\t244816629\t244816843\tregion_43739\t0\t+\n+chr1\t244960077\t244960670\tregion_3667\t0\t+\n+chr1\t244964442\t244964883\tregion_4000\t0\t+\n+chr1\t244977926\t244978123\tregion_62161\t0\t+\n+chr1\t244998664\t244998871\tregion_45776\t0\t+\n+chr1\t244999700\t244999749\tregion_64060\t0\t+\n+chr1\t245027598\t245028412\tregion_45678\t0\t+\n+chr1\t245082167\t245082439\tregion_32500\t0\t+\n+chr1\t245089144\t245089214\tregion_61069\t0\t+\n+chr1\t245104430\t245104711\tregion_54830\t0\t+\n+chr1\t245132833\t245133399\tregion_50061\t0\t+\n+chr1\t245133982\t245134853\tregion_36772\t0\t+\n+chr1\t245205811\t245206410\tregion_2491\t0\t+\n+chr1\t245242370\t245242694\tregion_44150\t0\t+\n+chr1\t245316247\t245316689\tregion_12572\t0\t+\n+chr1\t245319751\t245320102\tregion_9366\t0\t+\n+chr1\t245440732\t245440821\tregion_44353\t0\t+\n+chr1\t245544137\t245544435\tregion_25207\t0\t+\n+chr1\t245812331\t245812832\tregion_26685\t0\t+\n+chr1\t245836924\t245836965\tregion_64061\t0\t+\n+chr1\t245961057\t245961257\tregion_35514\t0\t+\n+chr1\t245970420\t245970527\tregion_55859\t0\t+\n+chr1\t246022365\t246022648\tregion_29024\t0\t+\n+chr1\t246052061\t246052491\tregion_7741\t0\t+\n+chr1\t246058193\t246058476\tregion_41032\t0\t+\n+chr1\t246132825\t246132850\tregion_42910\t0\t+\n+chr1\t246163046\t246163396\tregion_41673\t0\t+\n+chr1\t246166202\t246166839\tregion_940\t0\t+\n+chr1\t246175298\t246176192\tregion_6252\t0\t+\n+chr1\t246183508\t246183683\tregion_43947\t0\t+\n+chr1\t246280470\t246280911\tregion_49424\t0\t+\n+chr1\t246411660\t246411787\tregion_47485\t0\t+\n+chr1\t246443894\t246444226\tregion_50380\t0\t+\n+chr1\t246493106\t246493746\tregion_59251\t0\t+\n+chr1\t246558661\t246558668\tregion_48341\t0\t+\n+chr1\t246613874\t246614432\tregion_9016\t0\t+\n+chr1\t246655959\t246656299\tregion_16594\t0\t+\n+chr1\t246660508\t246661194\tregion_5420\t0\t+\n+chr1\t246670422\t246670483\tregion_61070\t0\t+\n+chr1\t246695979\t246696047\tregion_55860\t0\t+\n+chr1\t246729300\t246730422\tregion_25377\t0\t+\n+chr1\t246730707\t246730763\tregion_58278\t0\t+\n+chr1\t246732917\t246732950\tregion_42911\t0\t+\n+chr1\t246736975\t246736977\tregion_48342\t0\t+\n+chr1\t246754892\t246755092\tregion_59714\t0\t+\n+chr1\t246764750\t246764802\tregion_40640\t0\t+\n+chr1\t246776613\t246776667\tregion_42912\t0\t+\n+chr1\t246852800\t246853214\tregion_6202\t0\t+\n+chr1\t246859805\t246860134\tregion_25491\t0\t+\n+chr1\t246861934\t246861938\tregion_48343\t0\t+\n+chr1\t246862419\t246862876\tregion_8305\t0\t+\n+chr1\t246917141\t246917603\tregion_7126\t0\t+\n+chr1\t246972894\t246972990\tregion_53526\t0\t+\n+chr1\t247070840\t247071139\tregion_28439\t0\t+\n+chr1\t247123397\t247123696\tregion_28646\t0\t+\n+chr1\t247134651\t247135021\tregion_10077\t0\t+\n+chr1\t247240590\t247240817\tregion_41639\t0\t+\n+chr1\t247282285\t247282547\tregion_23774\t0\t+\n+chr1\t247373607\t247373677\tregion_55861\t0\t+\n+chr1\t247375366\t247375713\tregion_46666\t0\t+\n+chr1\t247494433\t247494633\tregion_49920\t0\t+\n+chr1\t247495777\t247495849\tregion_58279\t0\t+\n+chr1\t247496586\t247496645\tregion_61071\t0\t+\n+chr1\t247536009\t247536390\tregion_6529\t0\t+\n+chr1\t247537197\t247537559\tregion_19742\t0\t+\n+chr1\t247549666\t247549825\tregion_56398\t0\t+\n+chr1\t247553255\t247554052\tregion_5344\t0\t+\n+chr1\t247570450\t247570888\tregion_55239\t0\t+\n+chr1\t247573185\t247573749\tregion_37144\t0\t+\n+chr1\t247603341\t247603923\tregion_27793\t0\t+\n+chr1\t247650185\t247650794\tregion_6978\t0\t+\n+chr1\t247739860\t247740190\tregion_26084\t0\t+\n+chr1\t247844637\t247844986\tregion_43198\t0\t+\n+chr1\t248100167\t248100642\tregion_3825\t0\t+\n+chr1\t248406422\t248407032\tregion_6185\t0\t+\n+chr1\t248567324\t248567772\tregion_21120\t0\t+\n+chr1\t248595731\t248595786\tregion_54123\t0\t+\n+chr1\t248596049\t248596213\tregion_50862\t0\t+\n+chr1\t248598404\t248598485\tregion_51656\t0\t+\n+chr1\t248602309\t248602362\tregion_51657\t0\t+\n+chr1\t248602932\t248602948\tregion_51658\t0\t+\n+chr1\t248609314\t248609317\tregion_54124\t0\t+\n+chr1\t248613753\t248613809\tregion_51659\t0\t+\n+chr1\t248624246\t248624516\tregion_31214\t0\t+\n+chr1\t248630072\t248630123\tregion_61072\t0\t+\n+chr1\t248644915\t248645001\tregion_42913\t0\t+\n+chr1\t248645583\t248645930\tregion_37430\t0\t+\n+chr1\t248848783\t248848866\tregion_61073\t0\t+\n+chr1\t248849610\t248850639\tregion_5597\t0\t+\n+chr1\t248851498\t248852591\tregion_23251\t0\t+\n+chr1\t248859535\t248859989\tregion_10778\t0\t+\n+chr1\t248866958\t248867370\tregion_34602\t0\t+\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicValidateLocations/loops_1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/loops_1.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,1007 @@\n+1\t10000\t20000\t1\t250000\t260000\t0.001\n+1\t10000\t20000\t1\t243180000\t243190000\t0.001\n+1\t140000\t150000\t1\t680000\t690000\t0.001\n+1\t540000\t550000\t1\t640000\t650000\t0.001\n+1\t720000\t730000\t1\t224200000\t224210000\t0.001\n+1\t630000\t640000\t1\t1140000\t1150000\t0.001\n+1\t650000\t660000\t1\t145910000\t145920000\t0.001\n+1\t1050000\t1060000\t1\t1180000\t1190000\t0.001\n+1\t1310000\t1320000\t1\t1410000\t1420000\t0.001\n+1\t1710000\t1720000\t1\t1830000\t1840000\t0.001\n+1\t1870000\t1880000\t1\t3340000\t3350000\t0.0019430592210407135\n+1\t2110000\t2120000\t1\t2710000\t2720000\t0.001\n+1\t2130000\t2140000\t1\t3570000\t3580000\t0.001\n+1\t2080000\t2090000\t1\t3330000\t3340000\t0.001\n+1\t2120000\t2130000\t1\t2310000\t2320000\t0.001\n+1\t2120000\t2130000\t1\t2480000\t2490000\t0.001\n+1\t2480000\t2490000\t1\t3570000\t3580000\t0.001\n+1\t2340000\t2350000\t1\t3340000\t3350000\t0.001\n+1\t2340000\t2350000\t1\t2480000\t2490000\t0.001\n+1\t2590000\t2600000\t1\t3300000\t3310000\t0.001\n+1\t2580000\t2590000\t1\t2680000\t2690000\t0.001\n+1\t2600000\t2610000\t1\t3170000\t3180000\t0.001\n+1\t2850000\t2860000\t1\t4400000\t4410000\t0.001\n+1\t2860000\t2870000\t1\t4770000\t4780000\t0.001\n+1\t2850000\t2860000\t1\t4160000\t4170000\t0.001\n+1\t2860000\t2870000\t1\t5220000\t5230000\t0.001\n+1\t3070000\t3080000\t1\t4190000\t4200000\t0.001\n+1\t3110000\t3120000\t1\t4480000\t4490000\t0.001\n+1\t3240000\t3250000\t1\t4220000\t4230000\t0.001\n+1\t3290000\t3300000\t1\t4380000\t4390000\t0.001\n+1\t3400000\t3410000\t1\t3530000\t3540000\t0.001\n+1\t3820000\t3830000\t1\t5960000\t5970000\t0.001\n+1\t3820000\t3830000\t1\t5510000\t5520000\t0.001\n+1\t3820000\t3830000\t1\t5800000\t5810000\t0.001\n+1\t3820000\t3830000\t1\t4880000\t4890000\t0.001\n+1\t3840000\t3850000\t1\t4430000\t4440000\t0.001\n+1\t3830000\t3840000\t1\t4710000\t4720000\t0.001\n+1\t3840000\t3850000\t1\t3990000\t4000000\t0.001\n+1\t4190000\t4200000\t1\t5430000\t5440000\t0.001\n+1\t4010000\t4020000\t1\t5790000\t5800000\t0.001\n+1\t4150000\t4160000\t1\t5660000\t5670000\t0.001\n+1\t4710000\t4720000\t1\t4880000\t4890000\t0.001\n+1\t4280000\t4290000\t1\t5250000\t5260000\t0.001\n+1\t5570000\t5580000\t1\t5970000\t5980000\t0.001\n+1\t6770000\t6780000\t1\t7700000\t7710000\t0.001\n+1\t6510000\t6520000\t1\t17020000\t17030000\t0.001\n+1\t6540000\t6550000\t1\t6700000\t6710000\t0.001\n+1\t6780000\t6790000\t1\t7130000\t7140000\t0.001\n+1\t6770000\t6780000\t1\t7270000\t7280000\t0.001\n+1\t6850000\t6860000\t1\t6950000\t6960000\t0.001\n+1\t7100000\t7110000\t1\t7700000\t7710000\t0.001\n+1\t7450000\t7460000\t1\t7550000\t7560000\t0.001\n+1\t8080000\t8090000\t1\t8370000\t8380000\t0.001\n+1\t8050000\t8060000\t1\t8800000\t8810000\t0.001\n+1\t8620000\t8630000\t1\t8730000\t8740000\t0.001\n+1\t8960000\t8970000\t1\t9060000\t9070000\t0.001\n+1\t9340000\t9350000\t1\t9510000\t9520000\t0.001\n+1\t9650000\t9660000\t1\t10460000\t10470000\t0.001\n+1\t9680000\t9690000\t1\t9780000\t9790000\t0.001\n+1\t9830000\t9840000\t1\t9930000\t9940000\t0.001\n+1\t10270000\t10280000\t1\t10390000\t10400000\t0.001\n+1\t10560000\t10570000\t1\t11700000\t11710000\t0.001\n+1\t10560000\t10570000\t1\t10920000\t10930000\t0.001\n+1\t11090000\t11100000\t1\t11700000\t11710000\t0.001\n+1\t11390000\t11400000\t1\t11700000\t11710000\t0.001\n+1\t12170000\t12180000\t1\t12270000\t12280000\t0.001\n+1\t12400000\t12410000\t1\t13470000\t13480000\t0.001\n+1\t12370000\t12380000\t1\t12670000\t12680000\t0.001\n+1\t12600000\t12610000\t1\t13160000\t13170000\t0.001\n+1\t13110000\t13120000\t1\t13630000\t13640000\t0.001\n+1\t13160000\t13170000\t1\t14520000\t14530000\t0.001\n+1\t12960000\t12970000\t1\t14300000\t14310000\t0.001\n+1\t13010000\t13020000\t1\t13120000\t13130000\t0.001\n+1\t13030000\t13040000\t1\t13320000\t13330000\t0.001\n+1\t13320000\t13330000\t1\t13440000\t13450000\t0.001\n+1\t13350000\t13360000\t1\t13630000\t13640000\t0.008995826687529431\n+1\t13500000\t13510000\t1\t13720000\t13730000\t0.001\n+1\t13690000\t13700000\t1\t15390000\t15400000\t0.001\n+1\t13660000\t13670000\t1\t145980000\t145990000\t0.001\n+1\t13740000\t13750000\t1\t33440000\t33450000\t0.001\n+1\t13990000\t14000000\t1\t14280000\t14290000\t0.001\n+1\t13990000\t14000000\t1\t14130000\t14140000\t0.001\n+1\t14280000\t14290000\t1\t15370000\t15380000\t0.001\n+1\t14150000\t14160000\t1\t14280000\t14290000\t0.001\n+1\t14420000\t14430000\t1\t15620000\t15630000\t0.001\n+1\t14430000\t14440000\t1\t14890000\t14900000\t0.001\n+1\t14430000\t14440000\t1\t15370000\t15380000\t0.001\n+1\t14940000\t14950000\t1\t15050000\t15060000\t0.001\n+1\t14720000\t14730000\t1\t15380000\t15390000\t0.001\n+1\t15450000\t'..b'0000\t227900000\t0.001\n+1\t228790000\t228800000\t1\t229360000\t229370000\t0.001\n+1\t228790000\t228800000\t1\t229640000\t229650000\t0.001\n+1\t228880000\t228890000\t1\t228990000\t229000000\t0.001\n+1\t229390000\t229400000\t1\t230440000\t230450000\t0.001\n+1\t229390000\t229400000\t1\t229610000\t229620000\t0.001\n+1\t229850000\t229860000\t1\t230440000\t230450000\t0.001\n+1\t231050000\t231060000\t1\t231340000\t231350000\t0.001\n+1\t231490000\t231500000\t1\t231720000\t231730000\t0.001\n+1\t231990000\t232000000\t1\t233140000\t233150000\t0.001\n+1\t232000000\t232010000\t1\t233370000\t233380000\t0.001\n+1\t232000000\t232010000\t1\t232760000\t232770000\t0.001\n+1\t232770000\t232780000\t1\t233370000\t233380000\t0.001\n+1\t232770000\t232780000\t1\t233160000\t233170000\t0.001\n+1\t233480000\t233490000\t1\t234460000\t234470000\t0.001\n+1\t233730000\t233740000\t1\t234380000\t234390000\t0.001\n+1\t233530000\t233540000\t1\t234200000\t234210000\t0.001\n+1\t233570000\t233580000\t1\t233920000\t233930000\t0.001\n+1\t233620000\t233630000\t1\t233720000\t233730000\t0.001\n+1\t234340000\t234350000\t1\t234440000\t234450000\t0.001\n+1\t234610000\t234620000\t1\t235580000\t235590000\t0.001\n+1\t234630000\t234640000\t1\t235240000\t235250000\t0.001\n+1\t234630000\t234640000\t1\t235140000\t235150000\t0.001\n+1\t234630000\t234640000\t1\t234730000\t234740000\t0.001\n+1\t234740000\t234750000\t1\t234860000\t234870000\t0.001\n+1\t234860000\t234870000\t1\t234970000\t234980000\t0.001\n+1\t235140000\t235150000\t1\t235240000\t235250000\t0.001\n+1\t235410000\t235420000\t1\t235570000\t235580000\t0.001\n+1\t235670000\t235680000\t1\t235940000\t235950000\t0.001\n+1\t235670000\t235680000\t1\t236130000\t236140000\t0.001\n+1\t236020000\t236030000\t1\t236130000\t236140000\t0.001\n+1\t236270000\t236280000\t1\t236650000\t236660000\t0.001\n+1\t236320000\t236330000\t1\t236440000\t236450000\t0.001\n+1\t236260000\t236270000\t1\t237030000\t237040000\t0.001\n+1\t236770000\t236780000\t1\t237720000\t237730000\t0.001\n+1\t236770000\t236780000\t1\t237540000\t237550000\t0.001\n+1\t236910000\t236920000\t1\t237540000\t237550000\t0.001\n+1\t236920000\t236930000\t1\t237720000\t237730000\t0.001\n+1\t237080000\t237090000\t1\t237730000\t237740000\t0.001\n+1\t237970000\t237980000\t1\t240060000\t240070000\t0.001\n+1\t238010000\t238020000\t1\t239100000\t239110000\t0.001\n+1\t238400000\t238410000\t1\t240050000\t240060000\t0.001\n+1\t238610000\t238620000\t1\t240070000\t240080000\t0.001\n+1\t239570000\t239580000\t1\t240050000\t240060000\t0.001\n+1\t240890000\t240900000\t1\t241640000\t241650000\t0.001\n+1\t241050000\t241060000\t1\t241650000\t241660000\t0.001\n+1\t241770000\t241780000\t1\t242000000\t242010000\t0.001\n+1\t241690000\t241700000\t1\t241790000\t241800000\t0.001\n+1\t242180000\t242190000\t1\t243200000\t243210000\t0.001\n+1\t242630000\t242640000\t1\t243490000\t243500000\t0.001\n+1\t242630000\t242640000\t1\t243180000\t243190000\t0.001\n+1\t243370000\t243380000\t1\t243470000\t243480000\t0.001\n+1\t243220000\t243230000\t1\t244120000\t244130000\t0.001\n+1\t243500000\t243510000\t1\t244430000\t244440000\t0.001\n+1\t243510000\t243520000\t1\t243910000\t243920000\t0.001\n+1\t243870000\t243880000\t1\t244430000\t244440000\t0.001\n+1\t244160000\t244170000\t1\t244270000\t244280000\t0.001\n+1\t244760000\t244770000\t1\t245200000\t245210000\t0.001\n+1\t244760000\t244770000\t1\t244960000\t244970000\t0.001\n+1\t245310000\t245320000\t1\t246160000\t246170000\t0.001\n+1\t245310000\t245320000\t1\t246860000\t246870000\t0.001\n+1\t245310000\t245320000\t1\t246610000\t246620000\t0.001\n+1\t245310000\t245320000\t1\t246440000\t246450000\t0.001\n+1\t245680000\t245690000\t1\t246620000\t246630000\t0.001\n+1\t245820000\t245830000\t1\t246600000\t246610000\t0.001\n+1\t246170000\t246180000\t1\t246610000\t246620000\t0.001\n+1\t246050000\t246060000\t1\t246160000\t246170000\t0.001\n+1\t246170000\t246180000\t1\t246880000\t246890000\t0.001\n+1\t246660000\t246670000\t1\t246860000\t246870000\t0.001\n+1\t247190000\t247200000\t1\t247300000\t247310000\t0.001\n+1\t247370000\t247380000\t1\t247490000\t247500000\t0.001\n+1\t247550000\t247560000\t1\t247650000\t247660000\t0.001\n+1\t247840000\t247850000\t1\t249100000\t249110000\t0.001\n+1\t248090000\t248100000\t1\t249100000\t249110000\t0.001\n+1\t248080000\t248090000\t1\t248240000\t248250000\t0.001\n+1\t248400000\t248410000\t1\t249100000\t249110000\t0.001\n+1\t248600000\t248610000\t1\t248810000\t248820000\t0.001\n+1\t248560000\t248570000\t1\t249100000\t249110000\t0.001\n+1\t248900000\t248910000\t1\t249070000\t249080000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicValidateLocations/overlap_smc3_matched_locations
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Mon Dec 16 15:27:02 2019 -0500
b
b'@@ -0,0 +1,530 @@\n+chr1\t1050000\t1060000\tchr1\t1180000\t1190000\t0.001\n+chr1\t1710000\t1720000\tchr1\t1830000\t1840000\t0.001\n+chr1\t1870000\t1880000\tchr1\t3340000\t3350000\t0.0019430592210407133\n+chr1\t2120000\t2130000\tchr1\t2310000\t2320000\t0.001\n+chr1\t2120000\t2130000\tchr1\t2480000\t2490000\t0.001\n+chr1\t2130000\t2140000\tchr1\t3570000\t3580000\t0.001\n+chr1\t2340000\t2350000\tchr1\t3340000\t3350000\t0.001\n+chr1\t2340000\t2350000\tchr1\t2480000\t2490000\t0.001\n+chr1\t2480000\t2490000\tchr1\t3570000\t3580000\t0.001\n+chr1\t3400000\t3410000\tchr1\t3530000\t3540000\t0.001\n+chr1\t3820000\t3830000\tchr1\t5800000\t5810000\t0.001\n+chr1\t3820000\t3830000\tchr1\t4880000\t4890000\t0.001\n+chr1\t3830000\t3840000\tchr1\t4710000\t4720000\t0.001\n+chr1\t4710000\t4720000\tchr1\t4880000\t4890000\t0.001\n+chr1\t5570000\t5580000\tchr1\t5970000\t5980000\t0.001\n+chr1\t6540000\t6550000\tchr1\t6700000\t6710000\t0.001\n+chr1\t6770000\t6780000\tchr1\t7700000\t7710000\t0.001\n+chr1\t6770000\t6780000\tchr1\t7270000\t7280000\t0.001\n+chr1\t6780000\t6790000\tchr1\t7130000\t7140000\t0.001\n+chr1\t6850000\t6860000\tchr1\t6950000\t6960000\t0.001\n+chr1\t7100000\t7110000\tchr1\t7700000\t7710000\t0.001\n+chr1\t8080000\t8090000\tchr1\t8370000\t8380000\t0.001\n+chr1\t8620000\t8630000\tchr1\t8730000\t8740000\t0.001\n+chr1\t9340000\t9350000\tchr1\t9510000\t9520000\t0.001\n+chr1\t9680000\t9690000\tchr1\t9780000\t9790000\t0.001\n+chr1\t10270000\t10280000\tchr1\t10390000\t10400000\t0.001\n+chr1\t10560000\t10570000\tchr1\t11700000\t11710000\t0.001\n+chr1\t10560000\t10570000\tchr1\t10920000\t10930000\t0.001\n+chr1\t11090000\t11100000\tchr1\t11700000\t11710000\t0.001\n+chr1\t11390000\t11400000\tchr1\t11700000\t11710000\t0.001\n+chr1\t12370000\t12380000\tchr1\t12670000\t12680000\t0.001\n+chr1\t13990000\t14000000\tchr1\t14280000\t14290000\t0.001\n+chr1\t13990000\t14000000\tchr1\t14130000\t14140000\t0.001\n+chr1\t14150000\t14160000\tchr1\t14280000\t14290000\t0.001\n+chr1\t14280000\t14290000\tchr1\t15370000\t15380000\t0.001\n+chr1\t15450000\t15460000\tchr1\t15590000\t15600000\t0.001\n+chr1\t15650000\t15660000\tchr1\t15750000\t15760000\t0.001\n+chr1\t15920000\t15930000\tchr1\t16060000\t16070000\t0.001\n+chr1\t16400000\t16410000\tchr1\t16510000\t16520000\t0.001\n+chr1\t16570000\t16580000\tchr1\t16680000\t16690000\t0.001\n+chr1\t16920000\t16930000\tchr1\t21790000\t21800000\t0.001\n+chr1\t17270000\t17280000\tchr1\t17370000\t17380000\t0.001\n+chr1\t17450000\t17460000\tchr1\t17560000\t17570000\t0.001\n+chr1\t17820000\t17830000\tchr1\t17930000\t17940000\t0.001\n+chr1\t17980000\t17990000\tchr1\t18900000\t18910000\t0.001\n+chr1\t17980000\t17990000\tchr1\t18420000\t18430000\t0.001\n+chr1\t18310000\t18320000\tchr1\t18900000\t18910000\t0.001\n+chr1\t18920000\t18930000\tchr1\t19140000\t19150000\t0.001\n+chr1\t19230000\t19240000\tchr1\t19420000\t19430000\t0.001\n+chr1\t20240000\t20250000\tchr1\t20470000\t20480000\t0.001\n+chr1\t20240000\t20250000\tchr1\t20820000\t20830000\t0.001\n+chr1\t20840000\t20850000\tchr1\t20960000\t20970000\t0.001\n+chr1\t21020000\t21030000\tchr1\t21520000\t21530000\t0.001\n+chr1\t21020000\t21030000\tchr1\t21690000\t21700000\t0.001\n+chr1\t21580000\t21590000\tchr1\t21690000\t21700000\t0.001\n+chr1\t22450000\t22460000\tchr1\t22960000\t22970000\t0.001\n+chr1\t22450000\t22460000\tchr1\t22740000\t22750000\t0.001\n+chr1\t22740000\t22750000\tchr1\t22960000\t22970000\t0.001\n+chr1\t23030000\t23040000\tchr1\t23210000\t23220000\t0.001\n+chr1\t23860000\t23870000\tchr1\t23960000\t23970000\t0.001\n+chr1\t24130000\t24140000\tchr1\t24240000\t24250000\t0.001\n+chr1\t24520000\t24530000\tchr1\t24710000\t24720000\t0.001\n+chr1\t24740000\t24750000\tchr1\t24860000\t24870000\t0.001\n+chr1\t25010000\t25020000\tchr1\t25150000\t25160000\t0.001\n+chr1\t25720000\t25730000\tchr1\t26130000\t26140000\t0.001\n+chr1\t25930000\t25940000\tchr1\t26120000\t26130000\t0.001\n+chr1\t26220000\t26230000\tchr1\t26320000\t26330000\t0.001\n+chr1\t26360000\t26370000\tchr1\t26470000\t26480000\t0.001\n+chr1\t26930000\t26940000\tchr1\t27110000\t27120000\t0.001\n+chr1\t27430000\t27440000\tchr1\t27610000\t27620000\t0.001\n+chr1\t27620000\t27630000\tchr1\t27720000\t27730000\t0.001\n+chr1\t27720000\t27730000\tchr1\t27930000\t27940000\t0.001\n+chr1\t28180000\t28190000\tchr1\t28300000\t28310000\t0.001\n+chr1\t28180000\t28190000\tchr1\t28530000\t28540000\t0.001\n+chr1\t28410000\t28420000\tchr1\t28530000\t28540000\t0.001\n+chr1\t28570000\t28580000\tchr1\t28680000\t28690000\t0.001\n+chr1\t28680000\t28690000\tchr1\t29200000'..b'00\t0.001\n+chr1\t220460000\t220470000\tchr1\t220950000\t220960000\t0.001\n+chr1\t221040000\t221050000\tchr1\t221370000\t221380000\t0.001\n+chr1\t221040000\t221050000\tchr1\t221600000\t221610000\t0.001\n+chr1\t221040000\t221050000\tchr1\t222620000\t222630000\t0.001\n+chr1\t221650000\t221660000\tchr1\t222340000\t222350000\t0.001\n+chr1\t221650000\t221660000\tchr1\t222620000\t222630000\t0.001\n+chr1\t221910000\t221920000\tchr1\t222010000\t222020000\t0.001\n+chr1\t221910000\t221920000\tchr1\t222620000\t222630000\t0.001\n+chr1\t222630000\t222640000\tchr1\t223250000\t223260000\t0.001\n+chr1\t222960000\t222970000\tchr1\t223260000\t223270000\t0.001\n+chr1\t222960000\t222970000\tchr1\t223870000\t223880000\t0.001\n+chr1\t223300000\t223310000\tchr1\t223870000\t223880000\t0.001\n+chr1\t223310000\t223320000\tchr1\t223410000\t223420000\t0.001\n+chr1\t223880000\t223890000\tchr1\t224520000\t224530000\t0.001\n+chr1\t224300000\t224310000\tchr1\t224510000\t224520000\t0.001\n+chr1\t224700000\t224710000\tchr1\t225040000\t225050000\t0.001\n+chr1\t224880000\t224890000\tchr1\t225030000\t225040000\t0.001\n+chr1\t225660000\t225670000\tchr1\t226160000\t226170000\t0.001\n+chr1\t225960000\t225970000\tchr1\t226090000\t226100000\t0.001\n+chr1\t226170000\t226180000\tchr1\t226300000\t226310000\t0.001\n+chr1\t226730000\t226740000\tchr1\t227630000\t227640000\t0.001\n+chr1\t226820000\t226830000\tchr1\t227010000\t227020000\t0.001\n+chr1\t227660000\t227670000\tchr1\t228130000\t228140000\t0.001\n+chr1\t229390000\t229400000\tchr1\t230440000\t230450000\t0.001\n+chr1\t229390000\t229400000\tchr1\t229610000\t229620000\t0.001\n+chr1\t229850000\t229860000\tchr1\t230440000\t230450000\t0.001\n+chr1\t231050000\t231060000\tchr1\t231340000\t231350000\t0.001\n+chr1\t231490000\t231500000\tchr1\t231720000\t231730000\t0.001\n+chr1\t232000000\t232010000\tchr1\t233370000\t233380000\t0.001\n+chr1\t232000000\t232010000\tchr1\t232760000\t232770000\t0.001\n+chr1\t232770000\t232780000\tchr1\t233370000\t233380000\t0.001\n+chr1\t232770000\t232780000\tchr1\t233160000\t233170000\t0.001\n+chr1\t233530000\t233540000\tchr1\t234200000\t234210000\t0.001\n+chr1\t233570000\t233580000\tchr1\t233920000\t233930000\t0.001\n+chr1\t234340000\t234350000\tchr1\t234440000\t234450000\t0.001\n+chr1\t234610000\t234620000\tchr1\t235580000\t235590000\t0.001\n+chr1\t234630000\t234640000\tchr1\t235240000\t235250000\t0.001\n+chr1\t234630000\t234640000\tchr1\t235140000\t235150000\t0.001\n+chr1\t234630000\t234640000\tchr1\t234730000\t234740000\t0.001\n+chr1\t234740000\t234750000\tchr1\t234860000\t234870000\t0.001\n+chr1\t234860000\t234870000\tchr1\t234970000\t234980000\t0.001\n+chr1\t235140000\t235150000\tchr1\t235240000\t235250000\t0.001\n+chr1\t235410000\t235420000\tchr1\t235570000\t235580000\t0.001\n+chr1\t235670000\t235680000\tchr1\t235940000\t235950000\t0.001\n+chr1\t235670000\t235680000\tchr1\t236130000\t236140000\t0.001\n+chr1\t236020000\t236030000\tchr1\t236130000\t236140000\t0.001\n+chr1\t236260000\t236270000\tchr1\t237030000\t237040000\t0.001\n+chr1\t236270000\t236280000\tchr1\t236650000\t236660000\t0.001\n+chr1\t236320000\t236330000\tchr1\t236440000\t236450000\t0.001\n+chr1\t236770000\t236780000\tchr1\t237720000\t237730000\t0.001\n+chr1\t236770000\t236780000\tchr1\t237540000\t237550000\t0.001\n+chr1\t236910000\t236920000\tchr1\t237540000\t237550000\t0.001\n+chr1\t236920000\t236930000\tchr1\t237720000\t237730000\t0.001\n+chr1\t237970000\t237980000\tchr1\t240060000\t240070000\t0.001\n+chr1\t240890000\t240900000\tchr1\t241640000\t241650000\t0.001\n+chr1\t241690000\t241700000\tchr1\t241790000\t241800000\t0.001\n+chr1\t243500000\t243510000\tchr1\t244430000\t244440000\t0.001\n+chr1\t243510000\t243520000\tchr1\t243910000\t243920000\t0.001\n+chr1\t243870000\t243880000\tchr1\t244430000\t244440000\t0.001\n+chr1\t244760000\t244770000\tchr1\t245200000\t245210000\t0.001\n+chr1\t244760000\t244770000\tchr1\t244960000\t244970000\t0.001\n+chr1\t245310000\t245320000\tchr1\t246160000\t246170000\t0.001\n+chr1\t245310000\t245320000\tchr1\t246860000\t246870000\t0.001\n+chr1\t245310000\t245320000\tchr1\t246610000\t246620000\t0.001\n+chr1\t245310000\t245320000\tchr1\t246440000\t246450000\t0.001\n+chr1\t246050000\t246060000\tchr1\t246160000\t246170000\t0.001\n+chr1\t246170000\t246180000\tchr1\t246610000\t246620000\t0.001\n+chr1\t246660000\t246670000\tchr1\t246860000\t246870000\t0.001\n+chr1\t247370000\t247380000\tchr1\t247490000\t247500000\t0.001\n+chr1\t247550000\t247560000\tchr1\t247650000\t247660000\t0.001\n'
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/hicValidateLocations/overlap_smc3_statistics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,7 @@
+# HiCExplorer hicValidateLocations 3.3
+# Overlap of loop file /tmp/tmpo82hqd2o/files/4/a/4/dataset_4a45db46-19b9-4b40-9d5b-d049a100e2aa.dat with protein file /tmp/tmpo82hqd2o/files/3/5/8/dataset_358b0ce7-ab08-46fc-8968-195d416429ca.dat
+#
+Protein peaks: 3097
+Matched Loops: 530
+Total Loops: 1007
+Loops match protein: 0.5263157894736842
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/li_32-33mb_interactions.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/li_32-33mb_interactions.bedgraph Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,2 @@
+X 3139841 3367043 X 2851659 3139841 28764.634828529033
+X 3139841 3367043 X 3139841 3367043 139691.503741355060
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/li_viewpoint_32-33Mb.png
b
Binary file test-data/li_viewpoint_32-33Mb.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/li_viewpoint_32Mb.png
b
Binary file test-data/li_viewpoint_32Mb.png has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/raw_qc_report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_qc_report Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,29 @@
+
+File matrix.cool
+Sequenced reads 983
+Min rest. site distance 300
+Max library insert size 1000
+
+# count (percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality 300 (30.52)
+Hi-C contacts 215 (21.87)
+One mate unmapped 506 (51.48)
+One mate not unique 13 (1.32)
+Low mapping quality 164 (16.68)
+
+# count (percentage w.r.t. mappable, unique and high quality pairs)
+dangling end 0 (0.00)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 85 (28.33)
+self circle 0 (0.00)
+duplicated pairs 0 (0.00)
+
+# count (percentage w.r.t. total valid pairs used)
+inter chromosomal 24 (11.16)
+Intra short range (< 20kb) 61 (28.37)
+Intra long range (>= 20kb) 130 (60.47)
+Read pair type: inward pairs 42 (19.53)
+Read pair type: outward pairs 66 (30.70)
+Read pair type: left pairs 48 (22.33)
+Read pair type: right pairs 35 (16.28)
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regions.bed Mon Dec 16 15:27:02 2019 -0500
b
@@ -0,0 +1,2 @@
+chrX 10000000 15000000
+chrX 18000000 22000000
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/small_test_matrix.cool
b
Binary file test-data/small_test_matrix.cool has changed
b
diff -r 0c812ed34277 -r ce16a538ab46 test-data/small_test_matrix_result_sorted.bam
b
Binary file test-data/small_test_matrix_result_sorted.bam has changed