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Changeset 6:6001400eed99 (2021-03-16)

Previous changeset 5:6bc82c6d6620 (2020-12-11) Next changeset 7:6ef732512682 (2023-01-10)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

removed:
test-data/find_TADs/multiFDR_score.bedgraph

diff -r 6bc82c6d6620 -r 6001400eed99 chicSignificantInteractions.xml
--- a/chicSignificantInteractions.xml Fri Dec 11 21:43:10 2020 +0000
+++ b/chicSignificantInteractions.xml Tue Mar 16 15:33:42 2021 +0000

[

b'@@ -1,4 +1,4 @@\n-<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n+<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>computes viewpoints with the given reference points and a background model</description>\n <macros>\n <token name="@BINARY@">chicSignificantInteractions</token>\n@@ -17,8 +17,7 @@\n tar -C interactionFiles -xvf viewpoints.tar &&\n #else:\n #for $file in $tar_input_conditional.interactionFiles:\n- #set identifier = @ESCAPE_IDENTIFIER_FILE@\n- \n+ #set identifier = @ESCAPE_IDENTIFIER_FILE@ \n ln -s \'$file\' \'interactionFiles/$identifier\' &&\n #end for\n #end if\n@@ -30,9 +29,8 @@\n #if $batchmode_conditional.batchmode_selector == \'optionSinglemode\':\n --interactionFile $interactonfileslist\n --computeSampleNumber $batchmode_conditional.computeSampleNumber\n-\n #else:\n- --interactionFile $batchmode_conditional.interactionFilesOrderFile\n+ --interactionFile \'$batchmode_conditional.interactionFilesOrderFile\'\n --interactionFileFolder interactionFiles\n --batchMode\n --targetFileList targetListFile.txt\n@@ -71,7 +69,7 @@\n && rm -rf significantFilesFolder\n \n #end if\n- ]]></command>\n+ ]]> </command>\n <inputs>\n <conditional name="tar_input_conditional">\n <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">\n@@ -79,29 +77,26 @@\n <option value="interval_input" selected="True">Interval files</option>\n </param>\n <when value="tar_input">\n- <param name=\'interactionFiles\' type="data" format="tar" label="Interaction files" multiple="false"/>\n+ <param name=\'interactionFiles\' type="data" format="tar" label="Interaction files" multiple="false" />\n </when>\n <when value="interval_input">\n- <param name=\'interactionFiles\' type="data" format="interval" label="Interaction files" multiple="true"/>\n+ <param name=\'interactionFiles\' type="data" format="interval" label="Interaction files" multiple="true" />\n </when>\n </conditional>\n-\n-\n-\n <conditional name="batchmode_conditional">\n <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">\n <option value="optionBatchmode">Batch processing</option>\n <option value="optionSinglemode" selected="True">Single file processing</option>\n </param>\n <when value="optionBatchmode">\n- <param name=\'interactionFilesOrderFile\' type="data" format="txt" label="Interaction file order"/>\n- <param name=\'computeSampleNumber\' type="integer" value=\'2\' label="Create one target file for n consecutive files."/>\n+ <param name=\'interactionFilesOrderFile\' type="data" format="txt" label="Interaction file order" />\n+ <param name=\'computeSampleNumber\' type="integer" value=\'2\' label="Create one target file for n consecutive files." />\n </when>\n <when value="optionSinglemode">\n- <param name=\'computeSampleNumber\' type="integer" value=\'2\' label="Create one target file for n consecutive files."/>\n+ <param name=\'computeSampleNumber\' type="integer" value=\'2\' label="Create one target file for n consecutive files." />\n </when>\n </conditional>\n- <param name=\'pvalue\' type="float" value=\'0.05\' label="P-value of interaction to be accepted as significant"/>\n+ <param name=\'pvalue\' type="float" value=\'0.05\' label="P-value of interaction to be accepted as '..b'lue="cHi-C/chicViewpoint/viewpoints.tar" />\n+ </conditional>\n+ <conditional name="batchmode_conditional">\n+ <param name="batchmode_selector" value=\'optionBatchmode\' />\n+ <param name="interactionFilesOrderFile" value=\'cHi-C/chicViewpoint/fileNames_two_matrices.txt\' />\n+ <param name="computeSampleNumber" value=\'2\' />\n+ </conditional>\n+ <param name="pvalue" value=\'0.2\' />\n+\n+ <conditional name="filter_conditional">\n+ <param name="filter_selector" value=\'optionLoosePvalue\' />\n+ <param name="loosePvalue" value=\'0.5\' />\n+ </conditional>\n+\n+ <param name="backgroundModelFile" value="cHi-C/background.txt" />\n+ <param name="rangeUpstream" value="200000" />\n+ <param name="rangeDownstream" value="200000" />\n+\n+ <param name=\'tar\' value=\'True\' />\n \n <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n \n- <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n- <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n+ <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta=\'40000\' />\n+ <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta=\'40000\' />\n </test>\n-\n- <test>\n- <conditional name="tar_input_conditional">\n- <param name="tar_input_selector" value=\'tar_input\'/>\n- <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar"/>\n- </conditional>\n- <conditional name="batchmode_conditional">\n- <param name="batchmode_selector" value=\'optionBatchmode\'/>\n- <param name="interactionFilesOrderFile" value=\'cHi-C/chicViewpoint/fileNames_two_matrices.txt\'/>\n- <param name="computeSampleNumber" value=\'2\'/>\n- </conditional>\n- <param name="pvalue" value=\'0.2\'/>\n-\n- <conditional name="filter_conditional">\n- <param name="filter_selector" value=\'optionLoosePvalue\'/>\n- <param name="loosePvalue" value=\'0.5\'/>\n- </conditional>\n-\n- <param name="backgroundModelFile" value="cHi-C/background.txt"/>\n- <param name="rangeUpstream" value="200000"/>\n- <param name="rangeDownstream" value="200000"/>\n-\n- <param name=\'tar\' value=\'True\'/>\n-\n- <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n- <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype=\'tar\' compare="sim_size" delta=\'40000\' />\n-\n- <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n- <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta=\'40000\'/>\n- </test>\n-\n </tests>\n <help><![CDATA[\n \n@@ -298,6 +337,6 @@\n For more information about HiCExplorer please consider our documentation on readthedocs.io_\n \n .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html\n-]]></help>\n+]]> </help>\n <expand macro="citations" />\n </tool>\n'

diff -r 6bc82c6d6620 -r 6001400eed99 macros.xml
--- a/macros.xml Fri Dec 11 21:43:10 2020 +0000
+++ b/macros.xml Tue Mar 16 15:33:42 2021 +0000

b'@@ -1,6 +1,7 @@\n <macros>\n <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n- <token name="@WRAPPER_VERSION@">3.4.3</token>\n+ <token name="@TOOL_VERSION@">3.6</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n <token name="@USE_RANGE@">\n #if $use_range.select_use_range == "yes_use_range":\n --range $use_range.range_min:$use_range.range_max\n@@ -9,7 +10,7 @@\n \n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">hicexplorer</requirement>\n <yield />\n </requirements>\n <version_command>@BINARY@ --version</version_command>\n@@ -28,7 +29,7 @@\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+ <param argument="--chromosomes" type="text" value="">\n <validator type="empty_field" />\n </param>\n </repeat>\n@@ -40,17 +41,45 @@\n <yield />\n </citations>\n </xml>\n+ <xml name="dpi">\n+ <param argument=\'--dpi\' type=\'integer\' optional=\'true\' min="10" max="1000" label=\'DPI for image\' help=\'Change the default resolution of the plot.\' />\n+ </xml>\n+\n+ <xml name="restrictionCutFile">\n+ <param argument="--restrictionCutFile" type="data" format="bed" optional="false" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments\n+ (i.e. the region between one restriction site and the next)." />\n+ </xml>\n+\n+ <xml name="restrictionSequence">\n+ <param argument="--restrictionSequence" type="text" optional="false" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or\n+ "dangling-ends". If not given, such statistics will not be available.">\n+ <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>\n+ </param>\n+ </xml>\n+ <xml name="danglingSequence">\n+ <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.\n+ Each restriction enzyme recognizes a different DNA sequence and,\n+ after cutting, they leave behind a specific \xe2\x80\x98sticky\xe2\x80\x99 end or dangling end sequence.\n+ For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.\n+ For DpnII, the restriction site and dangling end sequence are the same: GATC.\n+ This information is easily found on the description of the restriction enzyme.\n+ The dangling sequence is used to classify and report reads whose 5\xe2\x80\x99 end starts with such sequence as dangling-end reads.\n+ A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">\n+ <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator>\n+ </param>\n+ </xml>\n \n <xml name="zMax">\n- <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> \n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />\n+ \n </xml>\n <xml name="use_range">\n- '..b' <param name="showOutputSettings" type="select" label="Show advanced output settings" >\n+ <conditional name="output">\n+ <param name="showOutputSettings" type="select" label="Show advanced output settings">\n <option value="no" selected="true">no</option>\n <option value="yes">yes</option>\n </param>\n <when value="no" />\n <when value="yes">\n <yield />\n- <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n- <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile" />\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap." />\n </when>\n </conditional>\n </xml>\n@@ -668,32 +643,33 @@\n </xml>\n \n <xml name="track_input_h5_macro">\n- <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n+ <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format" />\n </xml>\n <xml name="track_input_bed_macro">\n- <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n+ <param name="track_input_bed" type="data" format="bed" label="Track file BED format" />\n </xml>\n <xml name="track_input_bedgraph_macro">\n- <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" />\n </xml>\n <xml name="track_input_bigwig_macro">\n- <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" />\n </xml>\n <xml name="track_input_bedgraph_matrix_macro">\n- <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" />\n </xml>\n <xml name="track_input_tabular_macro">\n- <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n+ <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format" />\n </xml>\n <xml name="plot_title">\n- <param name="title" type="text" optional="true" label="Plot title"/>\n+ <param name="title" type="text" optional="true" label="Plot title">\n+ <validator type="expression" message="Only alphanumeric characters and a space are allowed.">value.isalnum()</validator>\n+ </param>\n </xml>\n \n <xml name="spacer_macro">\n- <param name="spacer_width" type="float" value="" optional="True"\n- label="Include spacer at the end of the track." help="Width of the spacer." />\n+ <param name="spacer_width" type="float" value="" min="0" optional="True" label="Include spacer at the end of the track" help="Width of the spacer." />\n </xml>\n <xml name="fontsize_macro">\n- <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ <param name="fontsize" type="integer" value="" min="5" optional="True" label="Fontsize" />\n </xml>\n </macros>\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/DpnII_10k.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DpnII_10k.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,5000 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No newline at end of file\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/background.txt
--- a/test-data/cHi-C/background.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/background.txt Tue Mar 16 15:33:42 2021 +0000

b'@@ -1,1002 +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\t0.0000'..b'000000000\t0.000382823833\n+444000\t144.859828494596\t0.996903162520\t1.400000000000\t0.000384117157\n+445000\t181.127453398191\t0.997559041921\t1.400000000000\t0.000384117157\n+446000\t160.136119588827\t0.997366406029\t1.600000000000\t0.000359893553\n+447000\t153.653411583530\t0.997172630419\t1.200000000000\t0.000375581220\n+448000\t141.661704353510\t0.997163979271\t1.400000000000\t0.000345930071\n+449000\t124.591789049055\t0.996755483579\t1.400000000000\t0.000346179660\n+450000\t140.232016383950\t0.997067070092\t1.200000000000\t0.000352107394\n+451000\t136.018310879152\t0.997198243244\t1.000000000000\t0.000330767552\n+452000\t246.419596102391\t0.998452925685\t1.000000000000\t0.000325917588\n+453000\t133.267828865974\t0.997093260709\t1.000000000000\t0.000330767552\n+454000\t111.562325167782\t0.996668013833\t1.000000000000\t0.000325432591\n+455000\t136.735744503062\t0.997168723327\t1.000000000000\t0.000331395194\n+456000\t107.078418601392\t0.996473504625\t1.000000000000\t0.000323467080\n+457000\t129.245163973247\t0.997085556223\t1.000000000000\t0.000322468725\n+458000\t105.576577704040\t0.996545373786\t1.000000000000\t0.000312171404\n+459000\t127.868794891999\t0.997409239339\t0.800000000000\t0.000283033695\n+460000\t106.303153236011\t0.997074941993\t0.600000000000\t0.000266120383\n+461000\t126.838873099817\t0.997248182634\t0.800000000000\t0.000298757789\n+462000\t142.511212214533\t0.997018798351\t0.800000000000\t0.000363705134\n+463000\t110.665900101286\t0.996960672273\t0.800000000000\t0.000288455796\n+464000\t95.203501929856\t0.995744217821\t1.800000000000\t0.000347324326\n+465000\t137.363904547769\t0.997021971833\t1.800000000000\t0.000352107394\n+466000\t118.557203735630\t0.996290881001\t2.400000000000\t0.000376758591\n+467000\t104.819090517074\t0.995525960971\t2.800000000000\t0.000402408450\n+468000\t114.597405436879\t0.995690757202\t2.800000000000\t0.000423382467\n+469000\t129.271097317921\t0.997170331551\t1.400000000000\t0.000314762670\n+470000\t192.030681022578\t0.997984998366\t1.400000000000\t0.000330423361\n+471000\t148.206038001898\t0.997389657398\t1.000000000000\t0.000331090883\n+472000\t97.546089803069\t0.995843333605\t1.200000000000\t0.000347128098\n+473000\t95.851837787801\t0.995983996487\t1.200000000000\t0.000330056224\n+474000\t99.818854582017\t0.996557343281\t1.000000000000\t0.000294342649\n+475000\t148.008769541300\t0.997902427625\t0.600000000000\t0.000265562479\n+476000\t148.345768593866\t0.997933098098\t0.600000000000\t0.000262644210\n+477000\t123.596807612976\t0.997297923191\t0.600000000000\t0.000284531228\n+478000\t204.246569441019\t0.998287432528\t1.000000000000\t0.000298757789\n+479000\t132.924248355030\t0.997278666969\t0.800000000000\t0.000309427710\n+480000\t136.416688826340\t0.997425348906\t0.800000000000\t0.000301268359\n+481000\t118.446922382493\t0.997078476496\t1.000000000000\t0.000296247219\n+482000\t118.529156084928\t0.997003411887\t1.200000000000\t0.000304092749\n+483000\t190.680584441799\t0.998045921750\t1.000000000000\t0.000318674975\n+484000\t192.305361142196\t0.998005560472\t1.200000000000\t0.000328791641\n+485000\t171.354362305989\t0.997464844394\t1.200000000000\t0.000373052054\n+486000\t120.791244594597\t0.996480163123\t1.600000000000\t0.000364199971\n+487000\t230.056159698575\t0.998148828248\t1.600000000000\t0.000364199971\n+488000\t195.433175858843\t0.997957440166\t1.400000000000\t0.000341437473\n+489000\t126.632801152788\t0.996613466031\t1.600000000000\t0.000367303948\n+490000\t169.329748474940\t0.997643487089\t1.200000000000\t0.000341437473\n+491000\t136.266699963976\t0.997144438338\t1.000000000000\t0.000336264178\n+492000\t132.474984457930\t0.997281892907\t1.000000000000\t0.000312171404\n+493000\t143.910368825532\t0.997529065543\t1.200000000000\t0.000304092749\n+494000\t115.246894063938\t0.997187873361\t1.200000000000\t0.000278027657\n+495000\t170.264731113853\t0.997728931336\t1.200000000000\t0.000331682117\n+496000\t150.361715442266\t0.997070480810\t1.200000000000\t0.000380834105\n+497000\t132.494299731452\t0.996465234668\t1.400000000000\t0.000400817903\n+498000\t197.912620506313\t0.997679641998\t1.200000000000\t0.000393395349\n+499000\t142.734281997358\t0.996531092376\t1.000000000000\t0.000426796841\n+500000\t10.000000000000\tnan\t0.000000000000\t0.000000000000\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicQualityControl/histogram.png

Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.4.3
+# Created with chicQualityControl version 3.6
# A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
# Used Matrices 0_matrix.cool 1_matrix.cool
# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.4.3
+# Created with chicQualityControl version 3.6
# QC report for matrices: 0_matrix.cool 1_matrix.cool
#Sparsity threshold for rejection: sparsity <= 0.05 are rejected.

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicQualityControl/sparsity.png

Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,8 +1,8 @@
# /home/wolffj/src/HiCExplorer/hicexplorer/test/test_data/cHi-C/FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
-chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.00703769867936687721 7.81112575817000021061 5.59999999999999964473
-chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864070004 3.78135593591500018817 39.00000000000000000000
-chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04850785315391703545 3.19033393500999995496 10.19999999999999928946
-chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.03491443188205700654 3.51709033858399999772 9.80000000000000071054
-chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000001048074382837 19.28508294646199772160 7.59999999999999875655
+chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.00706210137955387562 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10178166638720864690 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.04060984916018672841 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.02428991556274540109 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000047362266253348 19.28508294646199772160 7.59999999999999875655
chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000000011102 56.96782483342801128856 20.64999999999999857891

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt
# Mode: x-fold background with 1.5
# Used p-value: 0.2

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
# targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
# Mode: x-fold background with 1.5
# Used p-value: 0.2

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,8 +1,8 @@
# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
-chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885902431 9.15400589712000112286 7.00000000000000000000
-chr1 14295000 14372000 Eya1 673.0 -1000 0.73997028231099992723 0.00004780944416038491 71.55022378473699973256 497.99999999999977262632
-chr1 14391000 14404000 Eya1 673.0 99000 0.01485884100899999803 0.00001657170147506548 12.71460890380599906280 10.00000000000000000000
-chr1 14405000 14431000 Eya1 673.0 126000 0.01485884100399999762 0.00000000019301882315 16.50018487636599928692 10.00000000000000532907
-chr1 14447000 14465000 Eya1 673.0 150000 0.01485884100799999760 0.00000000084501772246 20.98645213257099939597 10.00000000000000177636
+chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00132401127244263783 9.15400589712000112286 7.00000000000000000000
+chr1 14295000 14372000 Eya1 673.0 -1000 0.73997028231099992723 0.00000273538672768137 71.55022378473699973256 497.99999999999977262632
+chr1 14391000 14404000 Eya1 673.0 99000 0.01485884100899999803 0.00000099822649402004 12.71460890380599906280 10.00000000000000000000
+chr1 14405000 14431000 Eya1 673.0 126000 0.01485884100399999762 0.00000000706881753132 16.50018487636599928692 10.00000000000000532907
+chr1 14447000 14465000 Eya1 673.0 150000 0.01485884100799999760 0.00000000163091362637 20.98645213257099939597 10.00000000000000177636
chr1 14476000 14501000 Eya1 673.0 200000 0.04494799405200000653 0.00000000000000011102 81.22289233532099217427 30.24999999999999644729

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,10 +1,10 @@
# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
-chr1 19088000 19093000 Tfap2d 472.0 -1000 0.25550847457600001089 0.11635169910476195199 8.11832748109999968733 120.59999999999999431566
-chr1 19094000 19118000 Tfap2d 472.0 1000 0.38686440678100009194 0.03474409585293225522 32.83428528261499934615 182.60000000000005115908
-chr1 19124000 19141000 Tfap2d 472.0 33000 0.04661016949300000184 0.00000002462477854959 22.39995010446000023308 22.00000000000000000000
-chr1 19143000 19150000 Tfap2d 472.0 52000 0.01059322034000000079 0.01821075341789391011 7.00310519245599927274 5.00000000000000000000
-chr1 19153000 19185000 Tfap2d 472.0 65000 0.03177966102100000800 0.00000000020590662508 24.96572554191800108470 14.99999999999999467093
-chr1 19186000 19210000 Tfap2d 472.0 108000 0.03177966101800000498 0.00000007308534966111 29.45424687062300250773 15.00000000000000000000
-chr1 19215000 19251000 Tfap2d 472.0 137000 0.04237288135900001140 0.00000000012967626972 56.40252329690899557590 19.99999999999999644729
-chr1 19252000 19264000 Tfap2d 472.0 163000 0.01694915254200000249 0.00000130986798663191 24.34766306781100198009 8.00000000000000000000
+chr1 19088000 19093000 Tfap2d 472.0 -1000 0.25550847457600001089 0.10302839603584690309 8.11832748109999968733 120.59999999999999431566
+chr1 19094000 19118000 Tfap2d 472.0 1000 0.38686440678100009194 0.02157410618457478169 32.83428528261499934615 182.60000000000005115908
+chr1 19124000 19141000 Tfap2d 472.0 33000 0.04661016949300000184 0.00000000000393274302 22.39995010446000023308 22.00000000000000000000
+chr1 19143000 19150000 Tfap2d 472.0 52000 0.01059322034000000079 0.01905738347386221054 7.00310519245599927274 5.00000000000000000000
+chr1 19153000 19185000 Tfap2d 472.0 65000 0.03177966102100000800 0.00000000000269295697 24.96572554191800108470 14.99999999999999467093
+chr1 19186000 19210000 Tfap2d 472.0 108000 0.03177966101800000498 0.00000001275562755421 29.45424687062300250773 15.00000000000000000000
+chr1 19215000 19251000 Tfap2d 472.0 137000 0.04237288135900001140 0.00000000000112376775 56.40252329690899557590 19.99999999999999644729
+chr1 19252000 19264000 Tfap2d 472.0 163000 0.01694915254200000249 0.00000062934133893133 24.34766306781100198009 8.00000000000000000000

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,5 +1,5 @@
# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
-chr1 14290000 14439000 Eya1 832.0 -1000 0.77524038462200028921 0.00000214655292485322 124.40376311550902244107 645.00000000000000000000
+chr1 14290000 14439000 Eya1 832.0 -1000 0.77524038462200028921 0.00000003592597119795 124.40376311550902244107 645.00000000000000000000
chr1 14444000 14467000 Eya1 832.0 149000 0.03004807692100000191 0.00000000000000011102 43.43355247431500032462 25.00000000000000000000
chr1 14484000 14501000 Eya1 832.0 200000 0.02902644230799999656 0.00000000000000011102 53.10190206687700253951 24.15000000000000213163

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,6 +1,6 @@
# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
-chr1 19077000 19083000 Tfap2d 800.0 -15000 0.01875000000000000278 0.00087756598335464453 9.05078678760400023862 15.00000000000000000000
-chr1 19084000 19118000 Tfap2d 800.0 0 0.64874999999999971578 0.00000017949046560162 44.36507725070399033029 518.99999999999988631316
+chr1 19077000 19083000 Tfap2d 800.0 -15000 0.01875000000000000278 0.00009145581248537482 9.05078678760400023862 15.00000000000000000000
+chr1 19084000 19118000 Tfap2d 800.0 0 0.64874999999999971578 0.00000005045883955113 44.36507725070399033029 518.99999999999988631316
chr1 19120000 19249000 Tfap2d 800.0 105000 0.25625000000000008882 0.00000000000000011102 244.06286621622496113559 204.99999999999994315658
-chr1 19258000 19274000 Tfap2d 800.0 169000 0.01000000000000000021 0.00000195299526528636 14.62211731845800244400 8.00000000000000000000
+chr1 19258000 19274000 Tfap2d 800.0 169000 0.01000000000000000021 0.00000152506365280747 14.62211731845800244400 8.00000000000000000000

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt
# Mode: loose p-value with 0.5
# Used p-value: 0.2
@@ -6,4 +6,4 @@
chr1 14274000 14279000
chr1 14290000 14439000
chr1 14444000 14467000
-chr1 14476000 14501000
+chr1 14484000 14501000

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt
# Mode: loose p-value with 0.5
# Used p-value: 0.2

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
--- a/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.4.3
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.6
# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt
# Mode: loose p-value with 0.5
# Used p-value: 0.2

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt
--- a/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt Tue Mar 16 15:33:42 2021 +0000

b"@@ -1,4 +1,4 @@\n-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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@@ -42,11 +42,11 @@\n chr1\t14137000\t14138000\tEya1\t673.0\t-163000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14138000\t14139000\tEya1\t673.0\t-162000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14139000\t14140000\tEya1\t673.0\t-161000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t14140000\t14141000\tEya1\t673.0\t-160000\t0.000891530461\t0.012107544045\t4.242405017910\t0.600000000000\n-chr1\t14141000\t14142000\tEya1\t673.0\t-159000\t0.000891530461\t0.012107544045\t4.789812097144\t0.600000000000\n-chr1\t14142000\t14143000\tEya1\t673.0\t-158000\t0.000891530461\t0.012107544045\t4.303889149198\t0.600000000000\n-chr1\t14143000\t14144000\tEya1\t673.0\t-157000\t0.000891530461\t0.012107544045\t4.367181637306\t0.600000000000\n-chr1\t14144000\t14145000\tEya1\t673.0\t-156000\t0.000891530461\t0.012107544045\t5.120143967809\t0.600000000000\n+chr1\t14140000\t14141000\tEya1\t673.0\t-160000\t0.000891530461\t0.232516348110\t2.088887205761\t0.600000000000\n+chr1\t14141000\t14142000\tEya1\t673.0\t-159000\t0.000891530461\t0.232516348110\t2.274191716551\t0.600000000000\n+chr1\t14142000\t14143000\tEya1\t673.0\t-158000\t0.000891530461\t0.232516348110\t2.043476610792\t0.600000000000\n+chr1\t14143000\t14144000\tEya1\t673.0\t-157000\t0.000891530461\t0.232516348110\t2.303919713268\t0.600000000000\n+chr1\t14144000\t14145000\tEya1\t673.0\t-156000\t0.000891530461\t0.232516348110\t2.431032520312\t0.600000000000\n chr1\t14145000\t14146000\tEya1\t673.0\t-155000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14146000\t14147000\tEya1\t673.0\t-154000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14147000\t14148000\tEya1\t673.0\t-153000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n@@ -77,53 +77,53 @@\n chr1\t14172000\t14173000\tEya1\t673.0\t-128000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14173000\t14174000\tEya1\t673.0\t-127000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14174000\t14175000\tEya1\t673.0\t-126000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t14175000\t14176000\tEya1\t673.0\t-125000\t0.000297176820\t0.042850447268\t0.916568982282\t0.200000000000\n-chr1\t14176000\t14177000\tEya1\t673.0\t-124000\t0.000297176820\t0.042850447268\t0.908160092485\t0.200000000000\n-chr1\t14177000\t14178000\tEya1\t673.0\t-123000\t0.000297176820\t0.042850447268\t0.798302018335\t0.200000000000\n-chr1\t14178000\t14179000\tEya1\t673.0\t-122000\t0.000297176820\t0.042850447268\t0.925135047590\t0.200000000000\n-chr1\t14179000\t14180000\tEya1\t673.0\t-121000\t0.000297176820\t0.042850447268\t0.883834378206\t0.200000000000\n+chr1\t14175000\t14176000\tEya1\t673.0\t-125000\t0.000297176820\t0.378306706409\t0.499656661362\t0.200000000000\n+chr1\t14176000\t14177000\tEya1\t673.0\t-124000\t0.000297176820\t0.378306706409\t0.415222227347\t0.200000000000\n+chr1\t14177000\t14178000\tEya1\t673.0\t-123000\t0.000297176820\t0.378306706409\t0.393070172785\t0.200000000000\n+chr1\t14178000\t14179000\tEya1\t673.0\t-122000\t0.000297176820\t0.378306706409\t0.455520574435\t0.200000000000\n+chr1\t14179000\t14180000\tEya1\t673.0\t-121000\t0.000297176820\t0.378306706409\t0.450727149836\t0.200000000000\n chr1\t14180000\t14181000\tEya1\t673.0\t-120000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14181000\t14182000\tEya1\t673.0\t-119000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t14182000\t14183000\tEya1\t673.0\t-118000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t14183000\t14184000\tEya1\t673.0\t-117000\t0.000297176820\t0.042850447268\t0.860777829009\t0.200000000000\n-chr1\t14184000\t14185000\tEya1\t673.0\t-116000\t0.000297176820\t0.042850447268\t0.791915602137\t0.200000000000\n-chr1\t14185000\t14186000\tEya1\t673.0\t-115000\t0.000297176820\t0.04285"..b'14412\t0.800000000000\n-chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.000000000000\t2.140312436513\t0.800000000000\n-chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.000000000000\t1.058710697124\t0.400000000000\n-chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.000000000000\t0.575520059550\t0.200000000000\n-chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.000000000000\t0.578885673960\t0.200000000000\n-chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.000000000000\t3.849589730333\t1.400000000000\n-chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.000000000000\t5.982878858272\t2.200000000000\n-chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.000000000000\t5.892229182196\t2.000000000000\n-chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.000000000000\t6.294126893758\t2.200000000000\n-chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.000000000000\t6.680269651133\t2.200000000000\n-chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.000000000000\t6.072972410121\t2.000000000000\n-chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.000000000000\t3.937080406684\t1.400000000000\n-chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.000000000000\t4.852424033528\t2.000000000000\n-chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.000000000000\t5.830530441735\t2.250000000000\n-chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t0.000000000000\t7.575723225668\t3.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t1.000000000000\t0.377777473345\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t1.000000000000\t0.387710125250\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t1.000000000000\t0.804681391196\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t1.000000000000\t0.853631790099\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t1.000000000000\t2.209060071856\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t1.000000000000\t1.740739337114\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t1.000000000000\t1.946633238000\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t1.000000000000\t2.611109005672\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t1.000000000000\t3.150313631272\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t1.000000000000\t1.707263580199\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t1.000000000000\t1.814813352082\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t1.000000000000\t1.806605148755\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t1.000000000000\t0.912259118375\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t1.000000000000\t0.475667144687\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t1.000000000000\t0.488628585681\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t1.000000000000\t3.452466352281\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t1.000000000000\t5.155266499539\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t1.000000000000\t4.559079214345\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t1.000000000000\t5.423459548891\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t1.000000000000\t5.638713926662\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t1.000000000000\t5.019309740274\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t1.000000000000\t3.323229640928\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t1.000000000000\t4.181187622141\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t1.000000000000\t4.818931539295\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t6.794212212290\t3.000000000000\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt
--- a/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt Tue Mar 16 15:33:42 2021 +0000

b"@@ -1,4 +1,4 @@\n-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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@@ -195,75 +195,75 @@\n chr1\t4477000\t4478000\tSox17\t810.0\t-10000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t4478000\t4479000\tSox17\t810.0\t-9000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t4479000\t4480000\tSox17\t810.0\t-8000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t4480000\t4481000\tSox17\t810.0\t-7000\t0.002222222222\t0.000185972288\t0.779180117089\t1.800000000000\n-chr1\t4481000\t4482000\tSox17\t810.0\t-6000\t0.002222222222\t0.000185972288\t0.537170617614\t1.800000000000\n-chr1\t4482000\t4483000\tSox17\t810.0\t-5000\t0.002222222222\t0.000185972288\t0.379990303436\t1.800000000000\n-chr1\t4483000\t4484000\tSox17\t810.0\t-4000\t0.012098765432\t0.000000000000\t1.215347622436\t9.800000000000\n-chr1\t4484000\t4485000\tSox17\t810.0\t-3000\t0.032839506173\t0.000000000000\t1.523937459823\t26.600000000000\n-chr1\t4485000\t4486000\tSox17\t810.0\t-2000\t0.092592592593\t0.000000000000\t1.384128990547\t75.000000000000\n-chr1\t4486000\t4487000\tSox17\t810.0\t-1000\t0.111111111111\t0.000000000000\t1.453408818204\t90.000000000000\n-chr1\t4487000\t4488000\tSox17\t810.0\t0\t0.114567901235\t0.188793973612\t1.440149085516\t92.800000000000\n-chr1\t4488000\t4489000\tSox17\t810.0\t1000\t0.105432098765\t0.000000000000\t1.347376918585\t85.400000000000\n-chr1\t4489000\t4490000\tSox17\t810.0\t2000\t0.086913580247\t0.000000000000\t1.270443659967\t70.400000000000\n-chr1\t4490000\t4491000\tSox17\t810.0\t3000\t0.028395061728\t0.000000000000\t1.145359755892\t23.000000000000\n-chr1\t4491000\t4492000\tSox17\t810.0\t4000\t0.014320987654\t0.000000000000\t0.915431553855\t11.600000000000\n-chr1\t4492000\t4493000\tSox17\t810.0\t5000\t0.010864197531\t0.000000000000\t0.897089431163\t8.800000000000\n-chr1\t4493000\t4494000\tSox17\t810.0\t6000\t0.012345679012\t0.000000000000\t1.180011336066\t10.000000000000\n-chr1\t4494000\t4495000\tSox17\t810.0\t7000\t0.010123456790\t0.000000000000\t1.060081230757\t8.200000000000\n-chr1\t4495000\t4496000\tSox17\t810.0\t8000\t0.009382716049\t0.000000000000\t1.076973819704\t7.600000000000\n-chr1\t4496000\t4497000\tSox17\t810.0\t9000\t0.005432098765\t0.000000000000\t0.678705694908\t4.400000000000\n-chr1\t4497000\t4498000\tSox17\t810.0\t10000\t0.006666666667\t0.000000000000\t0.919910245827\t5.400000000000\n-chr1\t4498000\t4499000\tSox17\t810.0\t11000\t0.007407407407\t0.000000000000\t1.156776232338\t6.000000000000\n-chr1\t4499000\t4500000\tSox17\t810.0\t12000\t0.009876543210\t0.000000000000\t1.659037622278\t8.000000000000\n-chr1\t4500000\t4501000\tSox17\t810.0\t13000\t0.007654320988\t0.000000000000\t1.425181941894\t6.200000000000\n-chr1\t4501000\t4502000\tSox17\t810.0\t14000\t0.007654320988\t0.000000000000\t1.576778289436\t6.200000000000\n-chr1\t4502000\t4503000\tSox17\t810.0\t15000\t0.006666666667\t0.000000000000\t1.434537037015\t5.400000000000\n-chr1\t4503000\t4504000\tSox17\t810.0\t16000\t0.003950617284\t0.000000000000\t0.867467792926\t3.200000000000\n-chr1\t4504000\t4505000\tSox17\t810.0\t17000\t0.001975308642\t0.000000000000\t0.470317599024\t1.600000000000\n-chr1\t4505000\t4506000\tSox17\t810.0\t18000\t0.001728395062\t0.000000000000\t0.423640567251\t1.400000000000\n-chr1\t4506000\t4507000\tSox17\t810.0\t19000\t0.003456790123\t0.000000000000\t0.869022688092\t2.800000000000\n-chr1\t4507000\t4508000\tSox17\t810.0\t20000\t0.005185185185\t0.000000000000\t1.383960410629\t4.200000000000\n-chr1\t4508000\t4509000\tSox17\t810.0\t21000\t0.005432098765\t0.000000000000\t1.490469013972\t4.400000000000\n-chr1\t4509000\t4510000\tSox17\t810.0\t22000\t0.006419753086\t0.000000000000\t1.835550680659\t5.200000000000\n-chr1\t4510000\t4511000\tSox17\t810.0\t23000\t0.007160493827\t0.000000000000\t2.286823503223\t5.800000000000\n-chr1\t4511000\t4512000\tSox17\t810.0\t24000\t0.005679012346\t0.000000000000\t1.847340012418\t4.600000000000\n-chr1\t4512000\t4513000\tSox17\t810.0\t25000\t0.005679012346\t0.000000000000\t1.948173195509\t4.6000"..b'0.000493827160\t1.000000000000\t0.668580958364\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t1.000000000000\t0.354626046134\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t1.000000000000\t0.367085784780\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t1.000000000000\t0.361579498110\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t1.000000000000\t0.404346965794\t0.200000000000\n chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.000000000000\t0.401203854492\t0.200000000000\n-chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.000000000000\t0.395417260391\t0.200000000000\n-chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.000000000000\t0.437482925987\t0.200000000000\n-chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.000000000000\t0.444577243757\t0.200000000000\n-chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.000000000000\t0.879644813784\t0.400000000000\n-chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.000000000000\t0.478179012441\t0.200000000000\n-chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.000000000000\t0.480975380957\t0.200000000000\n-chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.000000000000\t1.370779835192\t0.600000000000\n-chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.000000000000\t1.355716320410\t0.600000000000\n-chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.000000000000\t1.468692681340\t0.600000000000\n-chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.000000000000\t1.426244915656\t0.600000000000\n-chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.000000000000\t1.513744604449\t0.600000000000\n-chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.000000000000\t1.009163069632\t0.400000000000\n-chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.000000000000\t0.934622615061\t0.400000000000\n-chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.000000000000\t0.403170540070\t0.200000000000\n-chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.000000000000\t0.538264332961\t0.250000000000\n-chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.000000000000\t0.699377466512\t0.333333333333\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t1.000000000000\t0.373926115317\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t1.000000000000\t0.354626046134\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t1.000000000000\t0.376965859861\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t1.000000000000\t0.375260884294\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t1.000000000000\t0.757963440329\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t1.000000000000\t0.395214800462\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t1.000000000000\t0.405983997732\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t1.000000000000\t1.229370293696\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t1.000000000000\t1.168179917236\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t1.000000000000\t1.136392707872\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t1.000000000000\t1.228952281617\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t1.000000000000\t1.277728778668\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t1.000000000000\t0.834072951902\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t1.000000000000\t0.788900722520\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t1.000000000000\t0.347399909840\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t1.000000000000\t0.444875298484\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t1.000000000000\t0.627229741958\t0.333333333333\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt
--- a/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt Tue Mar 16 15:33:42 2021 +0000

b"@@ -1,4 +1,4 @@\n-# Interaction file, created with HiCExplorer's chicViewpoint version 3.4.3\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.6\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@@ -95,18 +95,18 @@\n chr1\t18983000\t18984000\tTfap2d\t800.0\t-110000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t18984000\t18985000\tTfap2d\t800.0\t-109000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t18985000\t18986000\tTfap2d\t800.0\t-108000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t18986000\t18987000\tTfap2d\t800.0\t-107000\t0.000500000000\t0.023000625561\t1.387914584417\t0.400000000000\n-chr1\t18987000\t18988000\tTfap2d\t800.0\t-106000\t0.000500000000\t0.023000625561\t1.682320705695\t0.400000000000\n-chr1\t18988000\t18989000\tTfap2d\t800.0\t-105000\t0.000500000000\t0.023000625561\t1.734893228113\t0.400000000000\n-chr1\t18989000\t18990000\tTfap2d\t800.0\t-104000\t0.000500000000\t0.023000625561\t2.081871876625\t0.400000000000\n-chr1\t18990000\t18991000\tTfap2d\t800.0\t-103000\t0.000500000000\t0.023000625561\t2.281503428260\t0.400000000000\n+chr1\t18986000\t18987000\tTfap2d\t800.0\t-107000\t0.000500000000\t0.299067125362\t0.829824948245\t0.400000000000\n+chr1\t18987000\t18988000\tTfap2d\t800.0\t-106000\t0.000500000000\t0.299067125362\t0.946680867864\t0.400000000000\n+chr1\t18988000\t18989000\tTfap2d\t800.0\t-105000\t0.000500000000\t0.299067125362\t0.915248104257\t0.400000000000\n+chr1\t18989000\t18990000\tTfap2d\t800.0\t-104000\t0.000500000000\t0.299067125362\t1.134907650442\t0.400000000000\n+chr1\t18990000\t18991000\tTfap2d\t800.0\t-103000\t0.000500000000\t0.299067125362\t1.243734411173\t0.400000000000\n chr1\t18991000\t18992000\tTfap2d\t800.0\t-102000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t18992000\t18993000\tTfap2d\t800.0\t-101000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t18993000\t18994000\tTfap2d\t800.0\t-100000\t0.000250000000\t0.042850447268\t1.028084877240\t0.200000000000\n-chr1\t18994000\t18995000\tTfap2d\t800.0\t-99000\t0.000250000000\t0.042850447268\t0.946305397749\t0.200000000000\n-chr1\t18995000\t18996000\tTfap2d\t800.0\t-98000\t0.000250000000\t0.042850447268\t0.885902925125\t0.200000000000\n-chr1\t18996000\t18997000\tTfap2d\t800.0\t-97000\t0.000250000000\t0.042850447268\t0.832748749263\t0.200000000000\n-chr1\t18997000\t18998000\tTfap2d\t800.0\t-96000\t0.000250000000\t0.042850447268\t0.763989677803\t0.200000000000\n+chr1\t18993000\t18994000\tTfap2d\t800.0\t-100000\t0.000250000000\t0.378306706409\t0.614685146810\t0.200000000000\n+chr1\t18994000\t18995000\tTfap2d\t800.0\t-99000\t0.000250000000\t0.378306706409\t0.632353235816\t0.200000000000\n+chr1\t18995000\t18996000\tTfap2d\t800.0\t-98000\t0.000250000000\t0.378306706409\t0.591990263285\t0.200000000000\n+chr1\t18996000\t18997000\tTfap2d\t800.0\t-97000\t0.000250000000\t0.378306706409\t0.497894968781\t0.200000000000\n+chr1\t18997000\t18998000\tTfap2d\t800.0\t-96000\t0.000250000000\t0.378306706409\t0.470219209914\t0.200000000000\n chr1\t18998000\t18999000\tTfap2d\t800.0\t-95000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t18999000\t19000000\tTfap2d\t800.0\t-94000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t19000000\t19001000\tTfap2d\t800.0\t-93000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n@@ -125,11 +125,11 @@\n chr1\t19013000\t19014000\tTfap2d\t800.0\t-80000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t19014000\t19015000\tTfap2d\t800.0\t-79000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t19015000\t19016000\tTfap2d\t800.0\t-78000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t19016000\t19017000\tTfap2d\t800.0\t-77000\t0.000250000000\t0.042850447268\t0.578297742704\t0.200000000000\n-chr1\t19017000\t19018000\tTfap2d\t800.0\t-76000\t0.000250000000\t0.042850447268\t0.551489237898\t0.200000000000\n-chr1\t19018000\t19019000\tTfap2d\t800.0\t-75000\t0.000250000000\t0.042850447268\t0.603441123004\t0.200000000000\n-chr1\t1901"..b'0\t1.000000000000\t0.978483428599\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t1.000000000000\t0.676938220343\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t1.000000000000\t0.718117743421\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t1.000000000000\t0.371674357090\t0.200000000000\n chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.000000000000\t0.447714381549\t0.200000000000\n-chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.000000000000\t0.433723307028\t0.200000000000\n-chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.000000000000\t1.218656708021\t0.600000000000\n-chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.000000000000\t1.201079928437\t0.600000000000\n-chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.000000000000\t1.328854387687\t0.600000000000\n-chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.000000000000\t0.900268918608\t0.400000000000\n-chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.000000000000\t0.890640373956\t0.400000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t1.000000000000\t0.409401302867\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t1.000000000000\t0.366099241837\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t1.000000000000\t1.135800575275\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t1.000000000000\t1.077176615132\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t1.000000000000\t1.145033799329\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t1.000000000000\t0.759903290695\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t1.000000000000\t0.767437983333\t0.400000000000\n chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n-chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.000000000000\t0.486987573219\t0.200000000000\n-chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.000000000000\t0.462638194377\t0.200000000000\n-chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.000000000000\t0.457554258138\t0.200000000000\n-chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.000000000000\t0.991367559904\t0.400000000000\n-chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.000000000000\t0.962715318068\t0.400000000000\n-chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.000000000000\t0.510888804001\t0.200000000000\n-chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.000000000000\t0.510888804001\t0.200000000000\n-chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.000000000000\t0.473152698875\t0.200000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t1.000000000000\t0.411058797704\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t1.000000000000\t0.414912474122\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t1.000000000000\t0.394260722067\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t1.000000000000\t0.767065077813\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t1.000000000000\t0.829542790092\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t1.000000000000\t0.431233462800\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t1.000000000000\t0.422249431901\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t1.000000000000\t0.399380990776\t0.200000000000\n chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/find_TADs/multiFDR_score.bedgraph
--- a/test-data/find_TADs/multiFDR_score.bedgraph Fri Dec 11 21:43:10 2020 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,24097 +0,0 @@\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'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicDifferentialTAD/accepted.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt Tue Mar 16 15:33:42 2021 +0000

@@ -0,0 +1,4 @@
+# Created with HiCExplorer's hicDifferentialTAD version 3.6
+# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.
+# Accepted regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one
+# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicDifferentialTAD/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/multiNone_domains.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,1402 @@\n+chr3L\t165000\t260000\tID_0.01_1\t-0.103166750000\t.\t165000\t260000\t31,120,180\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655000000\t.\t260000\t335000\t51,160,44\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848000000\t.\t335000\t360000\t31,120,180\n+chr3L\t360000\t485000\tID_0.01_4\t-0.058081500000\t.\t360000\t485000\t51,160,44\n+chr3L\t485000\t525000\tID_0.01_5\t-0.071697750000\t.\t485000\t525000\t31,120,180\n+chr3L\t525000\t680000\tID_0.01_6\t-0.106040500000\t.\t525000\t680000\t51,160,44\n+chr3L\t680000\t705000\tID_0.01_7\t-0.014885500000\t.\t680000\t705000\t31,120,180\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784000000\t.\t705000\t740000\t51,160,44\n+chr3L\t740000\t870000\tID_0.01_9\t0.009499750000\t.\t740000\t870000\t31,120,180\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.095469750000\t.\t870000\t1010000\t51,160,44\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.051821750000\t.\t1010000\t1040000\t31,120,180\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.058748750000\t.\t1040000\t1110000\t51,160,44\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349000000\t.\t1110000\t1210000\t31,120,180\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.056756500000\t.\t1210000\t1245000\t51,160,44\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.064143500000\t.\t1245000\t1300000\t31,120,180\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379000000\t.\t1300000\t1465000\t51,160,44\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.013072250000\t.\t1465000\t1535000\t31,120,180\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.087115250000\t.\t1535000\t1580000\t51,160,44\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.082358750000\t.\t1580000\t1640000\t31,120,180\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.062875500000\t.\t1640000\t1670000\t51,160,44\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945000000\t.\t1670000\t1735000\t31,120,180\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313000000\t.\t1735000\t1815000\t51,160,44\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.017235250000\t.\t1815000\t1850000\t31,120,180\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.025997500000\t.\t1850000\t1925000\t51,160,44\n+chr3L\t1925000\t2155000\tID_0.01_25\t0.000083250000\t.\t1925000\t2155000\t31,120,180\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.040196500000\t.\t2155000\t2260000\t51,160,44\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.075185750000\t.\t2260000\t2390000\t31,120,180\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071000000\t.\t2390000\t2460000\t51,160,44\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.091323250000\t.\t2460000\t2560000\t31,120,180\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.091796750000\t.\t2560000\t2600000\t51,160,44\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.093485500000\t.\t2600000\t2740000\t31,120,180\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.089278750000\t.\t2740000\t2885000\t51,160,44\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.089725750000\t.\t2885000\t2945000\t31,120,180\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899000000\t.\t2945000\t2960000\t51,160,44\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.035686500000\t.\t2960000\t3045000\t31,120,180\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.004668750000\t.\t3045000\t3135000\t51,160,44\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702000000\t.\t3135000\t3220000\t31,120,180\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463000000\t.\t3220000\t3255000\t51,160,44\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796000000\t.\t3255000\t3315000\t31,120,180\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.054998750000\t.\t3315000\t3345000\t51,160,44\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.042340750000\t.\t3345000\t3475000\t31,120,180\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.050976750000\t.\t3475000\t3515000\t51,160,44\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488000000\t.\t3515000\t3545000\t31,120,180\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.024579250000\t.\t3545000\t3615000\t51,160,44\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683000000\t.\t3615000\t3670000\t31,120,180\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.099453250000\t.\t3670000\t3765000\t51,160,44\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454000000\t.\t3765000\t3785000\t31,120,180\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084000000\t.\t3785000\t3825000\t51,160,44\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.061011750000\t.\t3825000\t3900000\t31,120,180\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.068453500000\t.\t3900000\t4000000\t51,160,44\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.030078750000\t.\t4000000\t4120000\t31,120,180\n+chr3L\t4120000\t4165000\tID_0.01_5'..b'.\t22780000\t22885000\t31,120,180\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.056834750000\t.\t22885000\t22985000\t51,160,44\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.023781500000\t.\t22985000\t23110000\t31,120,180\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625000000\t.\t23110000\t23185000\t51,160,44\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.002947250000\t.\t23185000\t23195000\t31,120,180\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.002757750000\t.\t23195000\t23415000\t51,160,44\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027000000\t.\t23415000\t23560000\t31,120,180\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602000000\t.\t23560000\t23770000\t51,160,44\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.111910500000\t.\t23770000\t23815000\t31,120,180\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.066076500000\t.\t23815000\t23920000\t51,160,44\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.042184750000\t.\t23920000\t24030000\t31,120,180\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.055795750000\t.\t24030000\t24160000\t51,160,44\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.015467250000\t.\t24160000\t24205000\t31,120,180\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.032601500000\t.\t24205000\t24345000\t51,160,44\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.062306500000\t.\t24345000\t24375000\t31,120,180\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.074939500000\t.\t24375000\t24450000\t51,160,44\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.098360750000\t.\t24450000\t24625000\t31,120,180\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.031713750000\t.\t24625000\t24745000\t51,160,44\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.085896250000\t.\t24745000\t24885000\t31,120,180\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.093237250000\t.\t24885000\t24995000\t51,160,44\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.058978500000\t.\t24995000\t25090000\t31,120,180\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.036742250000\t.\t25090000\t25165000\t51,160,44\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.046246500000\t.\t25165000\t25330000\t31,120,180\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.083033250000\t.\t25330000\t25405000\t51,160,44\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.005462250000\t.\t25405000\t25570000\t31,120,180\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.046540750000\t.\t25570000\t25580000\t51,160,44\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.018715750000\t.\t25580000\t25730000\t31,120,180\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.008588750000\t.\t25730000\t25880000\t51,160,44\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.105816250000\t.\t25880000\t25990000\t31,120,180\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403000000\t.\t25990000\t26050000\t51,160,44\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.093531500000\t.\t26050000\t26180000\t31,120,180\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.114692750000\t.\t26180000\t26275000\t51,160,44\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.100273500000\t.\t26275000\t26330000\t31,120,180\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304000000\t.\t26330000\t26490000\t51,160,44\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.062796500000\t.\t26490000\t26565000\t31,120,180\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.019744750000\t.\t26565000\t26640000\t51,160,44\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.074307250000\t.\t26640000\t26715000\t31,120,180\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789000000\t.\t26715000\t26870000\t51,160,44\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.024990500000\t.\t26870000\t27045000\t31,120,180\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189000000\t.\t27045000\t27155000\t51,160,44\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.006099250000\t.\t27155000\t27185000\t31,120,180\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.012810250000\t.\t27185000\t27250000\t51,160,44\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.049902750000\t.\t27250000\t27385000\t31,120,180\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305000000\t.\t27385000\t27420000\t51,160,44\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.049929500000\t.\t27420000\t27570000\t31,120,180\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.080943250000\t.\t27570000\t27700000\t51,160,44\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.015350000000\t.\t27700000\t27750000\t31,120,180\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.013577250000\t.\t27750000\t27770000\t51,160,44\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicDifferentialTAD/rejected.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt Tue Mar 16 15:33:42 2021 +0000

b"@@ -0,0 +1,1402 @@\n+# Created with HiCExplorer's hicDifferentialTAD version 3.6\n+# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.\n+# Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one \n+# Chromosome\tstart\tend\tname\tscore\tstrand\tp-value left-inter-TAD\tp-value right-inter-TAD\tp-value intra-TAD\n+chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\tnan\t1.0\t1.0\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t1.0\t1.0\t1.0\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t1.0\t1.0\t1.0\n+chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t1.0\t1.0\t1.0\n+chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t1.0\t1.0\t1.0\n+chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t1.0\t1.0\t1.0\n+chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t1.0\t1.0\t1.0\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t1.0\t1.0\t1.0\n+chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t1.0\t1.0\t1.0\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t1.0\t1.0\t1.0\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1.0\t1.0\t1.0\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1.0\t1.0\t1.0\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1.0\t1.0\t1.0\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1.0\t1.0\t1.0\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1.0\t1.0\t1.0\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1.0\t1.0\t1.0\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1.0\t1.0\t1.0\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1.0\t1.0\t1.0\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1.0\t1.0\t1.0\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1.0\t1.0\t1.0\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1.0\t1.0\t1.0\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1.0\t1.0\t1.0\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1.0\t1.0\t1.0\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1.0\t1.0\t1.0\n+chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1.0\t1.0\t1.0\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t1.0\t1.0\t1.0\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t1.0\t1.0\t1.0\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t1.0\t1.0\t1.0\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t1.0\t1.0\t1.0\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t1.0\t1.0\t1.0\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t1.0\t1.0\t1.0\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t1.0\t1.0\t1.0\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t1.0\t1.0\t1.0\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t1.0\t1.0\t1.0\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t1.0\t1.0\t1.0\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t1.0\t1.0\t1.0\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t1.0\t1.0\t1.0\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t1.0\t1.0\t1.0\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t1.0\t1.0\t1.0\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t1.0\t1.0\t1.0\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t1.0\t1.0\t1.0\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t1.0\t1.0\t1.0\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t1.0\t1.0\t1.0\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t1.0\t1.0\t1.0\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t1.0\t1.0\t1.0\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t1.0\t1.0\t1.0\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t1.0\t1.0\t1.0\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t1.0\t1.0\t1.0\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t1.0\t1.0\t1.0\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t1.0\t1.0\t1.0\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t1.0\t1.0\t1.0\n+chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t1.0\t1.0\t1.0\n+chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t1.0\t1.0\t1.0\n+chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t1.0\t1.0\t1.0\n+chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t1.0\t1.0\t1.0\n+chr3L\t4270000\t4365000\tID_0.01_56\t-0.11633575\t.\t1.0\t1.0\t1.0\n+chr3L\t4365000\t4405000\tID_0.01_57\t-0.0944955\t.\t1.0\t1.0\t1.0\n+chr3L\t4405000\t4490000\tID_0.01_58\t-0.07463925\t.\t1.0\t1.0\t1.0\n+chr3L\t4490000\t4625000\tID_0.01_59\t0.00287075\t.\t1.0\t1.0\t1.0\n+chr3L\t4625000\t4650000\tID_0.01_60\t0.04064075\t.\t1.0\t1.0\t1.0\n+chr3L\t4650000\t4790000\tID_0.01_"..b'0.0932985\t.\t1.0\t1.0\t1.0\n+chr3R\t21615000\t21730000\tID_0.01_1340\t-0.081974\t.\t1.0\t1.0\t1.0\n+chr3R\t21730000\t21820000\tID_0.01_1341\t0.07025075\t.\t1.0\t1.0\t1.0\n+chr3R\t21820000\t21845000\tID_0.01_1342\t-0.00145975\t.\t1.0\t1.0\t1.0\n+chr3R\t21845000\t21950000\tID_0.01_1343\t0.0360515\t.\t1.0\t1.0\t1.0\n+chr3R\t21950000\t21990000\tID_0.01_1344\t0.002742\t.\t1.0\t1.0\t1.0\n+chr3R\t21990000\t22075000\tID_0.01_1345\t0.00713375\t.\t1.0\t1.0\t1.0\n+chr3R\t22075000\t22220000\tID_0.01_1346\t-0.087915\t.\t1.0\t1.0\t1.0\n+chr3R\t22220000\t22270000\tID_0.01_1347\t0.0614505\t.\t1.0\t1.0\t1.0\n+chr3R\t22270000\t22310000\tID_0.01_1348\t-0.02575325\t.\t1.0\t1.0\t1.0\n+chr3R\t22310000\t22380000\tID_0.01_1349\t-0.04946475\t.\t1.0\t1.0\t1.0\n+chr3R\t22380000\t22500000\tID_0.01_1350\t-0.055847\t.\t1.0\t1.0\t1.0\n+chr3R\t22500000\t22520000\tID_0.01_1351\t-0.0631105\t.\t1.0\t1.0\t1.0\n+chr3R\t22520000\t22605000\tID_0.01_1352\t-0.062648\t.\t1.0\t1.0\t1.0\n+chr3R\t22605000\t22695000\tID_0.01_1353\t-0.011252\t.\t1.0\t1.0\t1.0\n+chr3R\t22695000\t22780000\tID_0.01_1354\t-0.089033\t.\t1.0\t1.0\t1.0\n+chr3R\t22780000\t22885000\tID_0.01_1355\t-0.04050025\t.\t1.0\t1.0\t1.0\n+chr3R\t22885000\t22985000\tID_0.01_1356\t-0.05683475\t.\t1.0\t1.0\t1.0\n+chr3R\t22985000\t23110000\tID_0.01_1357\t-0.0237815\t.\t1.0\t1.0\t1.0\n+chr3R\t23110000\t23185000\tID_0.01_1358\t-0.100625\t.\t1.0\t1.0\t1.0\n+chr3R\t23185000\t23195000\tID_0.01_1359\t-0.00294725\t.\t1.0\t1.0\t1.0\n+chr3R\t23195000\t23415000\tID_0.01_1360\t-0.00275775\t.\t1.0\t1.0\t1.0\n+chr3R\t23415000\t23560000\tID_0.01_1361\t-0.090027\t.\t1.0\t1.0\t1.0\n+chr3R\t23560000\t23770000\tID_0.01_1362\t-0.104602\t.\t1.0\t1.0\t1.0\n+chr3R\t23770000\t23815000\tID_0.01_1363\t-0.1119105\t.\t1.0\t1.0\t1.0\n+chr3R\t23815000\t23920000\tID_0.01_1364\t-0.0660765\t.\t1.0\t1.0\t1.0\n+chr3R\t23920000\t24030000\tID_0.01_1365\t-0.04218475\t.\t1.0\t1.0\t1.0\n+chr3R\t24030000\t24160000\tID_0.01_1366\t-0.05579575\t.\t1.0\t1.0\t1.0\n+chr3R\t24160000\t24205000\tID_0.01_1367\t-0.01546725\t.\t1.0\t1.0\t1.0\n+chr3R\t24205000\t24345000\tID_0.01_1368\t-0.0326015\t.\t1.0\t1.0\t1.0\n+chr3R\t24345000\t24375000\tID_0.01_1369\t-0.0623065\t.\t1.0\t1.0\t1.0\n+chr3R\t24375000\t24450000\tID_0.01_1370\t-0.0749395\t.\t1.0\t1.0\t1.0\n+chr3R\t24450000\t24625000\tID_0.01_1371\t-0.09836075\t.\t1.0\t1.0\t1.0\n+chr3R\t24625000\t24745000\tID_0.01_1372\t-0.03171375\t.\t1.0\t1.0\t1.0\n+chr3R\t24745000\t24885000\tID_0.01_1373\t-0.08589625\t.\t1.0\t1.0\t1.0\n+chr3R\t24885000\t24995000\tID_0.01_1374\t-0.09323725\t.\t1.0\t1.0\t1.0\n+chr3R\t24995000\t25090000\tID_0.01_1375\t-0.0589785\t.\t1.0\t1.0\t1.0\n+chr3R\t25090000\t25165000\tID_0.01_1376\t0.03674225\t.\t1.0\t1.0\t1.0\n+chr3R\t25165000\t25330000\tID_0.01_1377\t-0.0462465\t.\t1.0\t1.0\t1.0\n+chr3R\t25330000\t25405000\tID_0.01_1378\t-0.08303325\t.\t1.0\t1.0\t1.0\n+chr3R\t25405000\t25570000\tID_0.01_1379\t-0.00546225\t.\t1.0\t1.0\t1.0\n+chr3R\t25570000\t25580000\tID_0.01_1380\t-0.04654075\t.\t1.0\t1.0\t1.0\n+chr3R\t25580000\t25730000\tID_0.01_1381\t-0.01871575\t.\t1.0\t1.0\t1.0\n+chr3R\t25730000\t25880000\tID_0.01_1382\t-0.00858875\t.\t1.0\t1.0\t1.0\n+chr3R\t25880000\t25990000\tID_0.01_1383\t-0.10581625\t.\t1.0\t1.0\t1.0\n+chr3R\t25990000\t26050000\tID_0.01_1384\t-0.090403\t.\t1.0\t1.0\t1.0\n+chr3R\t26050000\t26180000\tID_0.01_1385\t-0.0935315\t.\t1.0\t1.0\t1.0\n+chr3R\t26180000\t26275000\tID_0.01_1386\t-0.11469275\t.\t1.0\t1.0\t1.0\n+chr3R\t26275000\t26330000\tID_0.01_1387\t-0.1002735\t.\t1.0\t1.0\t1.0\n+chr3R\t26330000\t26490000\tID_0.01_1388\t-0.092304\t.\t1.0\t1.0\t1.0\n+chr3R\t26490000\t26565000\tID_0.01_1389\t0.0627965\t.\t1.0\t1.0\t1.0\n+chr3R\t26565000\t26640000\tID_0.01_1390\t-0.01974475\t.\t1.0\t1.0\t1.0\n+chr3R\t26640000\t26715000\tID_0.01_1391\t-0.07430725\t.\t1.0\t1.0\t1.0\n+chr3R\t26715000\t26870000\tID_0.01_1392\t-0.049789\t.\t1.0\t1.0\t1.0\n+chr3R\t26870000\t27045000\tID_0.01_1393\t-0.0249905\t.\t1.0\t1.0\t1.0\n+chr3R\t27045000\t27155000\tID_0.01_1394\t-0.074189\t.\t1.0\t1.0\t1.0\n+chr3R\t27155000\t27185000\tID_0.01_1395\t-0.00609925\t.\t1.0\t1.0\t1.0\n+chr3R\t27185000\t27250000\tID_0.01_1396\t-0.01281025\t.\t1.0\t1.0\t1.0\n+chr3R\t27250000\t27385000\tID_0.01_1397\t-0.04990275\t.\t1.0\t1.0\t1.0\n+chr3R\t27385000\t27420000\tID_0.01_1398\t-0.041305\t.\t1.0\t1.0\t1.0\n+chr3R\t27420000\t27570000\tID_0.01_1399\t-0.0499295\t.\t1.0\t1.0\t1.0\n+chr3R\t27570000\t27700000\tID_0.01_1400\t-0.08094325\t.\t1.0\t1.0\t1.0\n+chr3R\t27700000\t27750000\tID_0.01_1401\t-0.01535\t.\t1.0\tnan\t1.0\n+chr3R\t27750000\t27770000\tID_0.01_1402\t0.01357725\t.\t1.0\tnan\t1.0\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicHyperoptDetectLoops/loops.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph Tue Mar 16 15:33:42 2021 +0000

@@ -0,0 +1,3 @@
+# Created by HiCExplorer hicHyperoptDetectLoops 3.6
+
+{'matrixFile': 'matrix.cool', 'maxLoopDistance': 2600000, 'maximumNumberOfLoops': 5, 'oet': 4.594451600287669, 'p': 0.07561093779253786, 'peakWidth': 2, 'pit': 68.07931954714506, 'pp': 0.021875258449572325, 'proteinFile': 'hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak', 'resolution': 2, 'threads': 1, 'windowSize': 10}
\ No newline at end of file

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/100kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/100kbtad_domains.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,179 @@\n+1\t2600000\t3800000\tID_0.01_1\t-1.141686912309\t.\t2600000\t3800000\t31,120,180\n+1\t3800000\t6000000\tID_0.01_2\t-1.059483103498\t.\t3800000\t6000000\t51,160,44\n+1\t6000000\t7800000\tID_0.01_3\t-0.984430873493\t.\t6000000\t7800000\t31,120,180\n+1\t7800000\t8900000\tID_0.01_4\t-0.399067786162\t.\t7800000\t8900000\t51,160,44\n+1\t8900000\t9700000\tID_0.01_5\t-0.117593287650\t.\t8900000\t9700000\t31,120,180\n+1\t9700000\t10500000\tID_0.01_6\t-0.185496017524\t.\t9700000\t10500000\t51,160,44\n+1\t10500000\t11100000\tID_0.01_7\t-0.201392985635\t.\t10500000\t11100000\t31,120,180\n+1\t11100000\t12100000\tID_0.01_8\t-0.354700283296\t.\t11100000\t12100000\t51,160,44\n+1\t12100000\t13000000\tID_0.01_9\t-0.799256699715\t.\t12100000\t13000000\t31,120,180\n+1\t13000000\t13700000\tID_0.01_10\t-1.402270586960\t.\t13000000\t13700000\t51,160,44\n+1\t13700000\t15800000\tID_0.01_11\t-1.386012674902\t.\t13700000\t15800000\t31,120,180\n+1\t15800000\t16900000\tID_0.01_12\t-0.616324727763\t.\t15800000\t16900000\t51,160,44\n+1\t16900000\t18000000\tID_0.01_13\t-0.790309360336\t.\t16900000\t18000000\t31,120,180\n+1\t18000000\t19200000\tID_0.01_14\t-0.743221612017\t.\t18000000\t19200000\t51,160,44\n+1\t19200000\t20000000\tID_0.01_15\t-0.771014287578\t.\t19200000\t20000000\t31,120,180\n+1\t20000000\t21000000\tID_0.01_16\t-0.197406966417\t.\t20000000\t21000000\t51,160,44\n+1\t21000000\t23300000\tID_0.01_17\t-0.246857948260\t.\t21000000\t23300000\t31,120,180\n+1\t23300000\t24100000\tID_0.01_18\t-0.073204223258\t.\t23300000\t24100000\t51,160,44\n+1\t24100000\t25600000\tID_0.01_19\t-0.481483747078\t.\t24100000\t25600000\t31,120,180\n+1\t25600000\t26800000\tID_0.01_20\t-0.288019958082\t.\t25600000\t26800000\t51,160,44\n+1\t26800000\t27200000\tID_0.01_21\t-0.373426473072\t.\t26800000\t27200000\t31,120,180\n+1\t27200000\t28100000\tID_0.01_22\t-0.223857449717\t.\t27200000\t28100000\t51,160,44\n+1\t28100000\t29500000\tID_0.01_23\t-0.226553355171\t.\t28100000\t29500000\t31,120,180\n+1\t29500000\t31200000\tID_0.01_24\t-0.294342328563\t.\t29500000\t31200000\t51,160,44\n+1\t31200000\t32600000\tID_0.01_25\t-0.691915018713\t.\t31200000\t32600000\t31,120,180\n+1\t32600000\t34100000\tID_0.01_26\t-0.525120566221\t.\t32600000\t34100000\t51,160,44\n+1\t34100000\t35200000\tID_0.01_27\t-0.870691440603\t.\t34100000\t35200000\t31,120,180\n+1\t35200000\t36900000\tID_0.01_28\t-0.711717112535\t.\t35200000\t36900000\t51,160,44\n+1\t36900000\t37900000\tID_0.01_29\t-0.859237923761\t.\t36900000\t37900000\t31,120,180\n+1\t37900000\t39300000\tID_0.01_30\t-0.593840260031\t.\t37900000\t39300000\t51,160,44\n+1\t39300000\t40200000\tID_0.01_31\t-0.709231729337\t.\t39300000\t40200000\t31,120,180\n+1\t40200000\t40900000\tID_0.01_32\t-0.351235876672\t.\t40200000\t40900000\t51,160,44\n+1\t40900000\t41500000\tID_0.01_33\t-0.073064714746\t.\t40900000\t41500000\t31,120,180\n+1\t41500000\t43600000\tID_0.01_34\t-0.262432443657\t.\t41500000\t43600000\t51,160,44\n+1\t43600000\t44500000\tID_0.01_35\t0.149239103642\t.\t43600000\t44500000\t31,120,180\n+1\t44500000\t45200000\tID_0.01_36\t0.096413662017\t.\t44500000\t45200000\t51,160,44\n+1\t45200000\t46100000\tID_0.01_37\t-0.404853685700\t.\t45200000\t46100000\t31,120,180\n+1\t46100000\t46800000\tID_0.01_38\t-0.067313090808\t.\t46100000\t46800000\t51,160,44\n+1\t46800000\t47800000\tID_0.01_39\t-0.829091697703\t.\t46800000\t47800000\t31,120,180\n+1\t47800000\t49000000\tID_0.01_40\t-0.428048529291\t.\t47800000\t49000000\t51,160,44\n+1\t49000000\t50800000\tID_0.01_41\t-0.036098871211\t.\t49000000\t50800000\t31,120,180\n+1\t50800000\t51800000\tID_0.01_42\t-0.640230613455\t.\t50800000\t51800000\t51,160,44\n+1\t51800000\t52500000\tID_0.01_43\t-0.433531022931\t.\t51800000\t52500000\t31,120,180\n+1\t52500000\t53700000\tID_0.01_44\t-0.320908527204\t.\t52500000\t53700000\t51,160,44\n+1\t53700000\t55500000\tID_0.01_45\t-0.439064654323\t.\t53700000\t55500000\t31,120,180\n+1\t55500000\t57300000\tID_0.01_46\t-0.879707940385\t.\t55500000\t57300000\t51,160,44\n+1\t57300000\t59000000\tID_0.01_47\t-0.381026749753\t.\t57300000\t59000000\t31,120,180\n+1\t59000000\t60400000\tID_0.01_48\t-0.655963485561\t.\t59000000\t60400000\t51,160,44\n+1\t60400000\t61300000\tID_0.01_49\t-0.859845271814\t.\t60400000\t61300000\t31,120,180\n+1\t61300000\t62600000\tID_0.01_50\t-0.262470171293\t.\t61300000\t62600000\t51,160,44\n+1\t62600000\t63300000\tID_0.01_51\t-0.546928077555\t.\t62600000\t63300000\t31,120,180\n+1\t6330000'..b'.085993697651\t.\t183600000\t184700000\t51,160,44\n+1\t184700000\t186300000\tID_0.01_133\t-0.264326017277\t.\t184700000\t186300000\t31,120,180\n+1\t186300000\t187000000\tID_0.01_134\t-0.810844695593\t.\t186300000\t187000000\t51,160,44\n+1\t187000000\t189100000\tID_0.01_135\t-0.561032153453\t.\t187000000\t189100000\t31,120,180\n+1\t189100000\t190500000\tID_0.01_136\t-0.638786084967\t.\t189100000\t190500000\t51,160,44\n+1\t190500000\t192400000\tID_0.01_137\t-0.804987835576\t.\t190500000\t192400000\t31,120,180\n+1\t192400000\t193100000\tID_0.01_13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No newline at end of file\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/10kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/10kbtad_domains.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,769 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diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/50kbtad_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/50kbtad_domains.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,355 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No newline at end of file\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf

Binary file test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/ctcf_sorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/ctcf_sorted.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,3403 @@\n+chr1\t805186\t805436\t.\t0\t.\t59.5609057962358\t-1\t4.7429214225993\t125\n+chr1\t840030\t840280\t.\t0\t.\t83.6226028373057\t-1\t4.7429214225993\t125\n+chr1\t848233\t848483\t.\t0\t.\t21.7013707748217\t-1\t3.97409700379598\t125\n+chr1\t873538\t873788\t.\t0\t.\t19.5674784603862\t-1\t3.88351633069348\t125\n+chr1\t886823\t887073\t.\t0\t.\t22.5711320345953\t-1\t4.11312075496602\t125\n+chr1\t911486\t911736\t.\t0\t.\t31.509769734266\t-1\t4.27124510662348\t125\n+chr1\t919601\t919851\t.\t0\t.\t33.1859544183338\t-1\t4.7429214225993\t125\n+chr1\t937269\t937519\t.\t0\t.\t48.2208573550132\t-1\t4.7429214225993\t125\n+chr1\t950804\t951054\t.\t0\t.\t27.7376222191221\t-1\t4.296482367922\t125\n+chr1\t954689\t954939\t.\t0\t.\t19.1922365041399\t-1\t3.79979779059073\t125\n+chr1\t968355\t968605\t.\t0\t.\t27.9104706029461\t-1\t4.29525180136426\t125\n+chr1\t999239\t999489\t.\t0\t.\t67.3973204081303\t-1\t4.7429214225993\t125\n+chr1\t1057530\t1057780\t.\t0\t.\t88.0665088853952\t-1\t4.7429214225993\t125\n+chr1\t1166148\t1166398\t.\t0\t.\t27.9814352288374\t-1\t4.29482615193429\t125\n+chr1\t1200463\t1200713\t.\t0\t.\t33.5952614512378\t-1\t4.7429214225993\t125\n+chr1\t1225610\t1225860\t.\t0\t.\t73.9102584682168\t-1\t4.7429214225993\t125\n+chr1\t1227292\t1227542\t.\t0\t.\t69.7040984837778\t-1\t4.7429214225993\t125\n+chr1\t1235462\t1235712\t.\t0\t.\t45.538363572806\t-1\t4.7429214225993\t125\n+chr1\t1237377\t1237627\t.\t0\t.\t19.9924023420945\t-1\t3.87966283949506\t125\n+chr1\t1280051\t1280301\t.\t0\t.\t52.5126590486595\t-1\t4.7429214225993\t125\n+chr1\t1284662\t1284912\t.\t0\t.\t26.3007670733988\t-1\t4.30716073872335\t125\n+chr1\t1285194\t1285444\t.\t0\t.\t19.6869777946214\t-1\t3.882480265106\t125\n+chr1\t1307585\t1307668\t.\t0\t.\t98.4512721959962\t-1\t4.7429214225993\t33\n+chr1\t1334834\t1335084\t.\t0\t.\t45.7165675131359\t-1\t4.7429214225993\t125\n+chr1\t1337531\t1337625\t.\t0\t.\t129.568164313081\t-1\t4.7429214225993\t15\n+chr1\t1376405\t1376551\t.\t0\t.\t112.104098738192\t-1\t4.7429214225993\t78\n+chr1\t1440337\t1440587\t.\t0\t.\t50.3693879296427\t-1\t4.7429214225993\t125\n+chr1\t1486555\t1486805\t.\t0\t.\t23.5386437775045\t-1\t4.32716132803452\t125\n+chr1\t1509199\t1509449\t.\t0\t.\t24.0579975291309\t-1\t4.32323146812351\t125\n+chr1\t1533113\t1533363\t.\t0\t.\t28.1831148336541\t-1\t4.29344358599487\t125\n+chr1\t1597192\t1597442\t.\t0\t.\t40.4396667960704\t-1\t4.7429214225993\t125\n+chr1\t1610383\t1610633\t.\t0\t.\t18.8867819454862\t-1\t3.80287941044449\t125\n+chr1\t1720538\t1720788\t.\t0\t.\t20.2783981866113\t-1\t3.87717290488528\t125\n+chr1\t1790091\t1790341\t.\t0\t.\t20.1334751599979\t-1\t3.87840050291318\t125\n+chr1\t1837789\t1837915\t.\t0\t.\t147.268012144206\t-1\t4.7429214225993\t74\n+chr1\t1840463\t1840713\t.\t0\t.\t26.3851329756002\t-1\t4.30646077049034\t125\n+chr1\t1875555\t1875662\t.\t0\t.\t106.834270840707\t-1\t4.7429214225993\t32\n+chr1\t1891605\t1891733\t.\t0\t.\t131.407645767539\t-1\t4.7429214225993\t63\n+chr1\t1976452\t1976520\t.\t0\t.\t87.5358082894933\t-1\t4.7429214225993\t11\n+chr1\t1977991\t1978241\t.\t0\t.\t73.4031161610917\t-1\t4.7429214225993\t125\n+chr1\t1980938\t1981188\t.\t0\t.\t61.7452349072252\t-1\t4.7429214225993\t125\n+chr1\t2040119\t2040369\t.\t0\t.\t23.8201211984674\t-1\t4.32501595101874\t125\n+chr1\t2063702\t2063952\t.\t0\t.\t21.9975491279828\t-1\t3.97170648286736\t125\n+chr1\t2071507\t2071645\t.\t0\t.\t114.969306459524\t-1\t4.7429214225993\t67\n+chr1\t2105852\t2105978\t.\t0\t.\t122.600087913384\t-1\t4.7429214225993\t61\n+chr1\t2126654\t2126904\t.\t0\t.\t86.7497585482926\t-1\t4.7429214225993\t125\n+chr1\t2144503\t2144753\t.\t0\t.\t20.0994558159811\t-1\t3.87871962123126\t125\n+chr1\t2246665\t2246915\t.\t0\t.\t20.7731784135031\t-1\t3.9821096350928\t125\n+chr1\t2313240\t2313490\t.\t0\t.\t84.2342744659508\t-1\t4.7429214225993\t125\n+chr1\t2314098\t2314348\t.\t0\t.\t62.0405584533353\t-1\t4.7429214225993\t125\n+chr1\t2345876\t2346126\t.\t0\t.\t87.6097808292363\t-1\t4.7429214225993\t125\n+chr1\t2361551\t2361801\t.\t0\t.\t80.0672677773095\t-1\t4.7429214225993\t125\n+chr1\t2470816\t2471066\t.\t0\t.\t28.4737352542628\t-1\t4.29140585420779\t125\n+chr1\t2479588\t2479691\t.\t0\t.\t108.435096866948\t-1\t4.7429214225993\t75\n+chr1\t2493400\t2493650\t.\t0\t.\t34.0043068331574\t-1\t4.7429214225993\t125\n+chr1\t3236597\t3236847\t.\t0\t.\t26.8900011644677\t-1\t4.30265555395945\t125\n+chr1\t3333725\t3333975\t.\t0\t.\t31.1329672384982\t-1\t4.27373412851497\t125\n+chr1\t3341315\t3341565\t.\t0\t.\t74.7245302958789\t-1\t4.7429214225993\t125\n+chr1\t3369726\t3369976\t.\t0\t.\t106.444209601322\t-1\t4.74'..b'-1\t4.7429214225993\t125\n+chr1\t242161899\t242162149\t.\t0\t.\t44.297888867722\t-1\t4.7429214225993\t125\n+chr1\t242180997\t242181247\t.\t0\t.\t78.3741983761816\t-1\t4.7429214225993\t125\n+chr1\t242183188\t242183438\t.\t0\t.\t66.679819217778\t-1\t4.7429214225993\t125\n+chr1\t242292490\t242292740\t.\t0\t.\t32.4950929799733\t-1\t4.7429214225993\t125\n+chr1\t242588613\t242588863\t.\t0\t.\t21.7470007916771\t-1\t3.973780784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No newline at end of file\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/merged_list.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/merged_list.bed Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,1287 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\tID_1243\t-0.694851336560\t.\t240150000\t240300000\t51,160,44\n+1\t240150000\t240850000\tID_1244\t-0.918612135670\t.\t240150000\t240850000\t31,120,180\n+1\t240200000\t241600000\tID_1245\t-0.875271039667\t.\t240200000\t241600000\t31,120,180\n+1\t240300000\t240860000\tID_1246\t-0.619962352140\t.\t240300000\t240860000\t31,120,180\n+1\t240850000\t241650000\tID_1247\t-0.628106996684\t.\t240850000\t241650000\t51,160,44\n+1\t240860000\t241450000\tID_1248\t-0.536630482238\t.\t240860000\t241450000\t51,160,44\n+1\t241450000\t241490000\tID_1249\t-0.334722832403\t.\t241450000\t241490000\t31,120,180\n+1\t241490000\t241670000\tID_1250\t-0.328186142869\t.\t241490000\t241670000\t51,160,44\n+1\t241600000\t243400000\tID_1251\t-0.260297744910\t.\t241600000\t243400000\t51,160,44\n+1\t241650000\t242200000\tID_1252\t-0.572894062116\t.\t241650000\t242200000\t31,120,180\n+1\t241670000\t242040000\tID_1253\t-0.413822039303\t.\t241670000\t242040000\t31,120,180\n+1\t242040000\t242190000\tID_1254\t-0.383218117849\t.\t242040000\t242190000\t51,160,44\n+1\t242190000\t242420000\tID_1255\t-0.441379005101\t.\t242190000\t242420000\t31,120,180\n+1\t242200000\t242600000\tID_1256\t-0.629968298486\t.\t242200000\t242600000\t51,160,44\n+1\t242420000\t242590000\tID_1257\t-0.387824388577\t.\t242420000\t242590000\t51,160,44\n+1\t242590000\t243270000\tID_1258\t-0.559328577036\t.\t242590000\t243270000\t31,120,180\n+1\t242600000\t243350000\tID_1259\t-0.649483941807\t.\t242600000\t243350000\t31,120,180\n+1\t243270000\t243490000\tID_1260\t-0.966884087888\t.\t243270000\t243490000\t51,160,44\n+1\t243350000\t244600000\tID_1261\t-1.199504248183\t.\t243350000\t244600000\t51,160,44\n+1\t243400000\t244700000\tID_1262\t-0.933246847344\t.\t243400000\t244700000\t31,120,180\n+1\t243490000\t243910000\tID_1263\t-0.631207979149\t.\t243490000\t243910000\t31,120,180\n+1\t243910000\t244210000\tID_1264\t0.015886430508\t.\t243910000\t244210000\t51,160,44\n+1\t244210000\t244440000\tID_1265\t0.502079406996\t.\t244210000\t244440000\t31,120,180\n+1\t244440000\t244620000\tID_1266\t-0.340301300275\t.\t244440000\t244620000\t51,160,44\n+1\t244600000\t245250000\tID_1267\t-0.563530506582\t.\t244600000\t245250000\t31,120,180\n+1\t244620000\t244990000\tID_1268\t-0.466221331340\t.\t244620000\t244990000\t31,120,180\n+1\t244700000\t245200000\tID_1269\t-0.507093336860\t.\t244700000\t245200000\t51,160,44\n+1\t244990000\t245230000\tID_1270\t-0.195814914535\t.\t244990000\t245230000\t51,160,44\n+1\t245200000\t247000000\tID_1271\t-0.500640827349\t.\t245200000\t247000000\t31,120,180\n+1\t245230000\t245830000\tID_1272\t-0.487584169638\t.\t245230000\t245830000\t31,120,180\n+1\t245250000\t246150000\tID_1273\t-0.686787834796\t.\t245250000\t246150000\t51,160,44\n+1\t245830000\t246170000\tID_1274\t-0.007526753428\t.\t245830000\t246170000\t51,160,44\n+1\t246150000\t246650000\tID_1275\t-0.335558918395\t.\t246150000\t246650000\t31,120,180\n+1\t246170000\t246440000\tID_1276\t-0.396857166679\t.\t246170000\t246440000\t31,120,180\n+1\t246440000\t246650000\tID_1277\t0.008005968484\t.\t246440000\t246650000\t51,160,44\n+1\t246650000\t247000000\tID_1278\t-0.564013263776\t.\t246650000\t247000000\t51,160,44\n+1\t247000000\t247090000\tID_1279\t-0.548680889867\t.\t247000000\t247090000\t51,160,44\n+1\t247000000\t248050000\tID_1280\t-0.755580115849\t.\t247000000\t248050000\t31,120,180\n+1\t247090000\t247360000\tID_1281\t-0.540609317126\t.\t247090000\t247360000\t31,120,180\n+1\t247360000\t247530000\tID_1282\t-0.311813169196\t.\t247360000\t247530000\t51,160,44\n+1\t247530000\t247730000\tID_1283\t-0.510802935408\t.\t247530000\t247730000\t31,120,180\n+1\t247730000\t248090000\tID_1284\t-0.497993016061\t.\t247730000\t248090000\t51,160,44\n+1\t248090000\t248630000\tID_1285\t-0.633276044452\t.\t248090000\t248630000\t31,120,180\n+1\t248630000\t248750000\tID_1286\t-0.866530333656\t.\t248630000\t248750000\t51,160,44\n+1\t248750000\t249080000\tID_1287\t-0.884473908997\t.\t248750000\t249080000\t31,120,180\n'

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/relationship.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/relationship.txt Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,1456 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diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicMergeDomains/two_files_relation_ctcf.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeDomains/two_files_relation_ctcf.txt Tue Mar 16 15:33:42 2021 +0000

b'@@ -0,0 +1,581 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diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotMatrix/plot1.png

Binary file test-data/hicPlotMatrix/plot1.png has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotMatrix/plot2.pdf

Binary file test-data/hicPlotMatrix/plot2.pdf has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotMatrix/plot3_pca.svg
--- a/test-data/hicPlotMatrix/plot3_pca.svg Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg Tue Mar 16 15:33:42 2021 +0000

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diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotSVL/p_values.txt
--- a/test-data/hicPlotSVL/p_values.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.3
+# Created with HiCExplorer's hicPlotSVL 3.6
# 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

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotSVL/plot.png

Binary file test-data/hicPlotSVL/plot.png has changed

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicPlotSVL/ratios.txt
--- a/test-data/hicPlotSVL/ratios.txt Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Tue Mar 16 15:33:42 2021 +0000

@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.3
+# Created with HiCExplorer's hicPlotSVL 3.6
# Short range vs long range contacts per chromosome: raw data
# Short range contacts: <= 2000000
# 0_small_test_matrix.h5 1_small_test_matrix.h5

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicQuickQC/QC.log
--- a/test-data/hicQuickQC/QC.log Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/hicQuickQC/QC.log Tue Mar 16 15:33:42 2021 +0000

@@ -1,5 +1,5 @@

-File /tmp/tmpp4d6khlj.h5
+File /tmp/tmp12xmnm2f.h5
Sequenced reads 983
Min rest. site distance 300
Max library insert size 1000
@@ -12,11 +12,11 @@
Low mapping quality 164 (16.68)

# count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end 0 (0.00)
+dangling end GATC 1 (0.33)
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)
+same fragment 84 (28.00)
+self circle 33 (11.00)
duplicated pairs 0 (0.00)

# count (percentage w.r.t. total valid pairs used)

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/hicValidateLocations/overlap_smc3_statistics
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Tue Mar 16 15:33:42 2021 +0000

@@ -1,5 +1,5 @@
-# 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
+# HiCExplorer hicValidateLocations 3.6
+# Overlap of loop file /tmp/tmpd80q3k6g/files/a/4/0/dataset_a40f2565-c94b-4e73-9b47-ec233d99bda8.dat with protein file /tmp/tmpd80q3k6g/files/7/1/1/dataset_7116b645-b87b-49a2-a957-3ebe53aba250.dat
#
Protein peaks: 3097
Matched Loops: 530

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiNone_domains.bed Tue Mar 16 15:33:42 2021 +0000

diff -r 6bc82c6d6620 -r 6001400eed99 test-data/raw_qc_report
--- a/test-data/raw_qc_report Fri Dec 11 21:43:10 2020 +0000
+++ b/test-data/raw_qc_report Tue Mar 16 15:33:42 2021 +0000

@@ -1,5 +1,5 @@

-File matrix.cool
+File matrix.h5
Sequenced reads 983
Min rest. site distance 300
Max library insert size 1000
@@ -12,11 +12,11 @@
Low mapping quality 164 (16.68)

# count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end 0 (0.00)
+dangling end GATC 1 (0.33)
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)
+same fragment 84 (28.00)
+self circle 33 (11.00)
duplicated pairs 0 (0.00)

# count (percentage w.r.t. total valid pairs used)