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Changeset 12:6b7987d22eab (2019-12-16)

Previous changeset 11:6bda631b9239 (2019-12-16) Next changeset 13:d3fad161b318 (2020-02-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

modified:
hicFindTADs.xml
macros.xml

diff -r 6bda631b9239 -r 6b7987d22eab hicFindTADs.xml
--- a/hicFindTADs.xml Mon Dec 16 10:36:22 2019 -0500
+++ b/hicFindTADs.xml Mon Dec 16 15:48:31 2019 -0500

[

b'@@ -6,17 +6,28 @@\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n- hicFindTADs\n- --matrix \'$matrix_h5_cooler\'\n+ ln -s \'$matrix_h5_cooler\' \'matrix.$matrix_h5_cooler.ext\' &&\n+ \n+ #if $precomputedZscore_conditional.precomputedZscore_selector == \'precomputed\':\n+ ln -s \'$precomputedZscore_conditional.scoreFile\' \'prefix_tad_score.bm\' && \n+ ln -s \'$precomputedZscore_conditional.zscoreMatrix\' \'prefix_zscore_matrix.h5\' &&\n+ #end if\n+ @BINARY@\n+ --matrix \'matrix.$matrix_h5_cooler.ext\'\n \n --delta $delta\n \n #if $minBoundaryDistance:\n --minBoundaryDistance $minBoundaryDistance\n #end if\n- --minDepth $minDepth\n- --maxDepth $maxDepth\n- --step $step\n+\n+ #if $precomputedZscore_conditional.precomputedZscore_selector == \'scratch\':\n+ --minDepth $precomputedZscore_conditional.minDepth\n+ --maxDepth $precomputedZscore_conditional.maxDepth\n+ --step $precomputedZscore_conditional.step\n+ #elif $precomputedZscore_conditional.precomputedZscore_selector == \'precomputed\':\n+ --TAD_sep_score_prefix prefix\n+ #end if\n #if $multiple_comparison_conditional.multiple_comparison_selector == \'fdr\':\n --correctForMultipleTesting fdr\n --threshold $multiple_comparison_conditional.threshold\n@@ -29,22 +40,39 @@\n \n --numberOfProcessors @THREADS@\n --outPrefix galaxy_tad_prefix\n+ #if $chromosomes:\n+ --chromosomes #echo "\' \'".join([ "\'%s\'" % $chrom.chromosome for $chrom in $chromosomes ])#\n+ #end if\n ]]></command>\n <inputs>\n <expand macro=\'matrix_h5_cooler_macro\' />\n \n- <param argument="--minDepth" type="integer" value="40000"\n- label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n- help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>\n- <param argument="--maxDepth" type="integer" value="100000"\n- label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n- help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>\n- <param argument="--step" type="integer" value="10000"\n- label="Step size when moving from minDepth to maxDepth"\n- help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]\n- until it reaches maxDepth. For example, selecting step=10,000, minDepth=20,000\n- and maxDepth=150,000 will compute TAD-scores for window sizes:\n- 20,000, 30,000, 40,000, 70,000 and 100,000"/>\n+ <conditional name=\'precomputedZscore_conditional\'>\n+ <param name=\'precomputedZscore_selector\' type="select" label="Compute from scratch or use precomputed data">\n+ <option value=\'scratch\' selected=\'True\'>From scratch</option>\n+ <option value=\'precomputed\'>Precomputed z-score matrix</option>\n+ </param>\n+ <when value=\'scratch\'>\n+\n+ <param argument="--minDepth" type="integer" value="5000"\n+ label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n+ help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>\n+ <param argument="--maxDepth" type="integer" value="10000"\n+ label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."\n+ '..b'e="sim_size" delta="35000" />\n+ <output name="matrix_output" ftype="h5">\n+ <assert_contents>\n+ <has_h5_keys keys=\'intervals,matrix\'/>\n+ </assert_contents>\n+ </output>\n \n- <param name="minDepth" value="60000"/>\n- <param name="maxDepth" value="180000"/>\n- <param name="step" value="20000"/>\n- <param name="minBoundaryDistance" value="20000" />\n+ </test>\n+ <test>\n+ <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>\n+ <conditional name="precomputedZscore_conditional">\n+ <param name="precomputedZscore_selector" value="precomputed"/>\n+ <param name="scoreFile" value="find_TADs/multiFDR_tad_score.bm" />\n+ <param name="zscoreMatrix" value="find_TADs/multiFDR_zscore_matrix.h5"/>\n+ </conditional>\n+ <param name="minBoundaryDistance" value="5000" />\n <conditional name="multiple_comparison_conditional">\n <param name="multiple_comparison_selector" value="fdr"/>\n <param name="threshold" value="0.1" />\n@@ -107,7 +171,6 @@\n <output name="boundaries_bin" file="find_TADs/multiFDR_boundaries.gff" ftype="gff" compare="sim_size" delta="35000" />\n <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />\n <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />\n- <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />\n </test>\n </tests>\n <help><![CDATA[\n@@ -152,7 +215,7 @@\n - TAD boundaries positions with delta, p-value and TAD separation score as GFF.\n - TAD domains as a BED file.\n - TAD seperation score as bigwig (bw), bedgraph and numpy array (npz) format. These files can be used to plot the so-called TAD insulation score or TAD separation score along the genome or at specific regions. This score is much more reliable across samples than the number of TADs or the TADs width that can vary depending on the sequencing depth because of the lack of information at certain bins, and depending on the parameters used with this tool.\n-- Matrix with multi-scale TAD scores as a bed-matrix (bm) file that can be plotted inside ``hicPlotTADs`` to nicely display TAD insulation score alongside Hi-C heatmap and other datasets.\n+- Matrix with multi-scale TAD scores as a bed-matrix (bm) file that can be plotted inside ``pyGenomeTracks`` to nicely display TAD insulation score alongside Hi-C heatmap and other datasets.\n - Z-score matrix in h5 format that is useful to quickly test the --thresholdComparisons, --delta and --correctForMultipleTesting parameters by using the --TAD_sep_score_prefix option pointing to this zscore_matrix.h5 file (will be added in a future update).\n \n _________________\n@@ -160,7 +223,7 @@\n Usage hints\n -----------\n \n-It is mandatory to test multiple parameters of TAD calling with **hicFindTADs** before making conclusions about the number of TADs in a given sample or before comparing TAD calling between multiple conditions. In order to compare numerous TAD calling parameters at once, it is recommended to use ``hicPlotTADs``, below you can find a plot where multiple TAD calling parameters are displayed for *Drosophila melanogaster* embryos:\n+It is mandatory to test multiple parameters of TAD calling with **hicFindTADs** before making conclusions about the number of TADs in a given sample or before comparing TAD calling between multiple conditions. In order to compare numerous TAD calling parameters at once, it is recommended to use ``pyGenomeTracks``, below you can find a plot where multiple TAD calling parameters are displayed for *Drosophila melanogaster* embryos:\n \n .. image:: $PATH_TO_IMAGES/hicFindTADs_TAD_calling_comparison.png\n :width: 65 %\n'

diff -r 6bda631b9239 -r 6b7987d22eab macros.xml
--- a/macros.xml Mon Dec 16 10:36:22 2019 -0500
+++ b/macros.xml Mon Dec 16 15:48:31 2019 -0500

[

b'@@ -1,6 +1,6 @@\n <macros>\n <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n- <token name="@WRAPPER_VERSION@">2.1.4</token>\n+ <token name="@WRAPPER_VERSION@">3.3.1</token>\n <token name="@USE_RANGE@">\n #if $use_range.select_use_range == "yes_use_range":\n --range $range_min:$range_max\n@@ -15,6 +15,25 @@\n <version_command>@BINARY@ --version</version_command>\n </xml>\n \n+ <token name="@CHROMOSOME_LIST@">\n+ #if $chromosome_list:\n+ #set $chromosomes = []\n+ #for $chrom in $chromosome_list:\n+ #silent $chromosomes.append("\'%s\'" % $chrom.chromosomes)\n+ #end for\n+ #set $chromosome_string = \' \'.join($chromosomes)\n+ --chromosomes $chromosome_string\n+ #end if\n+ </token>\n+\n+ <xml name="chromosome_list">\n+ <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">\n+ <param argument="--chromosomes" type="text" value="" >\n+ <validator type="empty_field" />\n+ </param>\n+ </repeat>\n+ </xml>\n+\n <xml name="citations">\n <citations>\n <citation type="doi">10.5281/zenodo.1133705</citation>\n@@ -114,6 +133,7 @@\n <option value="brg">brg</option>\n <option value="jet">jet</option>\n <option value="afmhot">afmhot</option>\n+ <option value="plasma">plasma</option>\n <option value="Accent_r">Accent reversed</option>\n <option value="Spectral_r">Spectral reversed</option>\n <option value="Set1_r">Set1 reversed</option>\n@@ -183,10 +203,10 @@\n <option value="brg_r">brg reversed</option>\n <option value="jet_r">jet reversed</option>\n <option value="afmhot_r">afmhot reversed</option>\n+ <option value="plasma_r">plasma reversed</option>\n </param>\n </xml>\n \n-\n <xml name="multiple_input_matrices">\n <repeat name="input_files" title="Hi-C Matrix files" min="2">\n <param name="matrix" type="data" format="h5,cool"\n@@ -202,19 +222,22 @@\n #set $matrices = []\n #set $mlabels = []\n #for $counter, $i in enumerate($input_files):\n- ln -s $i.matrix #echo str($counter)+\'_matrix\'#;\n- #silent $matrices.append( \'%s_matrix\' % $counter )\n+ ln -s \'$i.matrix\' \'${counter}_matrix.$i.matrix.ext\'; \n+ #silent $matrices.append( \'\\\'%s_matrix.%s\\\'\' % ($counter, $i.matrix.ext))\n \n #if str($i.mlabel.value) != "":\n- #set $mlabels += [\'"%s"\' % ($i.mlabel.value)]\n+ #set $mlabels += [\'\\\'%s\\\'\' % ($i.mlabel.value)]\n #else\n- #set $mlabels += [\'"%s"\' % ($i.matrix.name)]\n+ #set $mlabels += [\'\\\'%s\\\'\' % ($i.matrix.name)]\n #end if\n #end for\n #set $mlabels = \' \'.join($mlabels)\n #set $matrices = \' \'.join($matrices)\n </token>\n \n+ <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($file.element_identifier))]]></token>\n+ <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($matrix.element_identifier))]]></token>\n+ <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($m.element_identifier))]]></token>\n \n <xml name="region">\n <param name="region" type="text" label="Region of the genome to limit the operation"\n@@ -330,6 +353,96 @@\n <param name=\'matrix_h5_cooler_multiple\' type="data" format="h5,cool"\n label="Matricies to compute on" multiple="true"/>\n </xml>\n+\n+ \n+\n+ <xml name=\'convertFormat_single_macro\'>\n+ <conditional name="inputFormat_conditional">\n+ <param name="inputFormat_selector" type="select" label="Choose input file type">\n+ <option value="optionCool" selected="True">cool</option>\n+ '..b'n" truevalue="yes" falsevalue="" label=\'Apply correction factors with a division instead multiplication\'/>\n+ <param name=\'chromosome\' type=\'text\' label=\'Load only one chromosome\'/>\n+ <param name=\'loadRawValues\' type="boolean" truevalue="yes" falsevalue="" label=\'Load raw data\'/>\n+\n+ </when>\n+ <when value="optionH5">\n+ <expand macro=\'matrix_h5_cooler_macro\' />\n+ </when>\n+  \n+\n+ <when value="optionHomer">\n+ <param name=\'matrixHomer\' type=\'data\' format=\'txt\' label=\'Homer interaction matrix\'/>\n+ </when>\n+\n+ <when value="optionHicpro">\n+ <param name=\'matrixHicpro\' type=\'data\' format=\'txt\' label=\'.hic matrix\'/>\n+ <param name=\'bedHicpro\' type=\'data\' format=\'bed\' label=\'HicPro bed file\'/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name=\'convertFormat_multiple_macro\'>\n+ <conditional name="inputFormat_conditional">\n+ <param name="inputFormat_selector" type="select" label="Choose input file type">\n+ <option value="optionCool" selected="True">cool</option>\n+ <option value="optionH5">h5</option>\n+ <option value="optionHomer">Homer</option>\n+ <option value="optionHicpro">HiCPro</option>\n+ </param>\n+ <when value="optionCool">\n+ <expand macro=\'matrix_h5_cooler_multiple_macro\' />\n+ <param name=\'correctionName\' type=\'text\' label=\'Correction factors column name\'/>\n+ <param name=\'correctionDivision\' type="boolean" truevalue="yes" falsevalue="" label=\'Apply correction factors with a division instead multiplication\'/>\n+ <param name=\'chromosome\' type=\'text\' label=\'Load only one chromosome\'/>\n+ <param name=\'loadRawValues\' type="boolean" truevalue="yes" falsevalue="" label=\'Load raw data\'/>\n+\n+ </when>\n+ <when value="optionH5">\n+ <expand macro=\'matrix_h5_cooler_multiple_macro\' />\n+ </when>\n+ \n+ <when value="optionHomer">\n+ <param name=\'matrixHomer\' type=\'data\' format=\'txt\' label=\'Homer interaction matrix\' multiple="true"/>\n+ </when>\n+\n+ <when value="optionHicpro">\n+ <param name=\'matrixHicpro\' type=\'data\' format=\'txt\' label=\'.hic matrix\' multiple="true"/>\n+ <param name=\'bedHicpro\' type=\'data\' format=\'bed\' label=\'HicPro bed file\' multiple="true"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name=\'convertFormat_single_output_macro\'>\n+ \n+\n+ <conditional name="outputFormat_conditional">\n+ <param name="outputFormat_selector" type="select" label="Choose output file type">\n+ <option value="cool" selected="True">cool</option>\n+ <option value="h5">h5</option>\n+ <option value="homer">Homer</option>\n+ <option value="ginteractions">ginteractions</option>\n+\n+ </param>\n+ <when value="cool">\n+ <param name=\'storeAppliedCorrection\' type="boolean" truevalue="yes" falsevalue="" label=\'Store applied correction factors in column count\'/>\n+ <param name=\'enforceInteger\' type="boolean" truevalue="yes" falsevalue="" label=\'Enforce integer for count column\'/>\n+ </when>\n+ <when value=\'h5\'/>\n+ <when value=\'homer\'/>\n+ <when value=\'ginteractions\'/>\n+\n+ </conditional>\n+ </xml>\n <token name="@REFERENCES@">\n \n .. class:: infomark\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/Li_et_al_2015.cool

Binary file test-data/Li_et_al_2015.cool has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/FL-E13-5_chr1.cool

Binary file test-data/cHi-C/FL-E13-5_chr1.cool has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/MB-E10-5_chr1.cool

Binary file test-data/cHi-C/MB-E10-5_chr1.cool has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/background.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/background.bed Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,1002 @@\n+Relative position\tsize nbinom\tprob nbinom\tmax value\tmean value\n+-500000\t58.254577634279\t0.998604709282\t1.333333333333\t0.000105073709\n+-499000\t10.000013353187\t0.991925224088\t1.500000000000\t0.000105073709\n+-498000\t72.266262784304\t0.998828265884\t1.200000000000\t0.000111077921\n+-497000\t51.093422441771\t0.998183086351\t1.000000000000\t0.000120084239\n+-496000\t86.575220693033\t0.998899865570\t0.800000000000\t0.000123086345\n+-495000\t72.441590407550\t0.998655447638\t0.800000000000\t0.000126088451\n+-494000\t75.085350270547\t0.998668414055\t1.000000000000\t0.000129090557\n+-493000\t71.967411178924\t0.998612779641\t1.000000000000\t0.000129090557\n+-492000\t77.026231982211\t0.998763649786\t1.200000000000\t0.000123086345\n+-491000\t96.154018360868\t0.999129584825\t1.000000000000\t0.000108075815\n+-490000\t70.641792331241\t0.998918479365\t1.400000000000\t0.000099069497\n+-489000\t72.297114570842\t0.998971709245\t0.800000000000\t0.000096067391\n+-488000\t55.276417890737\t0.998907322028\t0.800000000000\t0.000078054755\n+-487000\t75.866231077639\t0.999020037562\t0.600000000000\t0.000096067391\n+-486000\t77.908114872120\t0.999075493568\t0.600000000000\t0.000093065285\n+-485000\t70.196050128375\t0.998940963837\t0.600000000000\t0.000096067391\n+-484000\t48.306835304302\t0.998789125810\t0.600000000000\t0.000078054755\n+-483000\t65.826727385050\t0.999115985283\t0.600000000000\t0.000075052649\n+-482000\t10.000003651221\t0.996523342626\t0.400000000000\t0.000045031590\n+-481000\t48.188933357556\t0.999179280048\t0.400000000000\t0.000051035802\n+-480000\t10.000001173914\t0.997216871755\t0.400000000000\t0.000036025272\n+-479000\t10.000002160096\t0.996985563716\t0.400000000000\t0.000039027378\n+-478000\t61.980720096540\t0.999287603012\t0.800000000000\t0.000057040014\n+-477000\t47.193502172887\t0.999138448161\t0.600000000000\t0.000054037908\n+-476000\t75.435666576826\t0.999477638616\t0.600000000000\t0.000051035802\n+-475000\t83.258498044933\t0.999385868055\t0.600000000000\t0.000066046332\n+-474000\t64.452927063111\t0.999206823435\t0.600000000000\t0.000066046332\n+-473000\t68.592799621533\t0.999390093904\t0.600000000000\t0.000054037908\n+-472000\t48.567204011739\t0.999139405277\t0.600000000000\t0.000054037908\n+-471000\t10.000004448331\t0.996292395667\t0.600000000000\t0.000048033696\n+-470000\t10.000000920405\t0.995831238986\t1.400000000000\t0.000054037908\n+-469000\t10.000003872489\t0.994909340544\t1.400000000000\t0.000066046332\n+-468000\t63.250123985231\t0.999022818205\t1.400000000000\t0.000081056861\n+-467000\t51.399551404579\t0.998558644000\t1.400000000000\t0.000096067391\n+-466000\t64.883458129266\t0.998762977849\t1.000000000000\t0.000105073709\n+-465000\t86.383451689662\t0.999139519880\t0.800000000000\t0.000096067391\n+-464000\t64.657320565128\t0.998830168725\t1.000000000000\t0.000099069497\n+-463000\t69.011442263596\t0.998889631783\t1.000000000000\t0.000099069497\n+-462000\t120.365580780362\t0.999304923056\t1.000000000000\t0.000108075815\n+-461000\t83.873478804403\t0.999085832019\t1.000000000000\t0.000099069497\n+-460000\t76.791436688795\t0.998822607239\t0.800000000000\t0.000117082133\n+-459000\t71.300309154477\t0.998707418591\t1.000000000000\t0.000120084239\n+-458000\t70.551044686671\t0.998794143443\t0.600000000000\t0.000111077921\n+-457000\t88.657625851365\t0.999084917164\t0.800000000000\t0.000105073709\n+-456000\t66.985331452249\t0.998825498193\t0.800000000000\t0.000102071603\n+-455000\t212.376735013798\t0.999710065148\t0.600000000000\t0.000078054755\n+-454000\t62.703317289439\t0.999261443476\t0.600000000000\t0.000060042120\n+-453000\t45.696967611307\t0.998932417121\t0.600000000000\t0.000063044226\n+-452000\t82.313181248075\t0.999548168551\t0.600000000000\t0.000048033696\n+-451000\t61.955802866608\t0.999249835457\t0.600000000000\t0.000060042120\n+-450000\t71.163546816639\t0.999118429295\t1.000000000000\t0.000081056861\n+-449000\t57.404577886000\t0.998868956077\t1.000000000000\t0.000084058967\n+-448000\t78.889496868591\t0.999175114488\t1.000000000000\t0.000084058967\n+-447000\t59.455705064746\t0.998872066360\t1.000000000000\t0.000087061073\n+-446000\t69.521205032032\t0.998763823049\t1.000000000000\t0.000111077921\n+-445000\t99.901425243691\t0.999325366218\t0.800000000000\t0.0000870'..b'92515295592\t0.998432747334\t1.400000000000\t0.000222155842\n+444000\t82.443622273366\t0.997719903159\t1.400000000000\t0.000243170584\n+445000\t70.933399279725\t0.997396373546\t1.400000000000\t0.000243170584\n+446000\t95.161892262226\t0.998095770809\t1.600000000000\t0.000234164266\n+447000\t124.614672839908\t0.998565069417\t1.200000000000\t0.000231162160\n+448000\t77.860490008359\t0.997704488044\t1.400000000000\t0.000231162160\n+449000\t65.217115835699\t0.997403641809\t1.400000000000\t0.000219153736\n+450000\t75.445932132698\t0.998007293338\t1.200000000000\t0.000198138995\n+451000\t95.181162634818\t0.998473187366\t1.000000000000\t0.000186130571\n+452000\t94.977236808895\t0.998461455130\t1.000000000000\t0.000189132677\n+453000\t71.519354123232\t0.997988008873\t1.000000000000\t0.000186130571\n+454000\t75.038048093362\t0.998148510684\t1.000000000000\t0.000183128465\n+455000\t66.094167095466\t0.997699897371\t1.000000000000\t0.000198138995\n+456000\t111.325708146664\t0.998498182775\t1.000000000000\t0.000216151630\n+457000\t102.171886886530\t0.998454607629\t1.000000000000\t0.000204143206\n+458000\t88.125308869888\t0.998313915544\t1.000000000000\t0.000192134783\n+459000\t70.605027521073\t0.997930191387\t0.800000000000\t0.000189132677\n+460000\t100.268739339170\t0.998772290781\t0.600000000000\t0.000159111617\n+461000\t74.543018827171\t0.998473634038\t0.800000000000\t0.000147103193\n+462000\t63.337319446090\t0.998204073767\t0.800000000000\t0.000147103193\n+463000\t117.089896011864\t0.999027727546\t0.800000000000\t0.000147103193\n+464000\t91.138003901288\t0.998496746777\t1.800000000000\t0.000177124253\n+465000\t92.914491189803\t0.998350787907\t1.800000000000\t0.000198138995\n+466000\t52.209334348546\t0.997159438011\t2.400000000000\t0.000192134783\n+467000\t77.918569531358\t0.998034146232\t2.800000000000\t0.000198138995\n+468000\t40.028010375624\t0.996410794913\t2.800000000000\t0.000186130571\n+469000\t52.807401795042\t0.997408431862\t1.400000000000\t0.000177124253\n+470000\t105.325058737937\t0.998676526339\t1.400000000000\t0.000180126359\n+471000\t97.395447231439\t0.998474152554\t1.000000000000\t0.000192134783\n+472000\t71.036732364957\t0.998055374489\t1.200000000000\t0.000183128465\n+473000\t58.839853998831\t0.997768804625\t1.200000000000\t0.000174122147\n+474000\t109.506948227434\t0.998942877974\t1.000000000000\t0.000150105299\n+475000\t73.687080792836\t0.998676219719\t0.600000000000\t0.000126088451\n+476000\t86.562200266338\t0.998926533547\t0.600000000000\t0.000120084239\n+477000\t78.601283549403\t0.998670347780\t0.600000000000\t0.000135094769\n+478000\t77.287682759273\t0.998311780993\t1.000000000000\t0.000168117935\n+479000\t80.196363250368\t0.998336155363\t0.800000000000\t0.000174122147\n+480000\t95.618679354949\t0.998538823715\t0.800000000000\t0.000180126359\n+481000\t71.324679124414\t0.998079961192\t1.000000000000\t0.000177124253\n+482000\t98.947326582471\t0.998662082026\t1.200000000000\t0.000171120041\n+483000\t98.312778915279\t0.998677055532\t1.000000000000\t0.000168117935\n+484000\t80.536358888257\t0.998500685590\t1.200000000000\t0.000156109511\n+485000\t75.299149742118\t0.998174557637\t1.200000000000\t0.000177124253\n+486000\t80.676043504302\t0.998160484267\t1.600000000000\t0.000192134783\n+487000\t65.456290718619\t0.997731312445\t1.600000000000\t0.000192134783\n+488000\t135.605664962437\t0.998837097471\t1.400000000000\t0.000204143206\n+489000\t78.041126983216\t0.997890938542\t1.600000000000\t0.000213149524\n+490000\t73.842941938827\t0.998020155259\t1.200000000000\t0.000192134783\n+491000\t135.330452041151\t0.998884251454\t1.000000000000\t0.000195136889\n+492000\t70.441325198247\t0.997891524929\t1.000000000000\t0.000192134783\n+493000\t93.145208276513\t0.998579085962\t1.200000000000\t0.000171120041\n+494000\t93.195291870240\t0.998579645775\t1.200000000000\t0.000171120041\n+495000\t66.167995861224\t0.997615723218\t1.200000000000\t0.000204143206\n+496000\t68.869469387443\t0.998039511367\t1.200000000000\t0.000174122147\n+497000\t61.393255588548\t0.997958646123\t1.400000000000\t0.000162113723\n+498000\t64.393702971434\t0.998089554455\t1.200000000000\t0.000159111617\n+499000\t64.222140571019\t0.998102497389\t1.000000000000\t0.000157610564\n+500000\t10.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 673.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 14274000 14279000 Eya1 673.0 -22000    7.00000
+chr1 14285000 14308000 Eya1 673.0 7000 389.40000
+chr1 14310000 14322000 Eya1 673.0 21000   54.80000
+chr1 14361000 14407000 Eya1 673.0 106000   21.20000
+chr1 14426000 14432000 Eya1 673.0 131000    2.40000
+chr1 14447000 14455000 Eya1 673.0 154000    4.40000
+chr1 14460000 14465000 Eya1 673.0 164000    3.20000
+chr1 14491000 14500000 Eya1 673.0 199000   17.65000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 472.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 19077000 19114000 Tfap2d 472.0 20000 344.80000
+chr1 19125000 19129000 Tfap2d 472.0 35000    7.80000
+chr1 19134000 19139000 Tfap2d 472.0 45000    8.40000
+chr1 19141000 19238000 Tfap2d 472.0 144000   47.40000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,9 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 810.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 4472000 4503000 Sox17 810.0 15000 566.20000
+chr1 4507000 4516000 Sox17 810.0 28000   38.80000
+chr1 4520000 4531000 Sox17 810.0 43000   10.40000
+chr1 4533000 4543000 Sox17 810.0 55000    6.80000
+chr1 4562000 4593000 Sox17 810.0 105000   25.00000
+chr1 4664000 4669000 Sox17 810.0 181000    1.20000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10  Mbp 14.50  Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 14274000 14279000 Eya1 832.0 -22000    0.00000
+chr1 14285000 14308000 Eya1 832.0 7000 479.80000
+chr1 14310000 14322000 Eya1 832.0 21000   52.80000
+chr1 14361000 14407000 Eya1 832.0 106000   36.00000
+chr1 14426000 14432000 Eya1 832.0 131000    9.00000
+chr1 14447000 14455000 Eya1 832.0 154000   12.40000
+chr1 14460000 14465000 Eya1 832.0 164000    7.60000
+chr1 14491000 14500000 Eya1 832.0 199000   15.75000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,7 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89  Mbp 19.29  Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 19077000 19114000 Tfap2d 800.0 20000 527.80000
+chr1 19125000 19129000 Tfap2d 800.0 35000    8.80000
+chr1 19134000 19139000 Tfap2d 800.0 45000   11.20000
+chr1 19141000 19238000 Tfap2d 800.0 144000 163.00000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,9 @@
+# Aggregated file, created with HiCExplorer's chicAggregateStatistic version 3.3
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29  Mbp 4.69  Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Sum of interactions Relative distance Raw target
+chr1 4472000 4503000 Sox17 978.0 15000 724.40000
+chr1 4507000 4516000 Sox17 978.0 28000   19.00000
+chr1 4520000 4531000 Sox17 978.0 43000   22.20000
+chr1 4533000 4543000 Sox17 978.0 55000   12.20000
+chr1 4562000 4593000 Sox17 978.0 105000   23.20000
+chr1 4664000 4669000 Sox17 978.0 181000    5.40000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/batch_mode_file_names.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed Mon Dec 16 15:48:31 2019 -0500

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,17 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00335
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96904
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.21097
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.25281
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.10924
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.12863
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.32025
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.35033

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.25943
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.40802
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.60118
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00004

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by chi2 test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.43072
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00105
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.12754
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.40725
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.36639
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.16231

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:48:31 2019 -0500

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,13 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,14 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 19077000 19114000 Tfap2d 20000 472.00000 344.80000 800.00000 527.80000 0.27744
+chr1 19125000 19129000 Tfap2d 35000 472.00000 7.80000 800.00000 8.80000 0.45206
+chr1 19134000 19139000 Tfap2d 45000 472.00000 8.40000 800.00000 11.20000 0.65094
+chr1 19141000 19238000 Tfap2d 144000 472.00000 47.40000 800.00000 163.00000 0.00005

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.2-dev
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 4472000 4503000 Sox17 15000 810.00000 566.20000 978.00000 724.40000 0.44082
+chr1 4507000 4516000 Sox17 28000 810.00000 38.80000 978.00000 19.00000 0.00117
+chr1 4520000 4531000 Sox17 43000 810.00000 10.40000 978.00000 22.20000 0.16402
+chr1 4533000 4543000 Sox17 55000 810.00000 6.80000 978.00000 12.20000 0.37847
+chr1 4562000 4593000 Sox17 105000 810.00000 25.00000 978.00000 23.20000 0.46860
+chr1 4664000 4669000 Sox17 181000 810.00000 1.20000 978.00000 5.40000 0.30594

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,12 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,16 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,18 @@
+# Differential analysis result file of HiCExplorer's chicDifferentialTest version 3.3
+# This file contains the p-values computed by fisher test
+# To test the smoothed (float) values they were rounded up to the next integer
+#
+# Alpha level 0.5
+# Degrees of freedom 1
+#
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Relative distance sum of interactions 1 target_1 raw sum of interactions 2 target_2 raw p-value
+chr1 14274000 14279000 Eya1 -22000 673.00000 7.00000 832.00000 0.00000 0.00366
+chr1 14285000 14308000 Eya1 7000 673.00000 389.40000 832.00000 479.80000 0.96586
+chr1 14310000 14322000 Eya1 21000 673.00000 54.80000 832.00000 52.80000 0.23002
+chr1 14361000 14407000 Eya1 106000 673.00000 21.20000 832.00000 36.00000 0.34706
+chr1 14426000 14432000 Eya1 131000 673.00000 2.40000 832.00000 9.00000 0.24523
+chr1 14447000 14455000 Eya1 154000 673.00000 4.40000 832.00000 12.40000 0.23210
+chr1 14460000 14465000 Eya1 164000 673.00000 3.20000 832.00000 7.60000 0.56425
+chr1 14491000 14500000 Eya1 199000 673.00000 17.65000 832.00000 15.75000 0.38515

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicDifferentialTest/rejectedFilesList.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png

Binary file test-data/cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png

Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png

Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png

Binary file test-data/cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicQualityControl/histogram.png

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

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicQualityControl/new_referencepoints.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,35 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+chr1 24202042 24202042 Col9a1
+chr1 33776741 33776741 Rab23
+chr1 38684089 38684089 Aff3
+chr1 42753991 42753991 Pou3f3
+chr1 52176282 52176282 Stat1
+chr1 53118507 53118507 Mstn
+chr1 57028178 57028178 Satb2
+chr1 59821123 59821123 Bmpr2
+chr1 66991630 66991630 Myl1
+chr1 74648029 74648029 Stk36
+chr1 74818466 74818466 Wnt6
+chr1 75356867 75356867 Des
+chr1 77511663 77511663 Epha4
+chr1 78193711 78193711 Pax3
+chr1 89102386 89102386 Chrng
+chr1 93355905 93355905 Per2
+chr1 93698054 93698054 Twist2
+chr1 107677300 107677300 Tnfrsf11a
+chr1 120950196 120950196 Gli2
+chr1 122499064 122499064 En1
+chr1 127808791 127808791 Lypd1
+chr1 135934092 135934092 Fmod
+chr1 136186581 136186581 MyoG
+chr1 164004278 164006270 mm712
+chr1 164147754 164147754 Dnm3os
+chr1 165243781 165243781 Prrx1
+chr1 165333772 165333772 Gorab
+chr1 169619689 169619689 Lmx1a
+chr1 182823250 182823250 Lefty2
+chr1 182865170 182865170 Lefty1
+chr1 188529871 188529871 Tgfb2
+chr1 194979306 194979306 Irf6

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,45 @@
+# Created with chicQualityControl version 3.3
+# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
+chr1 4487435 4487435 Sox17 0.14485514485514486 0.16083916083916083
+chr1 14300280 14300280 Eya1 0.14285714285714285 0.1938061938061938
+chr1 19093103 19093103 Tfap2d 0.1048951048951049 0.16683316683316685
+chr1 19198995 19198995 Tfap2b 0.01898101898101898 0.016983016983016984
+chr1 24202042 24202042 Col9a1 0.10589410589410589 0.12787212787212787
+chr1 33776741 33776741 Rab23 0.15484515484515485 0.2137862137862138
+chr1 38684089 38684089 Aff3 0.11588411588411589 0.11388611388611389
+chr1 42753991 42753991 Pou3f3 0.04995004995004995 0.07592407592407592
+chr1 52176282 52176282 Stat1 0.19080919080919082 0.22777222777222778
+chr1 52557292 52557292 Nab1 0.02197802197802198 0.024975024975024976
+chr1 53118507 53118507 Mstn 0.3116883116883117 0.37462537462537465
+chr1 57028178 57028178 Satb2 0.12287712287712288 0.14385614385614387
+chr1 59821123 59821123 Bmpr2 0.14085914085914086 0.16983016983016982
+chr1 66991630 66991630 Myl1 0.0919080919080919 0.09290709290709291
+chr1 74648029 74648029 Stk36 0.2777222777222777 0.3356643356643357
+chr1 74818466 74818466 Wnt6 0.29270729270729273 0.34165834165834164
+chr1 74838593 74838593 Wnt10a 0.00999000999000999 0.008991008991008992
+chr1 74998246 74998246 Ihh 0.008991008991008992 0.003996003996003996
+chr1 75356867 75356867 Des 0.18081918081918083 0.21678321678321677
+chr1 77511663 77511663 Epha4 0.15684315684315683 0.22277722277722278
+chr1 78193711 78193711 Pax3 0.24375624375624375 0.3096903096903097
+chr1 89102386 89102386 Chrng 0.16783216783216784 0.2217782217782218
+chr1 93355905 93355905 Per2 0.15384615384615385 0.16483516483516483
+chr1 93698054 93698054 Twist2 0.22277722277722278 0.23476523476523475
+chr1 94076918 94076918 Hdac4 0.0 0.0
+chr1 107677300 107677300 Tnfrsf11a 0.14685314685314685 0.16383616383616384
+chr1 120950196 120950196 Gli2 0.13986013986013987 0.2007992007992008
+chr1 122499064 122499064 En1 0.1008991008991009 0.11988011988011989
+chr1 127808791 127808791 Lypd1 0.18681318681318682 0.22977022977022976
+chr1 135934092 135934092 Fmod 0.3516483516483517 0.4145854145854146
+chr1 136186581 136186581 MyoG 0.07392607392607392 0.09090909090909091
+chr1 152313295 152313295 Prg4 0.00999000999000999 0.006993006993006993
+chr1 164004278 164006270 mm712 0.26173826173826176 0.2867132867132867
+chr1 164147754 164147754 Dnm3os 0.24875124875124874 0.24675324675324675
+chr1 165243781 165243781 Prrx1 0.36063936063936064 0.34065934065934067
+chr1 165333772 165333772 Gorab 0.36863136863136864 0.3956043956043956
+chr1 169619689 169619689 Lmx1a 0.11888111888111888 0.16783216783216784
+chr1 170362300 170362300 Pbx1 0.003996003996003996 0.002997002997002997
+chr1 180249284 180249284 Gm16586 0.0 0.0
+chr1 182823250 182823250 Lefty2 0.27472527472527475 0.33266733266733267
+chr1 182865170 182865170 Lefty1 0.25674325674325676 0.3086913086913087
+chr1 188529871 188529871 Tgfb2 0.13486513486513488 0.16583416583416583
+chr1 194979306 194979306 Irf6 0.12987012987012986 0.15284715284715283

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_rejected_filter Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+chr1 19198995 19198995 Tfap2b
+chr1 52557292 52557292 Nab1
+chr1 74838593 74838593 Wnt10a
+chr1 74998246 74998246 Ihh
+chr1 94076918 94076918 Hdac4
+chr1 152313295 152313295 Prg4
+chr1 170362300 170362300 Pbx1
+chr1 180249284 180249284 Gm16586

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicQualityControl/sparsity.png

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

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 14274000 14278000 Eya1 673.0 -26000 0.00832095096400000019 0.01042503066537725509 7.81112575817000021061 5.59999999999999964473
+chr1 14296000 14298000 Eya1 673.0 -3000 0.05794947993999999963 0.10421572859864158822 3.78135593591500018817 39.00000000000000000000
+chr1 14314000 14316000 Eya1 673.0 14000 0.01515601783000000008 0.05171206541410811042 3.19033393500999995496 10.19999999999999928946
+chr1 14317000 14319000 Eya1 673.0 17000 0.01456166419000000031 0.04670037874744681350 3.51709033858399999772 9.80000000000000071054
+chr1 14480000 14488000 Eya1 673.0 184000 0.01129271916799999900 0.00000005723969254134 19.28508294646199772160 7.59999999999999875655
+chr1 14491000 14501000 Eya1 673.0 200000 0.03068350668399999828 0.00000000000003064216 56.96782483342801128856 20.64999999999999857891

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_1_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000
+chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605
+chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109
+chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783
+chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109
+chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_2_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 14274000 14279000
+chr1 14285000 14308000
+chr1 14310000 14322000
+chr1 14361000 14395000
+chr1 14491000 14500000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,7 @@
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 14295000 14298000 Eya1 832.0 -3000 0.05985576923100000002 0.06113759528369666629 4.79015312599299925012 49.79999999999999715783
+chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000
+chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891
+chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473
+chr1 14491000 14501000 Eya1 832.0 200000 0.02253605769199999720 0.00000000000003064216 41.39757163433100117800 18.75000000000000000000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14295000 14298000
+chr1 14426000 14432000
+chr1 14447000 14455000
+chr1 14460000 14465000
+chr1 14491000 14501000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 19089000 19091000 Tfap2d 472.0 -3000 0.06101694915199999680 0.18835888966198111039 4.06818820852600016025 28.80000000000000071054
+chr1 19104000 19106000 Tfap2d 472.0 11000 0.02245762711799999950 0.11671915718551462149 3.62722049649999966903 10.59999999999999964473
+chr1 19109000 19114000 Tfap2d 472.0 18000 0.03940677966200000631 0.00080680261510490681 9.61739201792699915927 18.60000000000000142109
+chr1 19125000 19129000 Tfap2d 472.0 33000 0.01652542372999999884 0.00829653069244939978 7.28507499155399962376 7.79999999999999982236
+chr1 19133000 19138000 Tfap2d 472.0 41000 0.01949152542399999744 0.00041957482022692005 9.72184228688099949522 9.19999999999999928946
+chr1 19197000 19202000 Tfap2d 472.0 108000 0.01059322033899999863 0.00398884532051024809 10.24326734149200035517 5.00000000000000000000
+chr1 19227000 19233000 Tfap2d 472.0 137000 0.01186440677899999914 0.00244241040005155341 14.41899403645599875290 5.59999999999999964473
+chr1 19254000 19261000 Tfap2d 472.0 163000 0.01355932203300000069 0.00004326025137579848 19.68794216164500454624 6.39999999999999946709

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 4509000 4515000 Sox17 810.0 23000 0.03432098765399999724 0.00000160319175224188 11.55191083898800030738 27.80000000000000071054
+chr1 4561000 4567000 Sox17 810.0 75000 0.01432098765400000029 0.00000102319718320310 11.23656007944399881637 11.59999999999999964473
+chr1 4585000 4590000 Sox17 810.0 98000 0.00987654320999999807 0.00037019878415911478 8.98479195802099894763 8.00000000000000000000
+chr1 4652000 4658000 Sox17 810.0 169000 0.00740740740700000008 0.00005538687174366785 11.12107213938599947767 6.00000000000000000000
+chr1 4499000 4500000 Sox17 810.0 12000 0.00987654320999999981 0.15859163588059266292 1.65903762227799989049 8.00000000000000000000
+chr1 4501000 4502000 Sox17 810.0 14000 0.00765432098799999957 0.17926099806325068720 1.57677828943600006895 6.20000000000000017764

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_significant_files.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 14274000 14278000
+chr1 14296000 14298000
+chr1 14314000 14319000
+chr1 14480000 14488000
+chr1 14491000 14501000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,13 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 19089000 19091000
+chr1 19104000 19106000
+chr1 19109000 19114000
+chr1 19125000 19129000
+chr1 19133000 19138000
+chr1 19197000 19202000
+chr1 19227000 19233000
+chr1 19254000 19261000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.2-dev
+# chicSignificantInteractions/output_4_target/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+# Mode: x-fold background with 1.5
+# Used p-value: 0.2
+#
+chr1 4499000 4502000
+chr1 4509000 4515000
+chr1 4561000 4567000
+chr1 4585000 4590000
+chr1 4652000 4658000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_4_target_list.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 673.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 14274000 14279000 Eya1 673.0 -26000 0.01040118870499999980 0.00284160000885891328 9.15400589712000112286 7.00000000000000000000
+chr1 14285000 14303000 Eya1 673.0 -1000 0.50282317979099999672 0.00136523720299208673 11.07298757284899970443 338.40000000000003410605
+chr1 14304000 14308000 Eya1 673.0 4000 0.05438335809800000364 0.04630738638109899163 4.54925916911999994596 36.60000000000000142109
+chr1 14310000 14322000 Eya1 673.0 11000 0.08142644873500000380 0.00000295000019367997 16.90046348151199850918 54.79999999999999715783
+chr1 14361000 14395000 Eya1 673.0 61000 0.01872213967299999823 0.00000368259652272496 14.85031269307799917101 12.60000000000000142109
+chr1 14491000 14500000 Eya1 673.0 199000 0.02622585438099999874 0.00000000000000932587 49.39210160776001146132 17.64999999999999857891

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 472.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 19097000 19099000 Tfap2d 472.0 4000 0.04322033898299999788 0.18510915606880684603 3.09466471690400002359 20.39999999999999857891
+chr1 19103000 19106000 Tfap2d 472.0 11000 0.03305084745700000159 0.03717817323565530963 5.08894228542100002244 15.60000000000000142109
+chr1 19110000 19114000 Tfap2d 472.0 18000 0.03135593220400000047 0.00456343459440844423 7.84960476513000049437 14.79999999999999893419
+chr1 19126000 19129000 Tfap2d 472.0 33000 0.01271186440799999991 0.01781395819889997068 5.68520760692500015665 6.00000000000000000000
+chr1 19134000 19137000 Tfap2d 472.0 41000 0.01271186440799999991 0.00778984492262324579 6.25346808942800080899 6.00000000000000000000
+chr1 19162000 19198000 Tfap2d 472.0 69000 0.02966101695299999674 0.00000060908645727054 24.93693789855100106934 14.00000000000000532907

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# FL-E13-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 810.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 4483000 4496000 Sox17 810.0 0 0.64098765432000004427 0.00000017949046104970 15.90973968251499925941 519.20000000000004547474
+chr1 4497000 4503000 Sox17 810.0 12000 0.04592592592699999698 0.00009501601454375841 8.17222136878799965132 37.19999999999999573674
+chr1 4507000 4516000 Sox17 810.0 23000 0.04790123456699999643 0.00000000479943529363 15.54534421085400097695 38.80000000000000426326
+chr1 4533000 4543000 Sox17 810.0 46000 0.00839506173000000022 0.00536916279076038450 5.36115769549400056349 6.79999999999999893419
+chr1 4562000 4565000 Sox17 810.0 75000 0.00814814814800000030 0.00087160464483748701 6.21039574622800039094 6.59999999999999964473
+chr1 4567000 4585000 Sox17 810.0 81000 0.00814814814699999987 0.00084968562666110081 6.38963961746400066488 6.60000000000000053291

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# MB-E10-5_chr1.cool chr1_14300280_14300280 14.10 Mbp 14.50 Mbp Eya1 Sum of interactions in fixate range: 832.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 14295000 14303000 Eya1 832.0 -1000 0.51754807692400006669 0.00019954744684358428 10.99424166368200062038 430.60000000000002273737
+chr1 14304000 14307000 Eya1 832.0 4000 0.03052884615399999862 0.12043367620410594387 2.40926082355099957510 25.39999999999999857891
+chr1 14311000 14322000 Eya1 832.0 11000 0.05841346153899999727 0.00001294028787446333 12.63215080382700250539 48.59999999999999431566
+chr1 14369000 14382000 Eya1 832.0 69000 0.00793269231000000123 0.00220510219722336309 6.44339861264899926852 6.59999999999999875655
+chr1 14391000 14407000 Eya1 832.0 106000 0.01201923077000000006 0.00000515283260571486 11.00547257592000072179 10.00000000000000000000
+chr1 14426000 14432000 Eya1 832.0 130000 0.01081730769300000110 0.00000042985602966006 13.72351582211000042832 9.00000000000000000000
+chr1 14447000 14455000 Eya1 832.0 149000 0.01490384615199999950 0.00000000000012301271 22.36493893927400122834 12.39999999999999857891
+chr1 14460000 14465000 Eya1 832.0 162000 0.00913461538499999934 0.00001124312488187673 12.15366029908999934150 7.59999999999999964473
+chr1 14491000 14500000 Eya1 832.0 199000 0.01893028846099999857 0.00000000000000932587 35.26961282318300305860 15.75000000000000000000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# MB-E10-5_chr1.cool chr1_19093103_19093103 18.89 Mbp 19.29 Mbp Tfap2d Sum of interactions in fixate range: 800.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 19077000 19082000 Tfap2d 800.0 -15000 0.01675000000000000100 0.00195382844240210574 8.20856302019300088091 13.40000000000000035527
+chr1 19083000 19095000 Tfap2d 800.0 0 0.41274999999999995026 0.00011621308769860228 18.49630381537900092326 330.19999999999998863132
+chr1 19096000 19114000 Tfap2d 800.0 3000 0.17700000000000001843 0.00042447176642534945 22.86014655871399980924 141.59999999999999431566
+chr1 19125000 19129000 Tfap2d 800.0 33000 0.01099999999999999936 0.00379145119303403444 4.83882643603000062171 8.80000000000000071054
+chr1 19135000 19139000 Tfap2d 800.0 43000 0.01175000000000000003 0.00015657417058367873 6.23967021246500053167 9.40000000000000035527
+chr1 19141000 19170000 Tfap2d 800.0 49000 0.02125000000000001193 0.00000543603606051324 15.65207577841900032922 17.00000000000000355271
+chr1 19195000 19208000 Tfap2d 800.0 105000 0.04900000000000001577 0.00000000000000000000 47.90516101420298866742 39.20000000000000284217
+chr1 19209000 19238000 Tfap2d 800.0 124000 0.09275000000000004075 0.00000000000000000000 112.06129567939001390187 74.20000000000000284217

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,9 @@
+# MB-E10-5_chr1.cool chr1_4487435_4487435 4.29 Mbp 4.69 Mbp Sox17 Sum of interactions in fixate range: 978.0
+#Chromosome Start End Gene Sum of interactions Relative position Relative interactions p-value x-fold Raw target
+chr1 4472000 4492000 Sox17 978.0 0 0.66196319018500004994 0.00000000202165995056 17.41734930604599895787 647.40000000000009094947
+chr1 4493000 4496000 Sox17 978.0 6000 0.02576687116499999652 0.03614683764250059550 2.69049295166299984317 25.20000000000000284217
+chr1 4497000 4503000 Sox17 978.0 12000 0.03946830265799999848 0.00007297810251505332 7.02344214143100042946 38.60000000000000142109
+chr1 4520000 4531000 Sox17 978.0 37000 0.02269938650399999994 0.00000000003034350549 10.91808266157200080215 22.20000000000000284217
+chr1 4562000 4566000 Sox17 978.0 78000 0.00920245398800000058 0.00000732123325153378 7.15040494335099996448 9.00000000000000000000
+chr1 4569000 4593000 Sox17 978.0 93000 0.01022494887899999885 0.00001986913191398543 8.54218878677400006438 9.99999999999999822364
+chr1 4664000 4669000 Sox17 978.0 179000 0.00552147239400000052 0.00001416173948909361 8.93206575494200016863 5.40000000000000035527

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_significant_files.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,13 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 14274000 14279000
+chr1 14285000 14308000
+chr1 14310000 14322000
+chr1 14361000 14407000
+chr1 14426000 14432000
+chr1 14447000 14455000
+chr1 14460000 14465000
+chr1 14491000 14500000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,9 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 19077000 19114000
+chr1 19125000 19129000
+chr1 19134000 19139000
+chr1 19141000 19238000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,11 @@
+# Significant interactions result file of HiCExplorer's chicSignificantInteractions version 3.3
+# targetFolder/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+# Mode: loose p-value with 0.5
+# Used p-value: 0.2
+#
+chr1 4472000 4503000
+chr1 4507000 4516000
+chr1 4520000 4531000
+chr1 4533000 4543000
+chr1 4562000 4593000
+chr1 4664000 4669000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicSignificantInteractions/output_5_target_list.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,3 @@
+FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed
+FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed
+FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/fileNames_one_matrix.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,3 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/fileNames_two_matrices.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,6 @@
+FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
+MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
+FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
+MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
+FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
+MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.2-dev\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t43"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 673.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t673.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t14101000\t14102000\tEya1\t673.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t14102000\t14103000\tEya1\t673.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t14103000\t14104000\tEya1\t673.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t14104000\t14105000\tEya1\t673.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t14105000\t14106000\tEya1\t673.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t673.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t673.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t673.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t673.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t673.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t673.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t673.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t673.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t673.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t673.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t673.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t673.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t673.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t673.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t673.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t673.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t673.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t673.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t673.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t673.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t673.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t673.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t673.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t673.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t673.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t673.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t673.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t673.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t673.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t673.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'44260\t0.800000000000\n+chr1\t14462000\t14463000\tEya1\t673.0\t162000\t0.001188707281\t0.591476571829\t1.616154290340\t0.800000000000\n+chr1\t14463000\t14464000\tEya1\t673.0\t163000\t0.000594353640\t0.593731273297\t0.821489212945\t0.400000000000\n+chr1\t14464000\t14465000\tEya1\t673.0\t164000\t0.000594353640\t0.604924746422\t0.857051516792\t0.400000000000\n+chr1\t14465000\t14466000\tEya1\t673.0\t165000\t0.000000000000\t0.620870359018\t0.000000000000\t0.000000000000\n+chr1\t14466000\t14467000\tEya1\t673.0\t166000\t0.000000000000\t0.653063136379\t0.000000000000\t0.000000000000\n+chr1\t14467000\t14468000\tEya1\t673.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t673.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t673.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t673.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t673.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t14472000\t14473000\tEya1\t673.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t14473000\t14474000\tEya1\t673.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t14474000\t14475000\tEya1\t673.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t14475000\t14476000\tEya1\t673.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t14476000\t14477000\tEya1\t673.0\t176000\t0.000297176820\t0.580281241496\t0.421231702882\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t673.0\t177000\t0.000297176820\t0.600664600573\t0.449952046478\t0.200000000000\n+chr1\t14478000\t14479000\tEya1\t673.0\t178000\t0.000594353640\t0.611923543314\t0.933862738240\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t673.0\t179000\t0.000594353640\t0.616982108456\t0.951821637197\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t673.0\t180000\t0.001485884101\t0.367009687936\t2.512422592521\t1.000000000000\n+chr1\t14481000\t14482000\tEya1\t673.0\t181000\t0.001188707281\t0.637219432588\t2.020192860178\t0.800000000000\n+chr1\t14482000\t14483000\tEya1\t673.0\t182000\t0.001188707281\t0.649572741436\t2.128805380321\t0.800000000000\n+chr1\t14483000\t14484000\tEya1\t673.0\t183000\t0.001783060921\t0.359231506903\t3.093420317586\t1.200000000000\n+chr1\t14484000\t14485000\tEya1\t673.0\t184000\t0.002080237741\t0.375416393977\t3.380127570538\t1.400000000000\n+chr1\t14485000\t14486000\tEya1\t673.0\t185000\t0.001188707281\t0.617559413959\t1.903643274393\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t673.0\t186000\t0.001188707281\t0.647906480781\t2.106158514412\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t673.0\t187000\t0.001188707281\t0.651241359569\t2.140312436513\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t673.0\t188000\t0.000594353640\t0.647869186187\t1.058710697124\t0.400000000000\n+chr1\t14489000\t14490000\tEya1\t673.0\t189000\t0.000297176820\t0.671654971880\t0.575520059550\t0.200000000000\n+chr1\t14490000\t14491000\tEya1\t673.0\t190000\t0.000297176820\t0.671941112135\t0.578885673960\t0.200000000000\n+chr1\t14491000\t14492000\tEya1\t673.0\t191000\t0.002080237741\t0.341250160004\t3.849589730333\t1.400000000000\n+chr1\t14492000\t14493000\tEya1\t673.0\t192000\t0.003268945022\t0.068166431915\t5.982878858272\t2.200000000000\n+chr1\t14493000\t14494000\tEya1\t673.0\t193000\t0.002971768202\t0.059322876246\t5.892229182196\t2.000000000000\n+chr1\t14494000\t14495000\tEya1\t673.0\t194000\t0.003268945022\t0.062511655285\t6.294126893758\t2.200000000000\n+chr1\t14495000\t14496000\tEya1\t673.0\t195000\t0.003268945022\t0.056441264815\t6.680269651133\t2.200000000000\n+chr1\t14496000\t14497000\tEya1\t673.0\t196000\t0.002971768202\t0.056496760292\t6.072972410121\t2.000000000000\n+chr1\t14497000\t14498000\tEya1\t673.0\t197000\t0.002080237741\t0.335210836347\t3.937080406684\t1.400000000000\n+chr1\t14498000\t14499000\tEya1\t673.0\t198000\t0.002971768202\t0.083110512066\t4.852424033528\t2.000000000000\n+chr1\t14499000\t14500000\tEya1\t673.0\t199000\t0.003343239227\t0.073447408129\t5.830530441735\t2.250000000000\n+chr1\t14500000\t14501000\tEya1\t673.0\t200000\t0.004457652303\t1.000000000000\t7.575723225668\t3.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 472.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t472.0\t-200000\t0.001412429379\t0.880044890460\t8.554173074049\t0.666666666667\n+chr1\t18894000\t18895000\tTfap2d\t472.0\t-199000\t0.001059322034\t0.852151439574\t5.040852007510\t0.500000000000\n+chr1\t18895000\t18896000\tTfap2d\t472.0\t-198000\t0.000847457627\t0.820756603944\t3.282415254892\t0.400000000000\n+chr1\t18896000\t18897000\tTfap2d\t472.0\t-197000\t0.000847457627\t0.814190727178\t3.136530131373\t0.400000000000\n+chr1\t18897000\t18898000\tTfap2d\t472.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t472.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t472.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t472.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t472.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t472.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t472.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t472.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t472.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t472.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t472.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t472.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t472.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t472.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t472.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t472.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t472.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t472.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t472.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t472.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t472.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t472.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t472.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t472.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t472.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t472.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t472.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t472.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t472.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t472.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t472.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'4\t0.591476571829\t2.304389486014\t0.800000000000\n+chr1\t19256000\t19257000\tTfap2d\t472.0\t163000\t0.002542372881\t0.406268726703\t3.513954917238\t1.200000000000\n+chr1\t19257000\t19258000\tTfap2d\t472.0\t164000\t0.002118644068\t0.395075253578\t3.055061815685\t1.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t472.0\t165000\t0.002118644068\t0.379129640982\t3.252162579500\t1.000000000000\n+chr1\t19259000\t19260000\tTfap2d\t472.0\t166000\t0.001694915254\t0.653063136379\t2.822877120847\t0.800000000000\n+chr1\t19260000\t19261000\tTfap2d\t472.0\t167000\t0.001694915254\t0.616215444951\t2.701317818024\t0.800000000000\n+chr1\t19261000\t19262000\tTfap2d\t472.0\t168000\t0.000847457627\t0.616137376589\t1.312966101957\t0.400000000000\n+chr1\t19262000\t19263000\tTfap2d\t472.0\t169000\t0.000423728814\t0.600847921629\t0.593041411154\t0.200000000000\n+chr1\t19263000\t19264000\tTfap2d\t472.0\t170000\t0.000423728814\t0.585658029501\t0.573755512251\t0.200000000000\n+chr1\t19264000\t19265000\tTfap2d\t472.0\t171000\t0.000000000000\t0.601961893812\t0.000000000000\t0.000000000000\n+chr1\t19265000\t19266000\tTfap2d\t472.0\t172000\t0.000000000000\t0.591031149544\t0.000000000000\t0.000000000000\n+chr1\t19266000\t19267000\tTfap2d\t472.0\t173000\t0.000000000000\t0.574110012150\t0.000000000000\t0.000000000000\n+chr1\t19267000\t19268000\tTfap2d\t472.0\t174000\t0.000000000000\t0.594064541193\t0.000000000000\t0.000000000000\n+chr1\t19268000\t19269000\tTfap2d\t472.0\t175000\t0.000423728814\t0.586742846341\t0.608378689139\t0.200000000000\n+chr1\t19269000\t19270000\tTfap2d\t472.0\t176000\t0.000423728814\t0.580281241496\t0.600612152627\t0.200000000000\n+chr1\t19270000\t19271000\tTfap2d\t472.0\t177000\t0.000423728814\t0.600664600573\t0.641562981525\t0.200000000000\n+chr1\t19271000\t19272000\tTfap2d\t472.0\t178000\t0.000423728814\t0.611923543314\t0.665772905546\t0.200000000000\n+chr1\t19272000\t19273000\tTfap2d\t472.0\t179000\t0.000423728814\t0.616982108456\t0.678576230756\t0.200000000000\n+chr1\t19273000\t19274000\tTfap2d\t472.0\t180000\t0.000000000000\t0.632990312064\t0.000000000000\t0.000000000000\n+chr1\t19274000\t19275000\tTfap2d\t472.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t472.0\t182000\t0.000423728814\t0.649572741436\t0.758837934828\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t472.0\t183000\t0.000423728814\t0.640768493097\t0.735124249200\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t472.0\t184000\t0.000423728814\t0.624583606023\t0.688506614701\t0.200000000000\n+chr1\t19278000\t19279000\tTfap2d\t472.0\t185000\t0.000423728814\t0.617559413959\t0.678576230756\t0.200000000000\n+chr1\t19279000\t19280000\tTfap2d\t472.0\t186000\t0.000423728814\t0.647906480781\t0.750765190784\t0.200000000000\n+chr1\t19280000\t19281000\tTfap2d\t472.0\t187000\t0.000000000000\t0.651241359569\t0.000000000000\t0.000000000000\n+chr1\t19281000\t19282000\tTfap2d\t472.0\t188000\t0.000000000000\t0.647869186187\t0.000000000000\t0.000000000000\n+chr1\t19282000\t19283000\tTfap2d\t472.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t472.0\t190000\t0.000000000000\t0.671941112135\t0.000000000000\t0.000000000000\n+chr1\t19284000\t19285000\tTfap2d\t472.0\t191000\t0.000000000000\t0.658749839996\t0.000000000000\t0.000000000000\n+chr1\t19285000\t19286000\tTfap2d\t472.0\t192000\t0.000000000000\t0.655383997647\t0.000000000000\t0.000000000000\n+chr1\t19286000\t19287000\tTfap2d\t472.0\t193000\t0.000000000000\t0.676994533785\t0.000000000000\t0.000000000000\n+chr1\t19287000\t19288000\tTfap2d\t472.0\t194000\t0.000000000000\t0.669325066593\t0.000000000000\t0.000000000000\n+chr1\t19288000\t19289000\tTfap2d\t472.0\t195000\t0.000000000000\t0.685162890895\t0.000000000000\t0.000000000000\n+chr1\t19289000\t19290000\tTfap2d\t472.0\t196000\t0.000000000000\t0.685254654751\t0.000000000000\t0.000000000000\n+chr1\t19290000\t19291000\tTfap2d\t472.0\t197000\t0.000000000000\t0.664789163653\t0.000000000000\t0.000000000000\n+chr1\t19291000\t19292000\tTfap2d\t472.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t472.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t472.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# FL-E13-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 810.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t810.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t810.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t810.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t810.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t810.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t810.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t810.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t810.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t810.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t810.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t810.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t810.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t810.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t810.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t810.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t810.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t810.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t810.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t810.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t810.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t810.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t810.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t810.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t810.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t810.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t810.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t810.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t810.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t810.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t810.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t810.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t810.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t810.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t810.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t810.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t810.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000493827160\t0.533506885425\t0.593839639683\t0.400000000000\n+chr1\t4649000\t4650000\tSox17\t810.0\t162000\t0.000493827160\t0.591476571829\t0.671402368765\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t810.0\t163000\t0.000493827160\t0.593731273297\t0.682545975694\t0.400000000000\n+chr1\t4651000\t4652000\tSox17\t810.0\t164000\t0.000493827160\t0.604924746422\t0.712093420742\t0.400000000000\n+chr1\t4652000\t4653000\tSox17\t810.0\t165000\t0.000987654321\t0.620870359018\t1.516069864221\t0.800000000000\n+chr1\t4653000\t4654000\tSox17\t810.0\t166000\t0.000987654321\t0.653063136379\t1.644935803753\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t810.0\t167000\t0.000987654321\t0.616215444951\t1.574101247046\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t810.0\t168000\t0.001481481481\t0.383862623411\t2.295259259717\t1.200000000000\n+chr1\t4656000\t4657000\tSox17\t810.0\t169000\t0.001728395062\t0.399152078371\t2.419023237597\t1.400000000000\n+chr1\t4657000\t4658000\tSox17\t810.0\t170000\t0.001234567901\t0.414341970499\t1.671682727052\t1.000000000000\n+chr1\t4658000\t4659000\tSox17\t810.0\t171000\t0.000987654321\t0.601961893812\t1.353856628464\t0.800000000000\n+chr1\t4659000\t4660000\tSox17\t810.0\t172000\t0.000987654321\t0.591031149544\t1.270220697103\t0.800000000000\n+chr1\t4660000\t4661000\tSox17\t810.0\t173000\t0.000493827160\t0.574110012150\t0.647612520865\t0.400000000000\n+chr1\t4661000\t4662000\tSox17\t810.0\t174000\t0.000246913580\t0.594064541193\t0.342694958640\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t810.0\t175000\t0.000246913580\t0.586742846341\t0.354512026264\t0.200000000000\n+chr1\t4663000\t4664000\tSox17\t810.0\t176000\t0.000246913580\t0.580281241496\t0.349986340790\t0.200000000000\n+chr1\t4664000\t4665000\tSox17\t810.0\t177000\t0.000246913580\t0.600664600573\t0.373849046024\t0.200000000000\n+chr1\t4665000\t4666000\tSox17\t810.0\t178000\t0.000493827160\t0.611923543314\t0.775913114612\t0.400000000000\n+chr1\t4666000\t4667000\tSox17\t810.0\t179000\t0.000246913580\t0.616982108456\t0.395417260391\t0.200000000000\n+chr1\t4667000\t4668000\tSox17\t810.0\t180000\t0.000246913580\t0.632990312064\t0.417496396239\t0.200000000000\n+chr1\t4668000\t4669000\tSox17\t810.0\t181000\t0.000246913580\t0.637219432588\t0.419626479907\t0.200000000000\n+chr1\t4669000\t4670000\tSox17\t810.0\t182000\t0.000246913580\t0.649572741436\t0.442187043505\t0.200000000000\n+chr1\t4670000\t4671000\tSox17\t810.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t4671000\t4672000\tSox17\t810.0\t184000\t0.000246913580\t0.624583606023\t0.401203854492\t0.200000000000\n+chr1\t4672000\t4673000\tSox17\t810.0\t185000\t0.000246913580\t0.617559413959\t0.395417260391\t0.200000000000\n+chr1\t4673000\t4674000\tSox17\t810.0\t186000\t0.000246913580\t0.647906480781\t0.437482925987\t0.200000000000\n+chr1\t4674000\t4675000\tSox17\t810.0\t187000\t0.000246913580\t0.651241359569\t0.444577243757\t0.200000000000\n+chr1\t4675000\t4676000\tSox17\t810.0\t188000\t0.000493827160\t0.647869186187\t0.879644813784\t0.400000000000\n+chr1\t4676000\t4677000\tSox17\t810.0\t189000\t0.000246913580\t0.671654971880\t0.478179012441\t0.200000000000\n+chr1\t4677000\t4678000\tSox17\t810.0\t190000\t0.000246913580\t0.671941112135\t0.480975380957\t0.200000000000\n+chr1\t4678000\t4679000\tSox17\t810.0\t191000\t0.000740740741\t0.658749839996\t1.370779835192\t0.600000000000\n+chr1\t4679000\t4680000\tSox17\t810.0\t192000\t0.000740740741\t0.655383997647\t1.355716320410\t0.600000000000\n+chr1\t4680000\t4681000\tSox17\t810.0\t193000\t0.000740740741\t0.676994533785\t1.468692681340\t0.600000000000\n+chr1\t4681000\t4682000\tSox17\t810.0\t194000\t0.000740740741\t0.669325066593\t1.426244915656\t0.600000000000\n+chr1\t4682000\t4683000\tSox17\t810.0\t195000\t0.000740740741\t0.685162890895\t1.513744604449\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t810.0\t196000\t0.000493827160\t0.685254654751\t1.009163069632\t0.400000000000\n+chr1\t4684000\t4685000\tSox17\t810.0\t197000\t0.000493827160\t0.664789163653\t0.934622615061\t0.400000000000\n+chr1\t4685000\t4686000\tSox17\t810.0\t198000\t0.000246913580\t0.623323575813\t0.403170540070\t0.200000000000\n+chr1\t4686000\t4687000\tSox17\t810.0\t199000\t0.000308641975\t0.643728679260\t0.538264332961\t0.250000000000\n+chr1\t4687000\t4688000\tSox17\t810.0\t200000\t0.000411522634\t0.637624930855\t0.699377466512\t0.333333333333\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_14300280_14300280\t14.10 Mbp\t14.50 Mbp\tEya1\tSum of interactions in fixate range: 832.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t14100000\t14101000\tEya1\t832.0\t-200000\t0.000400641026\t0.880044890460\t2.426424093120\t0.333333333333\n+chr1\t14101000\t14102000\tEya1\t832.0\t-199000\t0.000300480769\t0.852151439574\t1.429857059822\t0.250000000000\n+chr1\t14102000\t14103000\tEya1\t832.0\t-198000\t0.000240384615\t0.820756603944\t0.931069711724\t0.200000000000\n+chr1\t14103000\t14104000\tEya1\t832.0\t-197000\t0.000240384615\t0.814190727178\t0.889688835341\t0.200000000000\n+chr1\t14104000\t14105000\tEya1\t832.0\t-196000\t0.000240384615\t0.827190062074\t0.976487746811\t0.200000000000\n+chr1\t14105000\t14106000\tEya1\t832.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t14106000\t14107000\tEya1\t832.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t14107000\t14108000\tEya1\t832.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t14108000\t14109000\tEya1\t832.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t14109000\t14110000\tEya1\t832.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t14110000\t14111000\tEya1\t832.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t14111000\t14112000\tEya1\t832.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t14112000\t14113000\tEya1\t832.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t14113000\t14114000\tEya1\t832.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t14114000\t14115000\tEya1\t832.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t14115000\t14116000\tEya1\t832.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t14116000\t14117000\tEya1\t832.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t14117000\t14118000\tEya1\t832.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t14118000\t14119000\tEya1\t832.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t14119000\t14120000\tEya1\t832.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t14120000\t14121000\tEya1\t832.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t14121000\t14122000\tEya1\t832.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t14122000\t14123000\tEya1\t832.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t14123000\t14124000\tEya1\t832.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t14124000\t14125000\tEya1\t832.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t14125000\t14126000\tEya1\t832.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t14126000\t14127000\tEya1\t832.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t14127000\t14128000\tEya1\t832.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t14128000\t14129000\tEya1\t832.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t14129000\t14130000\tEya1\t832.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t14130000\t14131000\tEya1\t832.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t14131000\t14132000\tEya1\t832.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t14132000\t14133000\tEya1\t832.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t14133000\t14134000\tEya1\t832.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t14134000\t14135000\tEya1\t832.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t14135000\t14136000\tEya1\t832.0\t-165000\t0.000000000000\t0.847952610367\t0.0"..b'96844\t1.600000000000\n+chr1\t14462000\t14463000\tEya1\t832.0\t162000\t0.002163461538\t0.408523428171\t2.941420233350\t1.800000000000\n+chr1\t14463000\t14464000\tEya1\t832.0\t163000\t0.001682692308\t0.406268726703\t2.325742597467\t1.400000000000\n+chr1\t14464000\t14465000\tEya1\t832.0\t164000\t0.001682692308\t0.395075253578\t2.426424095919\t1.400000000000\n+chr1\t14465000\t14466000\tEya1\t832.0\t165000\t0.000721153846\t0.620870359018\t1.106986108791\t0.600000000000\n+chr1\t14466000\t14467000\tEya1\t832.0\t166000\t0.000240384615\t0.653063136379\t0.400359976274\t0.200000000000\n+chr1\t14467000\t14468000\tEya1\t832.0\t167000\t0.000000000000\t0.616215444951\t0.000000000000\t0.000000000000\n+chr1\t14468000\t14469000\tEya1\t832.0\t168000\t0.000000000000\t0.616137376589\t0.000000000000\t0.000000000000\n+chr1\t14469000\t14470000\tEya1\t832.0\t169000\t0.000000000000\t0.600847921629\t0.000000000000\t0.000000000000\n+chr1\t14470000\t14471000\tEya1\t832.0\t170000\t0.000000000000\t0.585658029501\t0.000000000000\t0.000000000000\n+chr1\t14471000\t14472000\tEya1\t832.0\t171000\t0.000480769231\t0.601961893812\t0.659028767461\t0.400000000000\n+chr1\t14472000\t14473000\tEya1\t832.0\t172000\t0.000480769231\t0.591031149544\t0.618316565296\t0.400000000000\n+chr1\t14473000\t14474000\tEya1\t832.0\t173000\t0.000480769231\t0.574110012150\t0.630488151323\t0.400000000000\n+chr1\t14474000\t14475000\tEya1\t832.0\t174000\t0.000480769231\t0.594064541193\t0.667266626197\t0.400000000000\n+chr1\t14475000\t14476000\tEya1\t832.0\t175000\t0.000480769231\t0.586742846341\t0.690275820369\t0.400000000000\n+chr1\t14476000\t14477000\tEya1\t832.0\t176000\t0.000240384615\t0.580281241496\t0.340731894279\t0.200000000000\n+chr1\t14477000\t14478000\tEya1\t832.0\t177000\t0.000480769231\t0.600664600573\t0.727927229038\t0.400000000000\n+chr1\t14478000\t14479000\tEya1\t832.0\t178000\t0.000480769231\t0.611923543314\t0.755396181293\t0.400000000000\n+chr1\t14479000\t14480000\tEya1\t832.0\t179000\t0.000480769231\t0.616982108456\t0.769923031050\t0.400000000000\n+chr1\t14480000\t14481000\tEya1\t832.0\t180000\t0.000480769231\t0.632990312064\t0.812913656138\t0.400000000000\n+chr1\t14481000\t14482000\tEya1\t832.0\t181000\t0.000240384615\t0.637219432588\t0.408530587410\t0.200000000000\n+chr1\t14482000\t14483000\tEya1\t832.0\t182000\t0.000000000000\t0.649572741436\t0.000000000000\t0.000000000000\n+chr1\t14483000\t14484000\tEya1\t832.0\t183000\t0.000000000000\t0.640768493097\t0.000000000000\t0.000000000000\n+chr1\t14484000\t14485000\tEya1\t832.0\t184000\t0.000240384615\t0.624583606023\t0.390595098725\t0.200000000000\n+chr1\t14485000\t14486000\tEya1\t832.0\t185000\t0.000961538462\t0.617559413959\t1.539846062099\t0.800000000000\n+chr1\t14486000\t14487000\tEya1\t832.0\t186000\t0.000961538462\t0.647906480781\t1.703659471393\t0.800000000000\n+chr1\t14487000\t14488000\tEya1\t832.0\t187000\t0.000961538462\t0.651241359569\t1.731286381939\t0.800000000000\n+chr1\t14488000\t14489000\tEya1\t832.0\t188000\t0.001201923077\t0.352130813813\t2.140962437394\t1.000000000000\n+chr1\t14489000\t14490000\tEya1\t832.0\t189000\t0.001442307692\t0.328345028120\t2.793209135173\t1.200000000000\n+chr1\t14490000\t14491000\tEya1\t832.0\t190000\t0.000721153846\t0.671941112135\t1.404771845823\t0.600000000000\n+chr1\t14491000\t14492000\tEya1\t832.0\t191000\t0.001442307692\t0.341250160004\t2.669066506024\t1.200000000000\n+chr1\t14492000\t14493000\tEya1\t832.0\t192000\t0.002403846154\t0.068166431915\t4.399560174407\t2.000000000000\n+chr1\t14493000\t14494000\tEya1\t832.0\t193000\t0.002163461538\t0.323005466215\t4.289571172663\t1.800000000000\n+chr1\t14494000\t14495000\tEya1\t832.0\t194000\t0.001682692308\t0.330674933407\t3.239907320421\t1.400000000000\n+chr1\t14495000\t14496000\tEya1\t832.0\t195000\t0.002163461538\t0.314837109105\t4.421153111551\t1.800000000000\n+chr1\t14496000\t14497000\tEya1\t832.0\t196000\t0.001682692308\t0.314745345249\t3.438674642317\t1.400000000000\n+chr1\t14497000\t14498000\tEya1\t832.0\t197000\t0.001442307692\t0.335210836347\t2.729727108893\t1.200000000000\n+chr1\t14498000\t14499000\tEya1\t832.0\t198000\t0.002644230769\t0.083110512066\t4.317607586564\t2.200000000000\n+chr1\t14499000\t14500000\tEya1\t832.0\t199000\t0.003305288462\t0.073447408129\t5.764345200343\t2.750000000000\n+chr1\t14500000\t14501000\tEya1\t832.0\t200000\t0.003605769231\t1.000000000000\t6.127958811148\t3.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_19093103_19093103\t18.89 Mbp\t19.29 Mbp\tTfap2d\tSum of interactions in fixate range: 800.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t18893000\t18894000\tTfap2d\t800.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t18894000\t18895000\tTfap2d\t800.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t18895000\t18896000\tTfap2d\t800.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t18896000\t18897000\tTfap2d\t800.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t18897000\t18898000\tTfap2d\t800.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t18898000\t18899000\tTfap2d\t800.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t18899000\t18900000\tTfap2d\t800.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t18900000\t18901000\tTfap2d\t800.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t18901000\t18902000\tTfap2d\t800.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t18902000\t18903000\tTfap2d\t800.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t18903000\t18904000\tTfap2d\t800.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t18904000\t18905000\tTfap2d\t800.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t18905000\t18906000\tTfap2d\t800.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t18906000\t18907000\tTfap2d\t800.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t18907000\t18908000\tTfap2d\t800.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t18908000\t18909000\tTfap2d\t800.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t18909000\t18910000\tTfap2d\t800.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t18910000\t18911000\tTfap2d\t800.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t18911000\t18912000\tTfap2d\t800.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t18912000\t18913000\tTfap2d\t800.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t18913000\t18914000\tTfap2d\t800.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t18914000\t18915000\tTfap2d\t800.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t18915000\t18916000\tTfap2d\t800.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t18916000\t18917000\tTfap2d\t800.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t18917000\t18918000\tTfap2d\t800.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t18918000\t18919000\tTfap2d\t800.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t18919000\t18920000\tTfap2d\t800.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t18920000\t18921000\tTfap2d\t800.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t18921000\t18922000\tTfap2d\t800.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t18922000\t18923000\tTfap2d\t800.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t18923000\t18924000\tTfap2d\t800.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t18924000\t18925000\tTfap2d\t800.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t18925000\t18926000\tTfap2d\t800.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t18926000\t18927000\tTfap2d\t800.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t18927000\t18928000\tTfap2d\t800.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr"..b'0\t0.591476571829\t0.000000000000\t0.000000000000\n+chr1\t19256000\t19257000\tTfap2d\t800.0\t163000\t0.000000000000\t0.593731273297\t0.000000000000\t0.000000000000\n+chr1\t19257000\t19258000\tTfap2d\t800.0\t164000\t0.000000000000\t0.604924746422\t0.000000000000\t0.000000000000\n+chr1\t19258000\t19259000\tTfap2d\t800.0\t165000\t0.000250000000\t0.620870359018\t0.383755184381\t0.200000000000\n+chr1\t19259000\t19260000\tTfap2d\t800.0\t166000\t0.000500000000\t0.653063136379\t0.832748750650\t0.400000000000\n+chr1\t19260000\t19261000\tTfap2d\t800.0\t167000\t0.000750000000\t0.616215444951\t1.195333134476\t0.600000000000\n+chr1\t19261000\t19262000\tTfap2d\t800.0\t168000\t0.000750000000\t0.616137376589\t1.161975000232\t0.600000000000\n+chr1\t19262000\t19263000\tTfap2d\t800.0\t169000\t0.001000000000\t0.600847921629\t1.399577730324\t0.800000000000\n+chr1\t19263000\t19264000\tTfap2d\t800.0\t170000\t0.000750000000\t0.585658029501\t1.015547256684\t0.600000000000\n+chr1\t19264000\t19265000\tTfap2d\t800.0\t171000\t0.000750000000\t0.601961893812\t1.028084877240\t0.600000000000\n+chr1\t19265000\t19266000\tTfap2d\t800.0\t172000\t0.000500000000\t0.591031149544\t0.643049227908\t0.400000000000\n+chr1\t19266000\t19267000\tTfap2d\t800.0\t173000\t0.000750000000\t0.574110012150\t0.983561516064\t0.600000000000\n+chr1\t19267000\t19268000\tTfap2d\t800.0\t174000\t0.000500000000\t0.594064541193\t0.693957291245\t0.400000000000\n+chr1\t19268000\t19269000\tTfap2d\t800.0\t175000\t0.000750000000\t0.586742846341\t1.076830279776\t0.600000000000\n+chr1\t19269000\t19270000\tTfap2d\t800.0\t176000\t0.000750000000\t0.580281241496\t1.063083510150\t0.600000000000\n+chr1\t19270000\t19271000\tTfap2d\t800.0\t177000\t0.000750000000\t0.600664600573\t1.135566477299\t0.600000000000\n+chr1\t19271000\t19272000\tTfap2d\t800.0\t178000\t0.000500000000\t0.611923543314\t0.785612028545\t0.400000000000\n+chr1\t19272000\t19273000\tTfap2d\t800.0\t179000\t0.000500000000\t0.616982108456\t0.800719952292\t0.400000000000\n+chr1\t19273000\t19274000\tTfap2d\t800.0\t180000\t0.000250000000\t0.632990312064\t0.422715101192\t0.200000000000\n+chr1\t19274000\t19275000\tTfap2d\t800.0\t181000\t0.000000000000\t0.637219432588\t0.000000000000\t0.000000000000\n+chr1\t19275000\t19276000\tTfap2d\t800.0\t182000\t0.000250000000\t0.649572741436\t0.447714381549\t0.200000000000\n+chr1\t19276000\t19277000\tTfap2d\t800.0\t183000\t0.000250000000\t0.640768493097\t0.433723307028\t0.200000000000\n+chr1\t19277000\t19278000\tTfap2d\t800.0\t184000\t0.000750000000\t0.624583606023\t1.218656708021\t0.600000000000\n+chr1\t19278000\t19279000\tTfap2d\t800.0\t185000\t0.000750000000\t0.617559413959\t1.201079928437\t0.600000000000\n+chr1\t19279000\t19280000\tTfap2d\t800.0\t186000\t0.000750000000\t0.647906480781\t1.328854387687\t0.600000000000\n+chr1\t19280000\t19281000\tTfap2d\t800.0\t187000\t0.000500000000\t0.651241359569\t0.900268918608\t0.400000000000\n+chr1\t19281000\t19282000\tTfap2d\t800.0\t188000\t0.000500000000\t0.647869186187\t0.890640373956\t0.400000000000\n+chr1\t19282000\t19283000\tTfap2d\t800.0\t189000\t0.000000000000\t0.671654971880\t0.000000000000\t0.000000000000\n+chr1\t19283000\t19284000\tTfap2d\t800.0\t190000\t0.000250000000\t0.671941112135\t0.486987573219\t0.200000000000\n+chr1\t19284000\t19285000\tTfap2d\t800.0\t191000\t0.000250000000\t0.658749839996\t0.462638194377\t0.200000000000\n+chr1\t19285000\t19286000\tTfap2d\t800.0\t192000\t0.000250000000\t0.655383997647\t0.457554258138\t0.200000000000\n+chr1\t19286000\t19287000\tTfap2d\t800.0\t193000\t0.000500000000\t0.676994533785\t0.991367559904\t0.400000000000\n+chr1\t19287000\t19288000\tTfap2d\t800.0\t194000\t0.000500000000\t0.669325066593\t0.962715318068\t0.400000000000\n+chr1\t19288000\t19289000\tTfap2d\t800.0\t195000\t0.000250000000\t0.685162890895\t0.510888804001\t0.200000000000\n+chr1\t19289000\t19290000\tTfap2d\t800.0\t196000\t0.000250000000\t0.685254654751\t0.510888804001\t0.200000000000\n+chr1\t19290000\t19291000\tTfap2d\t800.0\t197000\t0.000250000000\t0.664789163653\t0.473152698875\t0.200000000000\n+chr1\t19291000\t19292000\tTfap2d\t800.0\t198000\t0.000000000000\t0.623323575813\t0.000000000000\t0.000000000000\n+chr1\t19292000\t19293000\tTfap2d\t800.0\t199000\t0.000000000000\t0.643728679260\t0.000000000000\t0.000000000000\n+chr1\t19293000\t19294000\tTfap2d\t800.0\t200000\t0.000000000000\t0.637624930855\t0.000000000000\t0.000000000000\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed Mon Dec 16 15:48:31 2019 -0500

b"@@ -0,0 +1,405 @@\n+# Interaction file, created with HiCExplorer's chicViewpoint version 3.3\n+# MB-E10-5_chr1.cool\tchr1_4487435_4487435\t4.29 Mbp\t4.69 Mbp\tSox17\tSum of interactions in fixate range: 978.0\n+# Chromosome\tStart\tEnd\tGene\tSum of interactions\tRelative position\tRelative Interactions\tp-value\tx-fold\tRaw\n+#\n+chr1\t4287000\t4288000\tSox17\t978.0\t-200000\t0.000000000000\t0.880044890460\t0.000000000000\t0.000000000000\n+chr1\t4288000\t4289000\tSox17\t978.0\t-199000\t0.000000000000\t0.852151439574\t0.000000000000\t0.000000000000\n+chr1\t4289000\t4290000\tSox17\t978.0\t-198000\t0.000000000000\t0.820756603944\t0.000000000000\t0.000000000000\n+chr1\t4290000\t4291000\tSox17\t978.0\t-197000\t0.000000000000\t0.814190727178\t0.000000000000\t0.000000000000\n+chr1\t4291000\t4292000\tSox17\t978.0\t-196000\t0.000000000000\t0.827190062074\t0.000000000000\t0.000000000000\n+chr1\t4292000\t4293000\tSox17\t978.0\t-195000\t0.000000000000\t0.836281106114\t0.000000000000\t0.000000000000\n+chr1\t4293000\t4294000\tSox17\t978.0\t-194000\t0.000000000000\t0.849921252675\t0.000000000000\t0.000000000000\n+chr1\t4294000\t4295000\tSox17\t978.0\t-193000\t0.000000000000\t0.861786083744\t0.000000000000\t0.000000000000\n+chr1\t4295000\t4296000\tSox17\t978.0\t-192000\t0.000000000000\t0.859809384515\t0.000000000000\t0.000000000000\n+chr1\t4296000\t4297000\tSox17\t978.0\t-191000\t0.000000000000\t0.853754951451\t0.000000000000\t0.000000000000\n+chr1\t4297000\t4298000\tSox17\t978.0\t-190000\t0.000000000000\t0.873048946174\t0.000000000000\t0.000000000000\n+chr1\t4298000\t4299000\tSox17\t978.0\t-189000\t0.000000000000\t0.867850964512\t0.000000000000\t0.000000000000\n+chr1\t4299000\t4300000\tSox17\t978.0\t-188000\t0.000000000000\t0.860889061003\t0.000000000000\t0.000000000000\n+chr1\t4300000\t4301000\tSox17\t978.0\t-187000\t0.000000000000\t0.863889228734\t0.000000000000\t0.000000000000\n+chr1\t4301000\t4302000\tSox17\t978.0\t-186000\t0.000000000000\t0.853953368554\t0.000000000000\t0.000000000000\n+chr1\t4302000\t4303000\tSox17\t978.0\t-185000\t0.000000000000\t0.849507893763\t0.000000000000\t0.000000000000\n+chr1\t4303000\t4304000\tSox17\t978.0\t-184000\t0.000000000000\t0.846001342365\t0.000000000000\t0.000000000000\n+chr1\t4304000\t4305000\tSox17\t978.0\t-183000\t0.000000000000\t0.875951792135\t0.000000000000\t0.000000000000\n+chr1\t4305000\t4306000\tSox17\t978.0\t-182000\t0.000000000000\t0.882361637509\t0.000000000000\t0.000000000000\n+chr1\t4306000\t4307000\tSox17\t978.0\t-181000\t0.000000000000\t1.000000000000\t0.000000000000\t0.000000000000\n+chr1\t4307000\t4308000\tSox17\t978.0\t-180000\t0.000000000000\t0.859844304863\t0.000000000000\t0.000000000000\n+chr1\t4308000\t4309000\tSox17\t978.0\t-179000\t0.000000000000\t0.878506000461\t0.000000000000\t0.000000000000\n+chr1\t4309000\t4310000\tSox17\t978.0\t-178000\t0.000000000000\t0.873876939682\t0.000000000000\t0.000000000000\n+chr1\t4310000\t4311000\tSox17\t978.0\t-177000\t0.000000000000\t0.861822188997\t0.000000000000\t0.000000000000\n+chr1\t4311000\t4312000\tSox17\t978.0\t-176000\t0.000000000000\t0.863859548467\t0.000000000000\t0.000000000000\n+chr1\t4312000\t4313000\tSox17\t978.0\t-175000\t0.000000000000\t0.880027314411\t0.000000000000\t0.000000000000\n+chr1\t4313000\t4314000\tSox17\t978.0\t-174000\t0.000000000000\t0.879993062257\t0.000000000000\t0.000000000000\n+chr1\t4314000\t4315000\tSox17\t978.0\t-173000\t0.000000000000\t0.875972132345\t0.000000000000\t0.000000000000\n+chr1\t4315000\t4316000\tSox17\t978.0\t-172000\t0.000000000000\t0.869989217721\t0.000000000000\t0.000000000000\n+chr1\t4316000\t4317000\tSox17\t978.0\t-171000\t0.000000000000\t0.882140840596\t0.000000000000\t0.000000000000\n+chr1\t4317000\t4318000\tSox17\t978.0\t-170000\t0.000000000000\t0.859915954096\t0.000000000000\t0.000000000000\n+chr1\t4318000\t4319000\tSox17\t978.0\t-169000\t0.000000000000\t0.852922494459\t0.000000000000\t0.000000000000\n+chr1\t4319000\t4320000\tSox17\t978.0\t-168000\t0.000000000000\t0.858077240772\t0.000000000000\t0.000000000000\n+chr1\t4320000\t4321000\tSox17\t978.0\t-167000\t0.000000000000\t0.859961156614\t0.000000000000\t0.000000000000\n+chr1\t4321000\t4322000\tSox17\t978.0\t-166000\t0.000000000000\t0.839443928609\t0.000000000000\t0.000000000000\n+chr1\t4322000\t4323000\tSox17\t978.0\t-165000\t0.000000000000\t0.847952610367\t0.000000000000\t0.000000000000\n+chr1\t432300"..b'0.000613496933\t0.533506885425\t0.737745564637\t0.600000000000\n+chr1\t4649000\t4650000\tSox17\t978.0\t162000\t0.000408997955\t0.591476571829\t0.556069446523\t0.400000000000\n+chr1\t4650000\t4651000\tSox17\t978.0\t163000\t0.000204498978\t0.593731273297\t0.282649407113\t0.200000000000\n+chr1\t4651000\t4652000\tSox17\t978.0\t164000\t0.000204498978\t0.604924746422\t0.294885312271\t0.200000000000\n+chr1\t4652000\t4653000\tSox17\t978.0\t165000\t0.000204498978\t0.620870359018\t0.313910171273\t0.200000000000\n+chr1\t4653000\t4654000\tSox17\t978.0\t166000\t0.000817995910\t0.653063136379\t1.362370144213\t0.800000000000\n+chr1\t4654000\t4655000\tSox17\t978.0\t167000\t0.000817995910\t0.616215444951\t1.303703486817\t0.800000000000\n+chr1\t4655000\t4656000\tSox17\t978.0\t168000\t0.000817995910\t0.616137376589\t1.267321063648\t0.800000000000\n+chr1\t4656000\t4657000\tSox17\t978.0\t169000\t0.001226993865\t0.399152078371\t1.717273288741\t1.200000000000\n+chr1\t4657000\t4658000\tSox17\t978.0\t170000\t0.001226993865\t0.414341970499\t1.661427004800\t1.200000000000\n+chr1\t4658000\t4659000\tSox17\t978.0\t171000\t0.000613496933\t0.601961893812\t0.840969224736\t0.600000000000\n+chr1\t4659000\t4660000\tSox17\t978.0\t172000\t0.000613496933\t0.591031149544\t0.789017457556\t0.600000000000\n+chr1\t4660000\t4661000\tSox17\t978.0\t173000\t0.000613496933\t0.574110012150\t0.804549297394\t0.600000000000\n+chr1\t4661000\t4662000\tSox17\t978.0\t174000\t0.000204498978\t0.594064541193\t0.283827112984\t0.200000000000\n+chr1\t4662000\t4663000\tSox17\t978.0\t175000\t0.000000000000\t0.586742846341\t0.000000000000\t0.000000000000\n+chr1\t4663000\t4664000\tSox17\t978.0\t176000\t0.000408997955\t0.580281241496\t0.579731975542\t0.400000000000\n+chr1\t4664000\t4665000\tSox17\t978.0\t177000\t0.001022494888\t0.399335399427\t1.548147889979\t1.000000000000\n+chr1\t4665000\t4666000\tSox17\t978.0\t178000\t0.001022494888\t0.388076456686\t1.606568565531\t1.000000000000\n+chr1\t4666000\t4667000\tSox17\t978.0\t179000\t0.001226993865\t0.383017891544\t1.964956938139\t1.200000000000\n+chr1\t4667000\t4668000\tSox17\t978.0\t180000\t0.001226993865\t0.367009687936\t2.074675343272\t1.200000000000\n+chr1\t4668000\t4669000\tSox17\t978.0\t181000\t0.001022494888\t0.362780567412\t1.737717018021\t1.000000000000\n+chr1\t4669000\t4670000\tSox17\t978.0\t182000\t0.000408997955\t0.649572741436\t0.732457065928\t0.400000000000\n+chr1\t4670000\t4671000\tSox17\t978.0\t183000\t0.000613496933\t0.640768493097\t1.064351673689\t0.600000000000\n+chr1\t4671000\t4672000\tSox17\t978.0\t184000\t0.000817995910\t0.624583606023\t1.329141603840\t0.800000000000\n+chr1\t4672000\t4673000\tSox17\t978.0\t185000\t0.000817995910\t0.617559413959\t1.309971292093\t0.800000000000\n+chr1\t4673000\t4674000\tSox17\t978.0\t186000\t0.000817995910\t0.647906480781\t1.449329938854\t0.800000000000\n+chr1\t4674000\t4675000\tSox17\t978.0\t187000\t0.001226993865\t0.348758640431\t2.209248880021\t1.200000000000\n+chr1\t4675000\t4676000\tSox17\t978.0\t188000\t0.001022494888\t0.352130813813\t1.821350457987\t1.000000000000\n+chr1\t4676000\t4677000\tSox17\t978.0\t189000\t0.000817995910\t0.671654971880\t1.584151329559\t0.800000000000\n+chr1\t4677000\t4678000\tSox17\t978.0\t190000\t0.001022494888\t0.328058887865\t1.991769215618\t1.000000000000\n+chr1\t4678000\t4679000\tSox17\t978.0\t191000\t0.001226993865\t0.341250160004\t2.270616904920\t1.200000000000\n+chr1\t4679000\t4680000\tSox17\t978.0\t192000\t0.000817995910\t0.655383997647\t1.497110047078\t0.800000000000\n+chr1\t4680000\t4681000\tSox17\t978.0\t193000\t0.001022494888\t0.323005466215\t2.027336523322\t1.000000000000\n+chr1\t4681000\t4682000\tSox17\t978.0\t194000\t0.000817995910\t0.669325066593\t1.574994385387\t0.800000000000\n+chr1\t4682000\t4683000\tSox17\t978.0\t195000\t0.000613496933\t0.685162890895\t1.253714856445\t0.600000000000\n+chr1\t4683000\t4684000\tSox17\t978.0\t196000\t0.000204498978\t0.685254654751\t0.417904952148\t0.200000000000\n+chr1\t4684000\t4685000\tSox17\t978.0\t197000\t0.001022494888\t0.335210836347\t1.935184862473\t1.000000000000\n+chr1\t4685000\t4686000\tSox17\t978.0\t198000\t0.000817995910\t0.623323575813\t1.335657003912\t0.800000000000\n+chr1\t4686000\t4687000\tSox17\t978.0\t199000\t0.001022494888\t0.356271320740\t1.783206992633\t1.000000000000\n+chr1\t4687000\t4688000\tSox17\t978.0\t200000\t0.001363326517\t0.362375069145\t2.316956024029\t1.333333333333\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/referencePoints.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/referencePoints.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,43 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+chr1 19198995 19198995 Tfap2b
+chr1 24202042 24202042 Col9a1
+chr1 33776741 33776741 Rab23
+chr1 38684089 38684089 Aff3
+chr1 42753991 42753991 Pou3f3
+chr1 52176282 52176282 Stat1
+chr1 52557292 52557292 Nab1
+chr1 53118507 53118507 Mstn
+chr1 57028178 57028178 Satb2
+chr1 59821123 59821123 Bmpr2
+chr1 66991630 66991630 Myl1
+chr1 74648029 74648029 Stk36
+chr1 74818466 74818466 Wnt6
+chr1 74838593 74838593 Wnt10a
+chr1 74998246 74998246 Ihh
+chr1 75356867 75356867 Des
+chr1 77511663 77511663 Epha4
+chr1 78193711 78193711 Pax3
+chr1 89102386 89102386 Chrng
+chr1 93355905 93355905 Per2
+chr1 93698054 93698054 Twist2
+chr1 94076918 94076918 Hdac4
+chr1 107677300 107677300 Tnfrsf11a
+chr1 120950196 120950196 Gli2
+chr1 122499064 122499064 En1
+chr1 127808791 127808791 Lypd1
+chr1 135934092 135934092 Fmod
+chr1 136186581 136186581 MyoG
+chr1 152313295 152313295 Prg4
+chr1 164004278 164006270 mm712
+chr1 164147754 164147754 Dnm3os
+chr1 165243781 165243781 Prrx1
+chr1 165333772 165333772 Gorab
+chr1 169619689 169619689 Lmx1a
+chr1 170362300 170362300 Pbx1
+chr1 180249284 180249284 Gm16586
+chr1 182823250 182823250 Lefty2
+chr1 182865170 182865170 Lefty1
+chr1 188529871 188529871 Tgfb2
+chr1 194979306 194979306 Irf6

diff -r 6bda631b9239 -r 6b7987d22eab test-data/cHi-C/referencePoints_chicViewpoint.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,4 @@
+chr1 4487435 4487435 Sox17
+chr1 14300280 14300280 Eya1
+chr1 19093103 19093103 Tfap2d
+

diff -r 6bda631b9239 -r 6b7987d22eab test-data/distVsCounts.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/distVsCounts.txt Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,600 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\n+543\tsmall_test_matrix_h5\tall\t2720000\t0.0001432356943350283\n+544\tsmall_test_matrix_h5\tall\t2725000\t3.581918475535497e-05\n+545\tsmall_test_matrix_h5\tall\t2730000\t0.00014331780723754928\n+546\tsmall_test_matrix_h5\tall\t2735000\t0.00021503834850548347\n+547\tsmall_test_matrix_h5\tall\t2740000\t7.170000717000071e-05\n+548\tsmall_test_matrix_h5\tall\t2745000\t0.0003586028831671807\n+549\tsmall_test_matrix_h5\tall\t2750000\t0.00014348231580457708\n+550\tsmall_test_matrix_h5\tall\t2755000\t0.00014352350197344816\n+551\tsmall_test_matrix_h5\tall\t2760000\t7.178235589692053e-05\n+552\tsmall_test_matrix_h5\tall\t2765000\t0.00014360594528613484\n+553\tsmall_test_matrix_h5\tall\t2770000\t0.00025138260432378077\n+554\tsmall_test_matrix_h5\tall\t2775000\t0.00014368848336805806\n+555\tsmall_test_matrix_h5\tall\t2780000\t0.00014372978799856272\n+556\tsmall_test_matrix_h5\tall\t2785000\t0.0001437711163827187\n+557\tsmall_test_matrix_h5\tall\t2790000\t0.00025167181994678936\n+558\tsmall_test_matrix_h5\tall\t2795000\t0.0001438538444939941\n+559\tsmall_test_matrix_h5\tall\t2800000\t0.00010792143319663285\n+560\tsmall_test_matrix_h5\tall\t2805000\t0.00021590500179920834\n+561\tsmall_test_matrix_h5\tall\t2810000\t0.00017997264415808796\n+562\tsmall_test_matrix_h5\tall\t2815000\t3.600489666594657e-05\n+563\tsmall_test_matrix_h5\tall\t2820000\t0.0002160916228480876\n+564\tsmall_test_matrix_h5\tall\t2825000\t0.000144102601051949\n+565\tsmall_test_matrix_h5\tall\t2830000\t0.00014414414414414415\n+566\tsmall_test_matrix_h5\tall\t2835000\t0.0002523249945930358\n+567\tsmall_test_matrix_h5\tall\t2840000\t0.00018028412778538978\n+568\tsmall_test_matrix_h5\tall\t2845000\t0.00010820168794633196\n+569\tsmall_test_matrix_h5\tall\t2850000\t0.00018038819539649325\n+570\tsmall_test_matrix_h5\tall\t2855000\t7.217610970768675e-05\n+571\tsmall_test_matrix_h5\tall\t2860000\t0.0003248862897985705\n+572\tsmall_test_matrix_h5\tall\t2865000\t0.00018054452227919405\n+573\tsmall_test_matrix_h5\tall\t2870000\t0.0002889547063497797\n+574\tsmall_test_matrix_h5\tall\t2875000\t0.00036129778163162076\n+575\tsmall_test_matrix_h5\tall\t2880000\t0.00014456089627755693\n+576\tsmall_test_matrix_h5\tall\t2890000\t0.00021696680407897592\n+577\tsmall_test_matrix_h5\tall\t2895000\t0.0001808579903060117\n+578\tsmall_test_matrix_h5\tall\t2900000\t7.236413633403285e-05\n+579\tsmall_test_matrix_h5\tall\t2905000\t0.0002533478103510677\n+580\tsmall_test_matrix_h5\tall\t2910000\t0.00010860907971906451\n+581\tsmall_test_matrix_h5\tall\t2915000\t0.00010864054465126386\n+582\tsmall_test_matrix_h5\tall\t2920000\t0.00021734405564007825\n+583\tsmall_test_matrix_h5\tall\t2925000\t0.00010870352924124937\n+584\tsmall_test_matrix_h5\tall\t2930000\t0.0001812250815512867\n+585\tsmall_test_matrix_h5\tall\t2935000\t0.00010876658690450294\n+586\tsmall_test_matrix_h5\tall\t2940000\t0.00014506419090447523\n+587\tsmall_test_matrix_h5\tall\t2945000\t0.000290212580715374\n+588\tsmall_test_matrix_h5\tall\t2950000\t0.0001451484142535743\n+589\tsmall_test_matrix_h5\tall\t2955000\t0.00025408348457350274\n+590\tsmall_test_matrix_h5\tall\t2960000\t0.00010892455159392927\n+591\tsmall_test_matrix_h5\tall\t2965000\t7.263746640517178e-05\n+592\tsmall_test_matrix_h5\tall\t2970000\t3.6329288672527794e-05\n+593\tsmall_test_matrix_h5\tall\t2975000\t7.26797005596337e-05\n+594\tsmall_test_matrix_h5\tall\t2980000\t0.00010905125408942203\n+595\tsmall_test_matrix_h5\tall\t2985000\t0.00021816595156715876\n+596\tsmall_test_matrix_h5\tall\t2990000\t0.00010911471593802284\n+597\tsmall_test_matrix_h5\tall\t2995000\t0.00014552863275849522\n+598\tsmall_test_matrix_h5\tall\t3000000\t0.00029114200451270107\n'

diff -r 6bda631b9239 -r 6b7987d22eab test-data/find_TADs/multiFDR_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_score.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,24097 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\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 6bda631b9239 -r 6b7987d22eab test-data/find_TADs/multiFDR_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_tad_score.bm Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,24113 @@\n+#{"step":15000,"minDepth":15000,"maxDepth":30000,"binsize":5000}\n+chr2L\t0\t5000\t0.000000\t0.000000\n+chr2L\t5000\t10000\t-0.260846\t-0.229327\n+chr2L\t10000\t15000\t-0.244737\t-0.217294\n+chr2L\t15000\t20000\t0.038826\t0.457739\n+chr2L\t20000\t25000\t0.248816\t0.195739\n+chr2L\t25000\t30000\t0.248816\t0.322439\n+chr2L\t30000\t35000\t-0.234167\t0.241686\n+chr2L\t35000\t40000\t0.480531\t0.299615\n+chr2L\t40000\t45000\t0.207538\t0.213937\n+chr2L\t45000\t50000\t0.207538\t0.234405\n+chr2L\t50000\t55000\t0.038826\t0.192227\n+chr2L\t55000\t60000\t0.207538\t0.234405\n+chr2L\t60000\t65000\t0.207538\t0.234405\n+chr2L\t65000\t70000\t0.207538\t0.099412\n+chr2L\t70000\t75000\t-0.234167\t-0.189929\n+chr2L\t75000\t80000\t-0.234167\t-0.057202\n+chr2L\t80000\t85000\t-0.234167\t-0.057202\n+chr2L\t85000\t90000\t0.296739\t0.075525\n+chr2L\t90000\t95000\t0.176728\t0.178248\n+chr2L\t95000\t100000\t0.707634\t0.178248\n+chr2L\t100000\t105000\t0.038826\t0.011046\n+chr2L\t105000\t110000\t-0.234167\t-0.057202\n+chr2L\t110000\t115000\t-0.234167\t-0.069183\n+chr2L\t115000\t120000\t0.248816\t0.075082\n+chr2L\t120000\t125000\t0.248816\t0.075082\n+chr2L\t125000\t130000\t-0.234167\t0.075082\n+chr2L\t130000\t135000\t0.176728\t0.057060\n+chr2L\t135000\t140000\t0.176728\t0.057060\n+chr2L\t140000\t145000\t0.207538\t0.064762\n+chr2L\t145000\t150000\t0.753523\t0.221726\n+chr2L\t150000\t155000\t0.207538\t0.085230\n+chr2L\t155000\t160000\t-0.234167\t-0.025196\n+chr2L\t160000\t165000\t-0.234167\t-0.025196\n+chr2L\t165000\t170000\t-0.234167\t0.063544\n+chr2L\t170000\t175000\t0.248816\t0.063544\n+chr2L\t175000\t180000\t0.779722\t0.063544\n+chr2L\t180000\t185000\t0.207538\t0.173970\n+chr2L\t185000\t190000\t0.618432\t0.155948\n+chr2L\t190000\t195000\t0.618432\t0.023221\n+chr2L\t195000\t200000\t-0.234167\t-0.189929\n+chr2L\t200000\t205000\t0.038826\t-0.121680\n+chr2L\t205000\t210000\t-0.234167\t-0.069183\n+chr2L\t210000\t215000\t0.248816\t-0.069183\n+chr2L\t215000\t220000\t0.248816\t0.374742\n+chr2L\t220000\t225000\t0.248816\t0.195827\n+chr2L\t225000\t230000\t0.248816\t0.195827\n+chr2L\t230000\t235000\t0.248816\t0.195827\n+chr2L\t235000\t240000\t0.248816\t0.075082\n+chr2L\t240000\t245000\t-0.234167\t0.075082\n+chr2L\t245000\t250000\t-0.234167\t-0.045664\n+chr2L\t250000\t255000\t-0.234167\t0.103511\n+chr2L\t255000\t260000\t0.176728\t0.206234\n+chr2L\t260000\t265000\t0.176728\t0.206234\n+chr2L\t265000\t270000\t0.480531\t0.426450\n+chr2L\t270000\t275000\t0.207538\t0.358202\n+chr2L\t275000\t280000\t0.207538\t0.064762\n+chr2L\t280000\t285000\t-0.234167\t-0.045664\n+chr2L\t285000\t290000\t0.176728\t0.057060\n+chr2L\t290000\t295000\t0.176728\t0.206234\n+chr2L\t295000\t300000\t-0.234167\t-0.040754\n+chr2L\t300000\t305000\t-0.234167\t-0.040754\n+chr2L\t305000\t310000\t0.587622\t0.164693\n+chr2L\t310000\t315000\t0.587622\t0.164693\n+chr2L\t315000\t320000\t0.038826\t0.011046\n+chr2L\t320000\t325000\t0.449720\t0.113770\n+chr2L\t325000\t330000\t0.707634\t0.045522\n+chr2L\t330000\t335000\t-0.234167\t-0.057202\n+chr2L\t335000\t340000\t-0.234167\t-0.057202\n+chr2L\t340000\t345000\t-0.234167\t-0.189929\n+chr2L\t345000\t350000\t-0.234167\t-0.189929\n+chr2L\t350000\t355000\t-0.234167\t-0.025196\n+chr2L\t355000\t360000\t-0.234167\t-0.025196\n+chr2L\t360000\t365000\t-0.234167\t-0.025196\n+chr2L\t365000\t370000\t-0.234167\t-0.025196\n+chr2L\t370000\t375000\t0.176728\t-0.087205\n+chr2L\t375000\t380000\t0.176728\t-0.087205\n+chr2L\t380000\t385000\t0.176728\t-0.087205\n+chr2L\t385000\t390000\t0.618432\t0.023221\n+chr2L\t390000\t395000\t0.207538\t-0.079502\n+chr2L\t395000\t400000\t0.207538\t-0.079502\n+chr2L\t400000\t405000\t-0.234167\t-0.057202\n+chr2L\t405000\t410000\t0.038826\t0.011046\n+chr2L\t410000\t415000\t0.738444\t0.197489\n+chr2L\t415000\t420000\t0.207538\t0.197489\n+chr2L\t420000\t425000\t0.207538\t0.197489\n+chr2L\t425000\t430000\t0.480531\t0.299615\n+chr2L\t430000\t435000\t0.207538\t0.352112\n+chr2L\t435000\t440000\t0.690520\t0.352112\n+chr2L\t440000\t445000\t0.248816\t-0.069183\n+chr2L\t445000\t450000\t-0.234167\t-0.069183\n+chr2L\t450000\t455000\t0.176728\t-0.087205\n+chr2L\t455000\t460000\t0.176728\t-0.087205\n+chr2L\t460000\t465000\t-0.234167\t-0.069183\n+chr2L\t465000\t470000\t0.248816\t0.097421\n+chr2L\t470000\t475000\t0.248816\t0.097421\n+chr2L\t475000\t480000\t0.038826\t0.165669\n+chr2L\t480000\t485000\t0.618432\t0.023221\n+chr2L\t485000\t490000\t0.618432\t0.023221\n+chr2L\t490000\t495000\t1.026516\t0.125242\n+chr2L\t495000\t500000\t-0.234167'..b'36915\t-0.109242\n+chrX\t21985000\t21990000\t-0.136915\t-0.109242\n+chrX\t21990000\t21995000\t-0.136915\t-0.109242\n+chrX\t21995000\t22000000\t-0.136915\t-0.109242\n+chrX\t22000000\t22005000\t-0.136915\t-0.109242\n+chrX\t22005000\t22010000\t-0.136915\t-0.109242\n+chrX\t22010000\t22015000\t-0.136915\t-0.109242\n+chrX\t22015000\t22020000\t-0.136915\t-0.109242\n+chrX\t22020000\t22025000\t-0.136915\t-0.109242\n+chrX\t22025000\t22030000\t-0.136915\t-0.109242\n+chrX\t22030000\t22035000\t-0.136915\t-0.109242\n+chrX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diff -r 6bda631b9239 -r 6b7987d22eab test-data/find_TADs/multiFDR_zscore_matrix.h5

Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAggregateContacts/test_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAggregateContacts/test_regions.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,55 @@
+2R 5441451 5441452 msl2_peak_1532 9.54697
+2R 8291271 8291272 msl2_peak_1644 7.36770
+2R 14575573 14575574 msl2_peak_1947 4.41313
+3L 628463 628464 msl2_peak_2780 11.60203
+3L 3903421 3903422 msl2_peak_2958 4.32242
+3L 8759529 8759530 msl2_peak_3195 4.10429
+3R 2901523 2901524 msl2_peak_4559 2.22040
+3R 3932152 3932153 msl2_peak_4603 9.59945
+3R 11851634 11851635 msl2_peak_4969 8.43238
+3R 20545331 20545332 msl2_peak_5267 4.72876
+X 147841 147842 msl2_peak_22671 16.59036
+X 366894 366895 msl2_peak_22686 25.37647
+X 517100 517101 msl2_peak_22694 8.54298
+X 548547 548548 msl2_peak_22696 27.53758
+X 656427 656428 msl2_peak_22697 14.11897
+X 692287 692288 msl2_peak_22698 15.96065
+X 818016 818017 msl2_peak_22713 10.66184
+X 937135 937136 msl2_peak_22717 67.84654
+X 1112721 1112722 msl2_peak_22727 26.81313
+X 1268823 1268824 msl2_peak_22735 29.73846
+X 1356647 1356648 msl2_peak_22736 9.58288
+X 1375009 1375010 msl2_peak_22738 4.49598
+X 1375616 1375617 msl2_peak_22739 128.36397
+X 1409093 1409094 msl2_peak_22742 14.72497
+X 1588015 1588016 msl2_peak_22757 102.61334
+X 1679121 1679122 msl2_peak_22767 16.12354
+X 1754043 1754044 msl2_peak_22769 20.51431
+X 1775025 1775026 msl2_peak_22773 43.05813
+X 1787755 1787756 msl2_peak_22774 142.73460
+X 1798236 1798237 msl2_peak_22775 80.66115
+X 1819545 1819546 msl2_peak_22777 11.21560
+X 1918989 1918990 msl2_peak_22793 74.48118
+X 1956476 1956477 msl2_peak_22794 32.73601
+X 1972291 1972292 msl2_peak_22795 37.39349
+X 2007235 2007236 msl2_peak_22798 11.21560
+X 2015927 2015928 msl2_peak_22799 68.80555
+X 2044335 2044336 msl2_peak_22804 36.60362
+X 2050114 2050115 msl2_peak_22805 47.23102
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+X 2126007 2126008 msl2_peak_22808 42.23372
+X 2162302 2162303 msl2_peak_22810 78.64520
+X 2237610 2237611 msl2_peak_22817 43.05813
+X 2340287 2340288 msl2_peak_22825 14.72497
+X 2493295 2493296 msl2_peak_22827 23.47760
+X 2503119 2503120 msl2_peak_22828 80.83590
+X 2520611 2520612 msl2_peak_22839 17.87077
+X 2521079 2521080 msl2_peak_22840 60.08352
+X 2613112 2613113 msl2_peak_22844 43.87985
+X 2628624 2628625 msl2_peak_22847 115.37079
+X 3382405 3382406 msl2_peak_22879 6.13203
+X 3593688 3593689 msl2_peak_22908 10.66184
+X 3596515 3596516 msl2_peak_22909 6.59200
+X 3755342 3755343 msl2_peak_22919 164.76546
+X 3848197 3848198 msl2_peak_22920 74.65739
+X 4021813 4021814 msl2_peak_22929 32.73601

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAggregateContacts_results1.png

Binary file test-data/hicAggregateContacts_results1.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAverageRegions/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicAverageRegions/regions.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,6 @@
+chr2L 2500000
+chr2L 3500000
+chr2L 4500000
+chr2L 5500000
+chr2L 7000000
+chr2L 19000000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAverageRegions/result.npz

Binary file test-data/hicAverageRegions/result.npz has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAverageRegions/result_rangeInBins_100.npz

Binary file test-data/hicAverageRegions/result_rangeInBins_100.npz has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicAverageRegions/result_range_100000.npz

Binary file test-data/hicAverageRegions/result_range_100000.npz has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png

Binary file test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCompartmentsPolarization/pca1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicCompartmentsPolarization/pca1.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,449 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicConvertFormat/small_test_matrix_chr4.cool

Binary file test-data/hicConvertFormat/small_test_matrix_chr4.cool has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.ginteractions.tsv Mon Dec 16 15:48:31 2019 -0500

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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicConvertFormat/small_test_matrix_chr4.homer

Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicConvertFormat/test_matrix.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/test_matrix.bed Mon Dec 16 15:48:31 2019 -0500

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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCorrectMatrix/diagnostic_plot.png

Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5

Binary file test-data/hicCorrectMatrix/hicCorrectMatrix_result1.npz.h5 has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCorrelate_heatmap_result1.png

Binary file test-data/hicCorrelate_heatmap_result1.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicCorrelate_scatter_result1.png

Binary file test-data/hicCorrelate_scatter_result1.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicFindRestrictionSites/reference_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/reference_genome.fasta Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,2 @@
+>chr1
+CTACGGTACGAACGTACGGTACGcgtaCGNAGTCATG

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicFindRestrictionSites/restriction_sites.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindRestrictionSites/restriction_sites.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,4 @@
+chr1 5 9 . 0 +
+chr1 13 17 . 0 +
+chr1 18 22 . 0 +
+chr1 24 28 . 0 +

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicInfo/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.3
+File: matrix_name.h5
+Size: 33,754
+Bin_length: 5000
+Sum of matrix: 35778.0
+Chromosomes: chr2L, chr2LHet, chr2R, chr2RHet, chr3L, chr3LHet, chr3R, chr3RHet, chr4, chrM, chrUextra, chrU, chrX, chrXHet, chrYHet
+Non-zero elements: 69,213
+Minimum (non zero): 1
+Maximum: 8
+NaN bins: 0

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicInfo_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInfo_output.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,10 @@
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.1
+File: matrix_name.h5
+Size: 3,383
+Bin_length: 50000
+Sum of matrix: 32798.5
+Chromosomes: chr2RHet, chr3RHet, chr2LHet, chr4, chrYHet, chr3L, chr2L, chrU, chrX, chrXHet, chr2R, chr3R, chrUextra, chrM, chr3LHet
+Non-zero elements: 45,981
+Minimum (non zero): 1
+Maximum: 68
+NaN bins: 664
\ No newline at end of file

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicMergeLoops/gm12878_10kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_10kb.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,1028 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicMergeLoops/gm12878_25kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_25kb.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,402 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicMergeLoops/gm12878_5kb.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_5kb.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,323 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicMergeLoops/gm12878_all.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,1256 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicPlotSVL/p_values.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,4 @@
+# Created with HiCExplorer's hicPlotSVL 3.3
+# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
+# Short range contacts: <= 2000000
+0_small_test_matrix.h5 1_small_test_matrix.h5 1.0

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicPlotSVL/plot.png

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

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicPlotSVL/ratios.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,8 @@
+# Created with HiCExplorer's hicPlotSVL 3.3
+# Short range vs long range contacts per chromosome: raw data
+# Short range contacts: <= 2000000
+# 0_small_test_matrix.h5 1_small_test_matrix.h5
+# Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000
+chr2L 4.7639676113360325 11767 2470 4.7639676113360325 11767 2470
+chr3L 4.8960869565217395 11261 2300 4.8960869565217395 11261 2300
+chr4

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicQuickQC/QC.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicQuickQC/QC.log Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,29 @@
+
+File /tmp/tmpp4d6khlj.h5
+Sequenced reads 983
+Min rest. site distance 300
+Max library insert size 1000
+
+# count (percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality 300 (30.52)
+Hi-C contacts 215 (21.87)
+One mate unmapped 506 (51.48)
+One mate not unique 13 (1.32)
+Low mapping quality 164 (16.68)
+
+# count (percentage w.r.t. mappable, unique and high quality pairs)
+dangling end 0 (0.00)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 85 (28.33)
+self circle 0 (0.00)
+duplicated pairs 0 (0.00)
+
+# count (percentage w.r.t. total valid pairs used)
+inter chromosomal 24 (11.16)
+Intra short range (< 20kb) 61 (28.37)
+Intra long range (>= 20kb) 130 (60.47)
+Read pair type: inward pairs 42 (19.53)
+Read pair type: outward pairs 66 (30.70)
+Read pair type: left pairs 48 (22.33)
+Read pair type: right pairs 35 (16.28)

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicTransform/obs_exp_norm.h5

Binary file test-data/hicTransform/obs_exp_norm.h5 has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak Mon Dec 16 15:48:31 2019 -0500

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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicValidateLocations/loops_1.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/loops_1.bedgraph Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,1007 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicValidateLocations/overlap_smc3_matched_locations
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Mon Dec 16 15:48:31 2019 -0500

b'@@ -0,0 +1,530 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diff -r 6bda631b9239 -r 6b7987d22eab test-data/hicValidateLocations/overlap_smc3_statistics
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,7 @@
+# HiCExplorer hicValidateLocations 3.3
+# Overlap of loop file /tmp/tmpo82hqd2o/files/4/a/4/dataset_4a45db46-19b9-4b40-9d5b-d049a100e2aa.dat with protein file /tmp/tmpo82hqd2o/files/3/5/8/dataset_358b0ce7-ab08-46fc-8968-195d416429ca.dat
+#
+Protein peaks: 3097
+Matched Loops: 530
+Total Loops: 1007
+Loops match protein: 0.5263157894736842

diff -r 6bda631b9239 -r 6b7987d22eab test-data/li_32-33mb_interactions.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/li_32-33mb_interactions.bedgraph Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,2 @@
+X 3139841 3367043 X 2851659 3139841 28764.634828529033
+X 3139841 3367043 X 3139841 3367043 139691.503741355060

diff -r 6bda631b9239 -r 6b7987d22eab test-data/li_viewpoint_32-33Mb.png

Binary file test-data/li_viewpoint_32-33Mb.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/li_viewpoint_32Mb.png

Binary file test-data/li_viewpoint_32Mb.png has changed

diff -r 6bda631b9239 -r 6b7987d22eab test-data/raw_qc_report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_qc_report Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,29 @@
+
+File matrix.cool
+Sequenced reads 983
+Min rest. site distance 300
+Max library insert size 1000
+
+# count (percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality 300 (30.52)
+Hi-C contacts 215 (21.87)
+One mate unmapped 506 (51.48)
+One mate not unique 13 (1.32)
+Low mapping quality 164 (16.68)
+
+# count (percentage w.r.t. mappable, unique and high quality pairs)
+dangling end 0 (0.00)
+self ligation (removed) 0 (0.00)
+One mate not close to rest site 0 (0.00)
+same fragment 85 (28.33)
+self circle 0 (0.00)
+duplicated pairs 0 (0.00)
+
+# count (percentage w.r.t. total valid pairs used)
+inter chromosomal 24 (11.16)
+Intra short range (< 20kb) 61 (28.37)
+Intra long range (>= 20kb) 130 (60.47)
+Read pair type: inward pairs 42 (19.53)
+Read pair type: outward pairs 66 (30.70)
+Read pair type: left pairs 48 (22.33)
+Read pair type: right pairs 35 (16.28)

diff -r 6bda631b9239 -r 6b7987d22eab test-data/regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/regions.bed Mon Dec 16 15:48:31 2019 -0500

@@ -0,0 +1,2 @@
+chrX 10000000 15000000
+chrX 18000000 22000000

diff -r 6bda631b9239 -r 6b7987d22eab test-data/small_test_matrix.cool

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diff -r 6bda631b9239 -r 6b7987d22eab test-data/small_test_matrix_result_sorted.bam

Binary file test-data/small_test_matrix_result_sorted.bam has changed