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Changeset 0:369f6cb43a86 (2017-12-30)

Next changeset 1:0c13bd882a1a (2018-01-02)

Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5

diff -r 000000000000 -r 369f6cb43a86 hicTransform.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicTransform.xml Sat Dec 30 09:19:19 2017 -0500

[

@@ -0,0 +1,93 @@
+<tool id="hicexplorer_hictransform" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>transforms a matrix to a obs_exp, pearson and covariance matrix</description>
+    <macros>
+        <token name="@BINARY@">hicTransform</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+
+
+        hicTransform --matrix '$matrix_h5_cooler'
+        --method all
+
+        #if $outputFormat == 'h5'
+            --outFileName matrix.h5
+        #elif $outputFormat == 'cool'
+            --outFileName matrix.cool
+        #end if
+
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='h5'>HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="obs_exp_h5" from_work_dir="obs_exp_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="pearson_h5" from_work_dir="pearson_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="covariance_h5" from_work_dir="covariance_matrix.h5" format="h5">
+            <filter>outputFormat == 'h5'</filter>
+        </data>
+        <data name="obs_exp_cool" from_work_dir="obs_exp_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+        <data name="pearson_cool" from_work_dir="pearson_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+        <data name="covariance_cool" from_work_dir="covariance_matrix.cool" format="cool">
+            <filter>outputFormat == 'cool'</filter>
+        </data>
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+            <param name="outputFormat" value="h5" />
+            <output name="obs_exp_h5" file="obs_exp_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="pearson_h5" file="pearson_small_50kb.h5" ftype="h5" compare="sim_size"/>
+            <output name="covariance_h5" file="covariance_small_50kb.h5" ftype="h5" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
+            <param name="outputFormat" value="cool" />
+            <output name="obs_exp_cool" file="obs_exp_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="pearson_cool" file="pearson_small_50kb.cool" ftype="cool" compare="sim_size"/>
+            <output name="covariance_cool" file="covariance_small_50kb.cool" ftype="cool" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Transformation of matrix for plotting
+=====================================
+`hicTransform` computes three matrices: an observed/expected matrix based on it a
+pearson correlation matrix and based on it a covariance matrix. These three matrices
+can be used with `hicPlotMatrix` for an A / B compartment analysis.
+
+Input
+-----
+- the matrix to be transformed
+
+Parameters
+__________
+- Output file format: h5 or cool
+
+Output
+------
+- observed/expected matrix
+- pearson correlation matrix
+- covariance matrix.
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r 369f6cb43a86 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Dec 30 09:19:19 2017 -0500

[

b'@@ -0,0 +1,564 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+ <token name="@WRAPPER_VERSION@">2.0</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.1123667</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> \n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="YlGn">YlGn</option>\n+ <option value="PuBuGn">PuBuGn</option>\n+ <option value="RdYlGn">RdYlGn</option>\n+ <option value="YlGnBu">YlGnBu</option>\n+ <option value="YlOrBr">YlOrBr</option>\n+ <option value="YlOrRd">YlOrRd</option>\n+ <option value="gist_gray">gist_gray</option>\n+ <option value="gist_stern">gist_stern</option>\n+ <option value="gist_earth">gist_earth</option>\n+ <'..b' <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="track_input_h5_macro">\n+ <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n+ </xml>\n+ <xml name="track_input_bed_macro">\n+ <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_macro">\n+ <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n+ </xml>\n+ <xml name="track_input_bigwig_macro">\n+ <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_bedgraph_matrix_macro">\n+ <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n+ </xml>\n+ <xml name="track_input_tabular_macro">\n+ <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n+ </xml>\n+ <xml name="plot_title">\n+ <param name="title" type="text" optional="true" label="Plot title"/>\n+ </xml>\n+\n+ <xml name="spacer_macro">\n+ <param name="spacer_width" type="float" value="" optional="True"\n+ label="Include spacer at the end of the track." help="Width of the spacer." />\n+ </xml>\n+ <xml name="fontsize_macro">\n+ <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ </xml>\n+</macros>\n'

diff -r 000000000000 -r 369f6cb43a86 static/images/SRR027956.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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+++ b/test-data/domains.bed Sat Dec 30 09:19:19 2017 -0500

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diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiBonferroni_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiBonferroni_boundaries.bed Sat Dec 30 09:19:19 2017 -0500

@@ -0,0 +1,2 @@
+chr2L 22922500 22927500 B09504 -0.06825625 .
+chrX 87500 92500 B09542 -0.0720205 .

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiBonferroni_boundaries.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiBonferroni_boundaries.gff Sat Dec 30 09:19:19 2017 -0500

@@ -0,0 +1,2 @@
+chr2L HiCExplorer boundary 22922500 22927500 -0.06825625 . . ID=B09504;delta=0.0219547105263;pvalue=0.0547512191318;tad_sep=-0.06825625
+chrX HiCExplorer boundary 87500 92500 -0.0720205 . . ID=B09542;delta=0.0197999736842;pvalue=0.0890201733631;tad_sep=-0.0720205

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiBonferroni_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiBonferroni_score.bedgraph Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,23814 @@\n+chr2RHet\t2500\t3286880\t0.0\n+chr3RHet\t2500\t2516253\t0.0\n+chr2LHet\t2500\t366936\t0.0\n+chr4\t2500\t1350928\t0.0\n+chrYHet\t2500\t346019\t0.0\n+chr3L\t2500\t7500\t-0.15973725\n+chr3L\t7500\t12500\t-0.1550825\n+chr3L\t12500\t17500\t-0.1511685\n+chr3L\t17500\t22500\t-0.14787325\n+chr3L\t22500\t27500\t-0.14477275\n+chr3L\t27500\t32500\t-0.141869\n+chr3L\t32500\t37500\t-0.13920825\n+chr3L\t37500\t42500\t-0.13669525\n+chr3L\t42500\t47500\t-0.13435775\n+chr3L\t47500\t52500\t-0.13219825\n+chr3L\t52500\t57500\t-0.13013875\n+chr3L\t57500\t62500\t-0.09402375\n+chr3L\t62500\t67500\t-0.076427\n+chr3L\t67500\t72500\t-0.04183125\n+chr3L\t72500\t77500\t0.0197075\n+chr3L\t77500\t82500\t0.07052875\n+chr3L\t82500\t87500\t0.07283975\n+chr3L\t87500\t92500\t0.07045525\n+chr3L\t92500\t97500\t0.0683615\n+chr3L\t97500\t102500\t0.06999375\n+chr3L\t102500\t107500\t0.0683285\n+chr3L\t107500\t112500\t0.066853\n+chr3L\t112500\t117500\t0.06554\n+chr3L\t117500\t122500\t0.06436125\n+chr3L\t122500\t127500\t0.00960325\n+chr3L\t127500\t132500\t0.012285\n+chr3L\t132500\t137500\t-0.00142775\n+chr3L\t137500\t142500\t-0.060362\n+chr3L\t142500\t147500\t-0.05156225\n+chr3L\t147500\t152500\t-0.0552185\n+chr3L\t152500\t157500\t-0.06660375\n+chr3L\t157500\t162500\t-0.070088\n+chr3L\t162500\t167500\t-0.10316675\n+chr3L\t167500\t172500\t-0.10316675\n+chr3L\t172500\t177500\t-0.10316675\n+chr3L\t177500\t182500\t-0.089227\n+chr3L\t182500\t187500\t-0.0778915\n+chr3L\t187500\t192500\t-0.0547475\n+chr3L\t192500\t197500\t-0.06240725\n+chr3L\t197500\t202500\t-0.040267\n+chr3L\t202500\t207500\t-0.018089\n+chr3L\t207500\t212500\t-0.018089\n+chr3L\t212500\t217500\t-0.018089\n+chr3L\t217500\t222500\t0.0190635\n+chr3L\t222500\t227500\t0.01122225\n+chr3L\t227500\t232500\t-0.00338425\n+chr3L\t232500\t237500\t0.018671\n+chr3L\t237500\t242500\t0.015759\n+chr3L\t242500\t247500\t0.015759\n+chr3L\t247500\t252500\t-0.00807575\n+chr3L\t252500\t257500\t-0.01047525\n+chr3L\t257500\t262500\t-0.026655\n+chr3L\t262500\t267500\t-0.01461\n+chr3L\t267500\t272500\t-0.01739225\n+chr3L\t272500\t277500\t0.006616\n+chr3L\t277500\t282500\t0.02626725\n+chr3L\t282500\t287500\t0.02671675\n+chr3L\t287500\t292500\t0.04431375\n+chr3L\t292500\t297500\t0.075128\n+chr3L\t297500\t302500\t0.0517535\n+chr3L\t302500\t307500\t0.03498275\n+chr3L\t307500\t312500\t0.04280875\n+chr3L\t312500\t317500\t-0.00566075\n+chr3L\t317500\t322500\t-0.00566075\n+chr3L\t322500\t327500\t-0.01699625\n+chr3L\t327500\t332500\t0.0001575\n+chr3L\t332500\t337500\t-0.030848\n+chr3L\t337500\t342500\t-0.02264125\n+chr3L\t342500\t347500\t-0.01607175\n+chr3L\t347500\t352500\t-0.03003825\n+chr3L\t352500\t357500\t-0.0029145\n+chr3L\t357500\t362500\t-0.0580815\n+chr3L\t362500\t367500\t-0.042338\n+chr3L\t367500\t372500\t-0.0243195\n+chr3L\t372500\t377500\t-0.0233235\n+chr3L\t377500\t382500\t0.01665375\n+chr3L\t382500\t387500\t0.01665375\n+chr3L\t387500\t392500\t0.030134\n+chr3L\t392500\t397500\t0.01966325\n+chr3L\t397500\t402500\t0.0270555\n+chr3L\t402500\t407500\t0.03715275\n+chr3L\t407500\t412500\t0.03215025\n+chr3L\t412500\t417500\t0.007102\n+chr3L\t417500\t422500\t0.01531925\n+chr3L\t422500\t427500\t0.04944275\n+chr3L\t427500\t432500\t0.017395\n+chr3L\t432500\t437500\t0.0233485\n+chr3L\t437500\t442500\t0.010935\n+chr3L\t442500\t447500\t0.015241\n+chr3L\t447500\t452500\t-0.00172725\n+chr3L\t452500\t457500\t-0.006215\n+chr3L\t457500\t462500\t-0.0121685\n+chr3L\t462500\t467500\t-0.0042425\n+chr3L\t467500\t472500\t0.00083775\n+chr3L\t472500\t477500\t-0.02013475\n+chr3L\t477500\t482500\t-0.058266\n+chr3L\t482500\t487500\t-0.07169775\n+chr3L\t487500\t492500\t-0.04601075\n+chr3L\t492500\t497500\t-0.02333825\n+chr3L\t497500\t502500\t-0.00838725\n+chr3L\t502500\t507500\t-0.0641845\n+chr3L\t507500\t512500\t-0.067458\n+chr3L\t512500\t517500\t-0.067458\n+chr3L\t517500\t522500\t-0.09926975\n+chr3L\t522500\t527500\t-0.1060405\n+chr3L\t527500\t532500\t-0.07751675\n+chr3L\t532500\t537500\t-0.07751675\n+chr3L\t537500\t542500\t-0.07751675\n+chr3L\t542500\t547500\t-0.06945475\n+chr3L\t547500\t552500\t-0.06322125\n+chr3L\t552500\t557500\t0.00947925\n+chr3L\t557500\t562500\t-0.02586475\n+chr3L\t562500\t567500\t0.030247\n+chr3L\t567500\t572500\t0.04485875\n+chr3L\t572500\t577500\t0.0579985\n+chr3L\t577500\t582500\t0.085449\n+chr3L\t582500\t587500\t0.10347075\n+chr3L\t587500\t592500\t0.1197795\n+chr3L\t592500\t597500\t0.115187\n+chr3L\t597500\t602500\t0.099483\n+chr3L\t602500\t607500\t0.100333\n+chr3L\t607500\t612500\t0.1935635\n+chr3L\t612500\t6'..b'52500\t27357500\t0.02843225\n+chr3R\t27357500\t27362500\t0.003006\n+chr3R\t27362500\t27367500\t0.02624575\n+chr3R\t27367500\t27372500\t0.01185675\n+chr3R\t27372500\t27377500\t0.0101145\n+chr3R\t27377500\t27382500\t-0.005061\n+chr3R\t27382500\t27387500\t-0.041305\n+chr3R\t27387500\t27392500\t-0.00143125\n+chr3R\t27392500\t27397500\t0.04561275\n+chr3R\t27397500\t27402500\t0.02985575\n+chr3R\t27402500\t27407500\t0.0173185\n+chr3R\t27407500\t27412500\t0.0272775\n+chr3R\t27412500\t27417500\t0.01093175\n+chr3R\t27417500\t27422500\t-0.0499295\n+chr3R\t27422500\t27427500\t-0.04139125\n+chr3R\t27427500\t27432500\t-0.0366555\n+chr3R\t27432500\t27437500\t-0.0366555\n+chr3R\t27437500\t27442500\t-0.04748775\n+chr3R\t27442500\t27447500\t-0.05511025\n+chr3R\t27447500\t27452500\t-0.05736225\n+chr3R\t27452500\t27457500\t-0.0233205\n+chr3R\t27457500\t27462500\t-0.0020265\n+chr3R\t27462500\t27467500\t0.02501975\n+chr3R\t27467500\t27472500\t0.036331\n+chr3R\t27472500\t27477500\t0.036331\n+chr3R\t27477500\t27482500\t0.036331\n+chr3R\t27482500\t27487500\t0.06726625\n+chr3R\t27487500\t27492500\t0.06726625\n+chr3R\t27492500\t27497500\t0.0926245\n+chr3R\t27497500\t27502500\t0.098145\n+chr3R\t27502500\t27507500\t0.088452\n+chr3R\t27507500\t27512500\t0.0991195\n+chr3R\t27512500\t27517500\t0.07477075\n+chr3R\t27517500\t27522500\t0.07477075\n+chr3R\t27522500\t27527500\t0.07477075\n+chr3R\t27527500\t27532500\t0.07477075\n+chr3R\t27532500\t27537500\t0.07667425\n+chr3R\t27537500\t27542500\t0.08198875\n+chr3R\t27542500\t27547500\t0.068792\n+chr3R\t27547500\t27552500\t0.00660575\n+chr3R\t27552500\t27557500\t-0.06866275\n+chr3R\t27557500\t27562500\t-0.063076\n+chr3R\t27562500\t27567500\t-0.063076\n+chr3R\t27567500\t27572500\t-0.08094325\n+chr3R\t27572500\t27577500\t-0.07177225\n+chr3R\t27577500\t27582500\t0.00014175\n+chr3R\t27582500\t27587500\t-0.004425\n+chr3R\t27587500\t27592500\t-0.0055905\n+chr3R\t27592500\t27597500\t0.0107725\n+chr3R\t27597500\t27602500\t0.012076\n+chr3R\t27602500\t27607500\t0.00204375\n+chr3R\t27607500\t27612500\t0.01391525\n+chr3R\t27612500\t27617500\t0.02616875\n+chr3R\t27617500\t27622500\t0.02862975\n+chr3R\t27622500\t27627500\t0.02862975\n+chr3R\t27627500\t27632500\t0.03521625\n+chr3R\t27632500\t27637500\t0.00040125\n+chr3R\t27637500\t27642500\t0.0303095\n+chr3R\t27642500\t27647500\t0.090842\n+chr3R\t27647500\t27652500\t0.10491025\n+chr3R\t27652500\t27657500\t0.11880175\n+chr3R\t27657500\t27662500\t0.09649925\n+chr3R\t27662500\t27667500\t0.07636225\n+chr3R\t27667500\t27672500\t0.06380525\n+chr3R\t27672500\t27677500\t0.04760175\n+chr3R\t27677500\t27682500\t0.02274975\n+chr3R\t27682500\t27687500\t0.015637\n+chr3R\t27687500\t27692500\t0.015637\n+chr3R\t27692500\t27697500\t0.025063\n+chr3R\t27697500\t27702500\t-0.01535\n+chr3R\t27702500\t27707500\t-0.01535\n+chr3R\t27707500\t27712500\t0.00155075\n+chr3R\t27712500\t27717500\t0.006288\n+chr3R\t27717500\t27722500\t0.006288\n+chr3R\t27722500\t27727500\t-0.00858325\n+chr3R\t27727500\t27732500\t0.02622075\n+chr3R\t27732500\t27737500\t0.097312\n+chr3R\t27737500\t27742500\t0.067952\n+chr3R\t27742500\t27747500\t0.0387865\n+chr3R\t27747500\t27752500\t0.01357725\n+chr3R\t27752500\t27757500\t0.02531675\n+chr3R\t27757500\t27762500\t0.033303\n+chr3R\t27762500\t27767500\t0.050386\n+chr3R\t27767500\t27772500\t0.0229625\n+chr3R\t27772500\t27777500\t0.04058825\n+chr3R\t27777500\t27782500\t0.03747975\n+chr3R\t27782500\t27787500\t0.0294565\n+chr3R\t27787500\t27792500\t0.07453225\n+chr3R\t27792500\t27797500\t0.08362425\n+chr3R\t27797500\t27802500\t0.06882\n+chr3R\t27802500\t27807500\t0.075945\n+chr3R\t27807500\t27812500\t0.11806575\n+chr3R\t27812500\t27817500\t0.152855\n+chr3R\t27817500\t27822500\t0.1721425\n+chr3R\t27822500\t27827500\t0.17090925\n+chr3R\t27827500\t27832500\t0.15466375\n+chr3R\t27832500\t27837500\t0.1765955\n+chr3R\t27837500\t27842500\t0.16170225\n+chr3R\t27842500\t27847500\t0.16431675\n+chr3R\t27847500\t27852500\t0.20353925\n+chr3R\t27852500\t27857500\t0.19259975\n+chr3R\t27857500\t27862500\t0.13903775\n+chr3R\t27862500\t27867500\t0.1658075\n+chr3R\t27867500\t27872500\t0.033584\n+chr3R\t27872500\t27877500\t-0.044813\n+chr3R\t27877500\t27882500\t-0.1079445\n+chr3R\t27882500\t27887500\t-0.1024605\n+chr3R\t27887500\t27892500\t-0.09179375\n+chr3R\t27892500\t27897500\t-0.1533095\n+chr3R\t27897500\t27902500\t-0.15876925\n+chr3R\t27902500\t27905026\t0.0\n+chrUextra\t2500\t29002328\t0.0\n+chrM\t2500\t17258\t0.0\n+chr3LHet\t2500\t2555245\t0.0\n'

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiBonferroni_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiBonferroni_tad_score.bm Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,23830 @@\n+#{"step":20000,"minDepth":60000,"maxDepth":180000,"binsize":5000}\n+chr2RHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr2RHet\t3285000\t3288761\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3RHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3RHet\t2515000\t2517507\t0.000000\t0.000000\t0.000000\t0.000000\n+chr2LHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr2LHet\t365000\t368872\t0.000000\t0.000000\t0.000000\t0.000000\n+chr4\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr4\t1350000\t1351857\t0.000000\t0.000000\t0.000000\t0.000000\n+chrYHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chrYHet\t345000\t347038\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3L\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3L\t5000\t10000\t-0.185185\t-0.171295\t-0.149986\t-0.132483\n+chr3L\t10000\t15000\t-0.179233\t-0.165874\t-0.145865\t-0.129358\n+chr3L\t15000\t20000\t-0.174239\t-0.161260\t-0.142558\t-0.126617\n+chr3L\t20000\t25000\t-0.170014\t-0.157559\t-0.139686\t-0.124234\n+chr3L\t25000\t30000\t-0.165979\t-0.154152\t-0.136908\t-0.122052\n+chr3L\t30000\t35000\t-0.162203\t-0.150978\t-0.134318\t-0.119977\n+chr3L\t35000\t40000\t-0.158727\t-0.148088\t-0.131965\t-0.118053\n+chr3L\t40000\t45000\t-0.155567\t-0.145272\t-0.129738\t-0.116204\n+chr3L\t45000\t50000\t-0.152607\t-0.142713\t-0.127607\t-0.114504\n+chr3L\t50000\t55000\t-0.149926\t-0.140331\t-0.125612\t-0.112924\n+chr3L\t55000\t60000\t-0.147348\t-0.138093\t-0.123706\t-0.111408\n+chr3L\t60000\t65000\t-0.092610\t-0.096797\t-0.095758\t-0.090930\n+chr3L\t65000\t70000\t-0.063836\t-0.077794\t-0.082758\t-0.081320\n+chr3L\t70000\t75000\t-0.063836\t-0.013812\t-0.039782\t-0.049895\n+chr3L\t75000\t80000\t0.022439\t0.060152\t0.009858\t-0.013619\n+chr3L\t80000\t85000\t0.152571\t0.093803\t0.032622\t0.003119\n+chr3L\t85000\t90000\t0.214709\t0.074296\t0.013186\t-0.010832\n+chr3L\t90000\t95000\t0.214709\t0.074296\t0.007552\t-0.014736\n+chr3L\t95000\t100000\t0.214709\t0.074296\t0.002590\t-0.018149\n+chr3L\t100000\t105000\t0.221372\t0.078043\t0.000227\t-0.019667\n+chr3L\t105000\t110000\t0.221372\t0.078043\t-0.003723\t-0.022378\n+chr3L\t110000\t115000\t0.221372\t0.078043\t-0.007240\t-0.024763\n+chr3L\t115000\t120000\t0.221372\t0.078043\t-0.010366\t-0.026889\n+chr3L\t120000\t125000\t0.221372\t0.078043\t-0.013170\t-0.028800\n+chr3L\t125000\t130000\t0.111997\t0.016520\t-0.040513\t-0.049591\n+chr3L\t130000\t135000\t0.067050\t0.048925\t-0.026111\t-0.040724\n+chr3L\t135000\t140000\t0.016687\t0.046933\t-0.026996\t-0.042335\n+chr3L\t140000\t145000\t-0.076765\t-0.035198\t-0.063499\t-0.065986\n+chr3L\t145000\t150000\t-0.022697\t-0.059245\t-0.060247\t-0.064060\n+chr3L\t150000\t155000\t-0.030134\t-0.063428\t-0.062106\t-0.065206\n+chr3L\t155000\t160000\t-0.053449\t-0.076543\t-0.067935\t-0.068488\n+chr3L\t160000\t165000\t-0.076765\t-0.058294\t-0.073764\t-0.071529\n+chr3L\t165000\t170000\t-0.144931\t-0.096638\t-0.090806\t-0.080292\n+chr3L\t170000\t175000\t-0.144931\t-0.096638\t-0.090806\t-0.080292\n+chr3L\t175000\t180000\t-0.144931\t-0.096638\t-0.090806\t-0.080292\n+chr3L\t180000\t185000\t-0.089172\t-0.096638\t-0.090806\t-0.080292\n+chr3L\t185000\t190000\t-0.065857\t-0.083523\t-0.084977\t-0.077209\n+chr3L\t190000\t195000\t-0.042541\t-0.042285\t-0.066649\t-0.067515\n+chr3L\t195000\t200000\t-0.065857\t-0.055399\t-0.072477\t-0.055896\n+chr3L\t200000\t205000\t-0.051757\t-0.011064\t-0.052773\t-0.045474\n+chr3L\t205000\t210000\t-0.014382\t0.013201\t-0.041989\t-0.029186\n+chr3L\t210000\t215000\t-0.014382\t0.013201\t-0.041989\t-0.029186\n+chr3L\t215000\t220000\t-0.014382\t0.013201\t-0.041989\t-0.029186\n+chr3L\t220000\t225000\t0.093474\t0.037466\t-0.031204\t-0.023482\n+chr3L\t225000\t230000\t0.093474\t0.006101\t-0.031204\t-0.023482\n+chr3L\t230000\t235000\t0.056060\t-0.014945\t-0.040558\t-0.014094\n+chr3L\t235000\t240000\t0.108983\t0.014825\t-0.027327\t-0.021797\n+chr3L\t240000\t245000\t0.079375\t0.026294\t-0.016159\t-0.026474\n+chr3L\t245000\t250000\t0.079375\t0.026294\t-0.016159\t-0.026474\n+chr3L\t250000\t255000\t0.006063\t0.013179\t-0.021988\t-0.029557\n+chr3L\t255000\t260000\t0.012922\t-0.011086\t-0.016881\t-0.026856\n+chr3L\t260000\t265000\t-0.051797\t-0.011086\t-0.016881\t-0.026856\n+chr3L\t265000\t270000\t-0.002735\t-0.011612\t-0.017114\t-0.026979\n+chr3L\t270000\t275000\t-0.008457\t-0.014831\t-0.018545\t-0.027736\n+chr3L\t275000\t280000\t0.040924\t0.012946\t-0.006200\t-0.021206\n+chr3L\t280000\t285000\t0.043057\t0.0848'..b'867\n+chr3R\t27615000\t27620000\t0.096590\t0.009047\t-0.006829\t0.005867\n+chr3R\t27620000\t27625000\t0.088048\t0.036259\t-0.012602\t0.002814\n+chr3R\t27625000\t27630000\t0.088048\t0.036259\t-0.012602\t0.002814\n+chr3R\t27630000\t27635000\t0.088048\t0.036259\t0.004630\t0.011928\n+chr3R\t27635000\t27640000\t0.016439\t-0.004021\t-0.013272\t0.002459\n+chr3R\t27640000\t27645000\t0.067730\t0.028353\t0.001116\t0.024039\n+chr3R\t27645000\t27650000\t0.192236\t0.098387\t0.032243\t0.040502\n+chr3R\t27650000\t27655000\t0.221172\t0.114663\t0.039477\t0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diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiBonferroni_zscore_matrix.h5

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

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiFDR_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_boundaries.bed Sat Dec 30 09:19:19 2017 -0500

@@ -0,0 +1,2 @@
+chr2L 22922500 22927500 B09504 -0.0682563628914 .
+chrX 87500 92500 B09542 -0.0720204010166 .

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiFDR_boundaries.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_boundaries.gff Sat Dec 30 09:19:19 2017 -0500

@@ -0,0 +1,2 @@
+chr2L HiCExplorer boundary 22922500 22927500 -0.0682563628914 . . ID=B09504;delta=0.0219548467205;pvalue=3.39647761363e-05;tad_sep=-0.0682563628914
+chrX HiCExplorer boundary 87500 92500 -0.0720204010166 . . ID=B09542;delta=0.0197999801036;pvalue=5.52234326074e-05;tad_sep=-0.0720204010166

diff -r 000000000000 -r 369f6cb43a86 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 Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,23814 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r3R\t27492500\t27497500\t0.0926243695908\n+chr3R\t27497500\t27502500\t0.0981449030292\n+chr3R\t27502500\t27507500\t0.0884518556514\n+chr3R\t27507500\t27512500\t0.0991195811149\n+chr3R\t27512500\t27517500\t0.0747706741268\n+chr3R\t27517500\t27522500\t0.0747706741268\n+chr3R\t27522500\t27527500\t0.0747706741268\n+chr3R\t27527500\t27532500\t0.0747706741268\n+chr3R\t27532500\t27537500\t0.0766743472887\n+chr3R\t27537500\t27542500\t0.0819888617495\n+chr3R\t27542500\t27547500\t0.0687920794808\n+chr3R\t27547500\t27552500\t0.00660554313528\n+chr3R\t27552500\t27557500\t-0.068663015437\n+chr3R\t27557500\t27562500\t-0.0630758560148\n+chr3R\t27562500\t27567500\t-0.0630758560148\n+chr3R\t27567500\t27572500\t-0.0809430698515\n+chr3R\t27572500\t27577500\t-0.0717723999989\n+chr3R\t27577500\t27582500\t0.000141647672875\n+chr3R\t27582500\t27587500\t-0.00442507235603\n+chr3R\t27587500\t27592500\t-0.00559045677864\n+chr3R\t27592500\t27597500\t0.0107725606946\n+chr3R\t27597500\t27602500\t0.0120760744751\n+chr3R\t27602500\t27607500\t0.00204356889653\n+chr3R\t27607500\t27612500\t0.0139153913065\n+chr3R\t27612500\t27617500\t0.0261687926169\n+chr3R\t27617500\t27622500\t0.0286298507012\n+chr3R\t27622500\t27627500\t0.0286298507012\n+chr3R\t27627500\t27632500\t0.0352164944657\n+chr3R\t27632500\t27637500\t0.000401173118025\n+chr3R\t27637500\t27642500\t0.0303094054812\n+chr3R\t27642500\t27647500\t0.0908420094422\n+chr3R\t27647500\t27652500\t0.104910058763\n+chr3R\t27652500\t27657500\t0.118801510524\n+chr3R\t27657500\t27662500\t0.0964990987183\n+chr3R\t27662500\t27667500\t0.0763621831154\n+chr3R\t27667500\t27672500\t0.0638054902132\n+chr3R\t27672500\t27677500\t0.0476018389011\n+chr3R\t27677500\t27682500\t0.0227499384692\n+chr3R\t27682500\t27687500\t0.0156368494306\n+chr3R\t27687500\t27692500\t0.0156368494306\n+chr3R\t27692500\t27697500\t0.0250628717201\n+chr3R\t27697500\t27702500\t-0.0153501339631\n+chr3R\t27702500\t27707500\t-0.0153501339631\n+chr3R\t27707500\t27712500\t0.00155093677552\n+chr3R\t27712500\t27717500\t0.00628832953637\n+chr3R\t27717500\t27722500\t0.00628832953637\n+chr3R\t27722500\t27727500\t-0.00858313357697\n+chr3R\t27727500\t27732500\t0.0262206216996\n+chr3R\t27732500\t27737500\t0.0973120916552\n+chr3R\t27737500\t27742500\t0.0679519287234\n+chr3R\t27742500\t27747500\t0.0387863613672\n+chr3R\t27747500\t27752500\t0.0135773284877\n+chr3R\t27752500\t27757500\t0.0253166135267\n+chr3R\t27757500\t27762500\t0.0333030070633\n+chr3R\t27762500\t27767500\t0.0503863505993\n+chr3R\t27767500\t27772500\t0.0229622694476\n+chr3R\t27772500\t27777500\t0.0405881951039\n+chr3R\t27777500\t27782500\t0.037479587368\n+chr3R\t27782500\t27787500\t0.029456572128\n+chr3R\t27787500\t27792500\t0.0745322715233\n+chr3R\t27792500\t27797500\t0.0836243348379\n+chr3R\t27797500\t27802500\t0.0688200327796\n+chr3R\t27802500\t27807500\t0.0759450550149\n+chr3R\t27807500\t27812500\t0.118065986623\n+chr3R\t27812500\t27817500\t0.152855110565\n+chr3R\t27817500\t27822500\t0.172142533307\n+chr3R\t27822500\t27827500\t0.170909037821\n+chr3R\t27827500\t27832500\t0.154663891259\n+chr3R\t27832500\t27837500\t0.176595521439\n+chr3R\t27837500\t27842500\t0.161702307533\n+chr3R\t27842500\t27847500\t0.164316603264\n+chr3R\t27847500\t27852500\t0.203539265274\n+chr3R\t27852500\t27857500\t0.192599593633\n+chr3R\t27857500\t27862500\t0.139037714041\n+chr3R\t27862500\t27867500\t0.165807374217\n+chr3R\t27867500\t27872500\t0.0335840423644\n+chr3R\t27872500\t27877500\t-0.0448126165606\n+chr3R\t27877500\t27882500\t-0.107944679472\n+chr3R\t27882500\t27887500\t-0.102460435442\n+chr3R\t27887500\t27892500\t-0.0917938917283\n+chr3R\t27892500\t27897500\t-0.153309285822\n+chr3R\t27897500\t27902500\t-0.158769428921\n+chr3R\t27902500\t27905026\t0.0\n+chrUextra\t2500\t29002328\t0.0\n+chrM\t2500\t17258\t0.0\n+chr3LHet\t2500\t2555245\t0.0\n'

diff -r 000000000000 -r 369f6cb43a86 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 Sat Dec 30 09:19:19 2017 -0500

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiFDR_zscore_matrix.h5

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

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_boundaries.bed Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,1408 @@\n+chr3L\t162500\t167500\tB00043\t-0.10316675\t.\n+chr3L\t257500\t262500\tB00062\t-0.026655\t.\n+chr3L\t332500\t337500\tB00077\t-0.030848\t.\n+chr3L\t357500\t362500\tB00082\t-0.0580815\t.\n+chr3L\t482500\t487500\tB00107\t-0.07169775\t.\n+chr3L\t522500\t527500\tB00115\t-0.1060405\t.\n+chr3L\t677500\t682500\tB00146\t-0.0148855\t.\n+chr3L\t702500\t707500\tB00151\t0.002784\t.\n+chr3L\t737500\t742500\tB00158\t0.00949975\t.\n+chr3L\t867500\t872500\tB00184\t-0.09546975\t.\n+chr3L\t1007500\t1012500\tB00212\t-0.05182175\t.\n+chr3L\t1037500\t1042500\tB00218\t-0.05874875\t.\n+chr3L\t1107500\t1112500\tB00232\t-0.048349\t.\n+chr3L\t1207500\t1212500\tB00252\t-0.0567565\t.\n+chr3L\t1242500\t1247500\tB00259\t-0.0641435\t.\n+chr3L\t1297500\t1302500\tB00270\t-0.091379\t.\n+chr3L\t1462500\t1467500\tB00303\t-0.01307225\t.\n+chr3L\t1532500\t1537500\tB00317\t-0.08711525\t.\n+chr3L\t1577500\t1582500\tB00326\t-0.08235875\t.\n+chr3L\t1637500\t1642500\tB00338\t-0.0628755\t.\n+chr3L\t1667500\t1672500\tB00344\t-0.037945\t.\n+chr3L\t1732500\t1737500\tB00357\t-0.050313\t.\n+chr3L\t1812500\t1817500\tB00373\t-0.01723525\t.\n+chr3L\t1847500\t1852500\tB00380\t-0.0259975\t.\n+chr3L\t1922500\t1927500\tB00395\t8.325e-05\t.\n+chr3L\t2152500\t2157500\tB00441\t-0.0401965\t.\n+chr3L\t2257500\t2262500\tB00462\t-0.07518575\t.\n+chr3L\t2387500\t2392500\tB00488\t-0.072071\t.\n+chr3L\t2457500\t2462500\tB00502\t-0.09132325\t.\n+chr3L\t2557500\t2562500\tB00522\t-0.09179675\t.\n+chr3L\t2597500\t2602500\tB00530\t-0.0934855\t.\n+chr3L\t2737500\t2742500\tB00558\t-0.08927875\t.\n+chr3L\t2882500\t2887500\tB00587\t-0.08972575\t.\n+chr3L\t2942500\t2947500\tB00599\t0.029899\t.\n+chr3L\t2957500\t2962500\tB00602\t0.0356865\t.\n+chr3L\t3042500\t3047500\tB00619\t-0.00466875\t.\n+chr3L\t3132500\t3137500\tB00637\t0.055702\t.\n+chr3L\t3217500\t3222500\tB00654\t-0.059463\t.\n+chr3L\t3252500\t3257500\tB00661\t-0.045796\t.\n+chr3L\t3312500\t3317500\tB00673\t-0.05499875\t.\n+chr3L\t3342500\t3347500\tB00679\t-0.04234075\t.\n+chr3L\t3472500\t3477500\tB00705\t-0.05097675\t.\n+chr3L\t3512500\t3517500\tB00713\t-0.012488\t.\n+chr3L\t3542500\t3547500\tB00719\t0.02457925\t.\n+chr3L\t3612500\t3617500\tB00733\t0.019683\t.\n+chr3L\t3667500\t3672500\tB00744\t0.09945325\t.\n+chr3L\t3762500\t3767500\tB00763\t-0.047454\t.\n+chr3L\t3782500\t3787500\tB00767\t-0.041084\t.\n+chr3L\t3822500\t3827500\tB00775\t-0.06101175\t.\n+chr3L\t3897500\t3902500\tB00790\t-0.0684535\t.\n+chr3L\t3997500\t4002500\tB00810\t-0.03007875\t.\n+chr3L\t4117500\t4122500\tB00834\t-0.0807515\t.\n+chr3L\t4162500\t4167500\tB00843\t-0.088488\t.\n+chr3L\t4197500\t4202500\tB00850\t-0.098724\t.\n+chr3L\t4217500\t4222500\tB00854\t-0.088911\t.\n+chr3L\t4267500\t4272500\tB00864\t-0.11633575\t.\n+chr3L\t4362500\t4367500\tB00883\t-0.0944955\t.\n+chr3L\t4402500\t4407500\tB00891\t-0.07463925\t.\n+chr3L\t4487500\t4492500\tB00908\t0.00287075\t.\n+chr3L\t4622500\t4627500\tB00935\t0.04064075\t.\n+chr3L\t4647500\t4652500\tB00940\t0.03764975\t.\n+chr3L\t4787500\t4792500\tB00968\t-0.06999725\t.\n+chr3L\t4892500\t4897500\tB00989\t-0.076914\t.\n+chr3L\t4997500\t5002500\tB01010\t-0.0378805\t.\n+chr3L\t5107500\t5112500\tB01032\t-0.061049\t.\n+chr3L\t5237500\t5242500\tB01058\t0.07173475\t.\n+chr3L\t5277500\t5282500\tB01066\t0.02598475\t.\n+chr3L\t5357500\t5362500\tB01082\t-0.06976425\t.\n+chr3L\t5462500\t5467500\tB01103\t0.0082995\t.\n+chr3L\t5552500\t5557500\tB01121\t-0.03433\t.\n+chr3L\t5572500\t5577500\tB01125\t0.00900825\t.\n+chr3L\t5742500\t5747500\tB01159\t-0.09901225\t.\n+chr3L\t5812500\t5817500\tB01173\t-0.08504275\t.\n+chr3L\t5872500\t5877500\tB01185\t-0.107036\t.\n+chr3L\t5957500\t5962500\tB01202\t-0.0645035\t.\n+chr3L\t5987500\t5992500\tB01208\t-0.06534175\t.\n+chr3L\t6117500\t6122500\tB01234\t-0.06653425\t.\n+chr3L\t6192500\t6197500\tB01249\t-0.08219225\t.\n+chr3L\t6227500\t6232500\tB01256\t-0.07949925\t.\n+chr3L\t6252500\t6257500\tB01261\t-0.0959415\t.\n+chr3L\t6367500\t6372500\tB01284\t-0.0155925\t.\n+chr3L\t6442500\t6447500\tB01299\t-0.0843135\t.\n+chr3L\t6487500\t6492500\tB01308\t-0.07350925\t.\n+chr3L\t6557500\t6562500\tB01322\t0.050254\t.\n+chr3L\t6582500\t6587500\tB01327\t0.05181025\t.\n+chr3L\t6727500\t6732500\tB01356\t-0.08674075\t.\n+chr3L\t6872500\t6877500\tB01385\t0.015592\t.\n+chr3L\t6957500\t6962500\tB01402\t-0.06386025\t.\n+chr3L\t7072500\t7077500\tB01425\t-0.05008325\t.\n+chr3L\t7117500\t7122500\tB01434\t-0.04982075\t.\n+chr3L\t7142500\t7147500\tB01439\t-0.049721\t.\n+chr3L\t7302500\t7307500\tB01471\t-0.10379175\t.\n+chr3L\t7367500\t7372500\tB01484\t-0.0351445\t.\n+'..b'9697500\tB22180\t-0.10521125\t.\n+chr3R\t19737500\t19742500\tB22189\t-0.1117525\t.\n+chr3R\t19932500\t19937500\tB22228\t-0.10631075\t.\n+chr3R\t20017500\t20022500\tB22245\t-0.083403\t.\n+chr3R\t20047500\t20052500\tB22251\t-0.0909175\t.\n+chr3R\t20147500\t20152500\tB22271\t-0.0227935\t.\n+chr3R\t20217500\t20222500\tB22285\t-0.034021\t.\n+chr3R\t20332500\t20337500\tB22308\t-0.10360825\t.\n+chr3R\t20372500\t20377500\tB22316\t-0.11469275\t.\n+chr3R\t20452500\t20457500\tB22332\t-0.10752325\t.\n+chr3R\t20612500\t20617500\tB22364\t-0.099168\t.\n+chr3R\t20707500\t20712500\tB22383\t-0.07351875\t.\n+chr3R\t20717500\t20722500\tB22385\t-0.0705095\t.\n+chr3R\t20762500\t20767500\tB22394\t-0.0862985\t.\n+chr3R\t20857500\t20862500\tB22413\t-0.01276525\t.\n+chr3R\t20897500\t20902500\tB22421\t-0.02185325\t.\n+chr3R\t20932500\t20937500\tB22428\t-0.05891975\t.\n+chr3R\t20962500\t20967500\tB22434\t-0.0613935\t.\n+chr3R\t21082500\t21087500\tB22458\t-0.094928\t.\n+chr3R\t21172500\t21177500\tB22476\t-0.0413955\t.\n+chr3R\t21217500\t21222500\tB22485\t-0.05028725\t.\n+chr3R\t21317500\t21322500\tB22505\t-0.086029\t.\n+chr3R\t21332500\t21337500\tB22508\t-0.06100175\t.\n+chr3R\t21387500\t21392500\tB22519\t-0.0656765\t.\n+chr3R\t21472500\t21477500\tB22536\t-0.0932985\t.\n+chr3R\t21612500\t21617500\tB22564\t-0.081974\t.\n+chr3R\t21727500\t21732500\tB22587\t0.07025075\t.\n+chr3R\t21817500\t21822500\tB22605\t-0.00145975\t.\n+chr3R\t21842500\t21847500\tB22610\t0.0360515\t.\n+chr3R\t21947500\t21952500\tB22631\t0.002742\t.\n+chr3R\t21987500\t21992500\tB22639\t0.00713375\t.\n+chr3R\t22072500\t22077500\tB22656\t-0.087915\t.\n+chr3R\t22217500\t22222500\tB22685\t0.0614505\t.\n+chr3R\t22267500\t22272500\tB22695\t-0.02575325\t.\n+chr3R\t22307500\t22312500\tB22703\t-0.04946475\t.\n+chr3R\t22377500\t22382500\tB22717\t-0.055847\t.\n+chr3R\t22497500\t22502500\tB22741\t-0.0631105\t.\n+chr3R\t22517500\t22522500\tB22745\t-0.062648\t.\n+chr3R\t22602500\t22607500\tB22762\t-0.011252\t.\n+chr3R\t22692500\t22697500\tB22780\t-0.089033\t.\n+chr3R\t22777500\t22782500\tB22797\t-0.04050025\t.\n+chr3R\t22882500\t22887500\tB22818\t-0.05683475\t.\n+chr3R\t22982500\t22987500\tB22838\t-0.0237815\t.\n+chr3R\t23107500\t23112500\tB22863\t-0.100625\t.\n+chr3R\t23182500\t23187500\tB22878\t-0.00294725\t.\n+chr3R\t23192500\t23197500\tB22880\t-0.00275775\t.\n+chr3R\t23412500\t23417500\tB22924\t-0.090027\t.\n+chr3R\t23557500\t23562500\tB22953\t-0.104602\t.\n+chr3R\t23767500\t23772500\tB22995\t-0.1119105\t.\n+chr3R\t23812500\t23817500\tB23004\t-0.0660765\t.\n+chr3R\t23917500\t23922500\tB23025\t-0.04218475\t.\n+chr3R\t24027500\t24032500\tB23047\t-0.05579575\t.\n+chr3R\t24157500\t24162500\tB23073\t-0.01546725\t.\n+chr3R\t24202500\t24207500\tB23082\t-0.0326015\t.\n+chr3R\t24342500\t24347500\tB23110\t-0.0623065\t.\n+chr3R\t24372500\t24377500\tB23116\t-0.0749395\t.\n+chr3R\t24447500\t24452500\tB23131\t-0.09836075\t.\n+chr3R\t24622500\t24627500\tB23166\t-0.03171375\t.\n+chr3R\t24742500\t24747500\tB23190\t-0.08589625\t.\n+chr3R\t24882500\t24887500\tB23218\t-0.09323725\t.\n+chr3R\t24992500\t24997500\tB23240\t-0.0589785\t.\n+chr3R\t25087500\t25092500\tB23259\t0.03674225\t.\n+chr3R\t25162500\t25167500\tB23274\t-0.0462465\t.\n+chr3R\t25327500\t25332500\tB23307\t-0.08303325\t.\n+chr3R\t25402500\t25407500\tB23322\t-0.00546225\t.\n+chr3R\t25567500\t25572500\tB23355\t-0.04654075\t.\n+chr3R\t25577500\t25582500\tB23357\t-0.01871575\t.\n+chr3R\t25727500\t25732500\tB23387\t-0.00858875\t.\n+chr3R\t25877500\t25882500\tB23417\t-0.10581625\t.\n+chr3R\t25987500\t25992500\tB23439\t-0.090403\t.\n+chr3R\t26047500\t26052500\tB23451\t-0.0935315\t.\n+chr3R\t26177500\t26182500\tB23477\t-0.11469275\t.\n+chr3R\t26272500\t26277500\tB23496\t-0.1002735\t.\n+chr3R\t26327500\t26332500\tB23507\t-0.092304\t.\n+chr3R\t26487500\t26492500\tB23539\t0.0627965\t.\n+chr3R\t26562500\t26567500\tB23554\t-0.01974475\t.\n+chr3R\t26637500\t26642500\tB23569\t-0.07430725\t.\n+chr3R\t26712500\t26717500\tB23584\t-0.049789\t.\n+chr3R\t26867500\t26872500\tB23615\t-0.0249905\t.\n+chr3R\t27042500\t27047500\tB23650\t-0.074189\t.\n+chr3R\t27152500\t27157500\tB23672\t-0.00609925\t.\n+chr3R\t27182500\t27187500\tB23678\t-0.01281025\t.\n+chr3R\t27247500\t27252500\tB23691\t-0.04990275\t.\n+chr3R\t27382500\t27387500\tB23718\t-0.041305\t.\n+chr3R\t27417500\t27422500\tB23725\t-0.0499295\t.\n+chr3R\t27567500\t27572500\tB23755\t-0.08094325\t.\n+chr3R\t27697500\t27702500\tB23781\t-0.01535\t.\n+chr3R\t27747500\t27752500\tB23791\t0.01357725\t.\n+chr3R\t27767500\t27772500\tB23795\t0.0229625\t.\n'

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_boundaries.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_boundaries.gff Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,1408 @@\n+chr3L\tHiCExplorer\tboundary\t162500\t167500\t-0.10316675\t.\t.\tID=B00043;delta=0.0645107368421;pvalue=0.414620099134;tad_sep=-0.10316675\n+chr3L\tHiCExplorer\tboundary\t257500\t262500\t-0.026655\t.\t.\tID=B00062;delta=0.0383848026316;pvalue=0.674283084976;tad_sep=-0.026655\n+chr3L\tHiCExplorer\tboundary\t332500\t337500\t-0.030848\t.\t.\tID=B00077;delta=0.0331458421053;pvalue=0.748578488932;tad_sep=-0.030848\n+chr3L\tHiCExplorer\tboundary\t357500\t362500\t-0.0580815\t.\t.\tID=B00082;delta=0.0546451184211;pvalue=0.411792655248;tad_sep=-0.0580815\n+chr3L\tHiCExplorer\tboundary\t482500\t487500\t-0.07169775\t.\t.\tID=B00107;delta=0.0361521710526;pvalue=0.503736281368;tad_sep=-0.07169775\n+chr3L\tHiCExplorer\tboundary\t522500\t527500\t-0.1060405\t.\t.\tID=B00115;delta=0.0607123552632;pvalue=0.409780073639;tad_sep=-0.1060405\n+chr3L\tHiCExplorer\tboundary\t677500\t682500\t-0.0148855\t.\t.\tID=B00146;delta=0.131560763158;pvalue=0.100696558537;tad_sep=-0.0148855\n+chr3L\tHiCExplorer\tboundary\t702500\t707500\t0.002784\t.\t.\tID=B00151;delta=0.0290640789474;pvalue=0.0467137020614;tad_sep=0.002784\n+chr3L\tHiCExplorer\tboundary\t737500\t742500\t0.00949975\t.\t.\tID=B00158;delta=0.0521745789474;pvalue=0.489399813333;tad_sep=0.00949975\n+chr3L\tHiCExplorer\tboundary\t867500\t872500\t-0.09546975\t.\t.\tID=B00184;delta=0.0513249605263;pvalue=0.400201394819;tad_sep=-0.09546975\n+chr3L\tHiCExplorer\tboundary\t1007500\t1012500\t-0.05182175\t.\t.\tID=B00212;delta=0.0427919605263;pvalue=0.672733336625;tad_sep=-0.05182175\n+chr3L\tHiCExplorer\tboundary\t1037500\t1042500\t-0.05874875\t.\t.\tID=B00218;delta=0.0230098947368;pvalue=0.755560160507;tad_sep=-0.05874875\n+chr3L\tHiCExplorer\tboundary\t1107500\t1112500\t-0.048349\t.\t.\tID=B00232;delta=0.0230250526316;pvalue=0.888587028967;tad_sep=-0.048349\n+chr3L\tHiCExplorer\tboundary\t1207500\t1212500\t-0.0567565\t.\t.\tID=B00252;delta=0.0157581052632;pvalue=0.800037725246;tad_sep=-0.0567565\n+chr3L\tHiCExplorer\tboundary\t1242500\t1247500\t-0.0641435\t.\t.\tID=B00259;delta=0.0260385921053;pvalue=0.954297852598;tad_sep=-0.0641435\n+chr3L\tHiCExplorer\tboundary\t1297500\t1302500\t-0.091379\t.\t.\tID=B00270;delta=0.0368676315789;pvalue=0.631433509478;tad_sep=-0.091379\n+chr3L\tHiCExplorer\tboundary\t1462500\t1467500\t-0.01307225\t.\t.\tID=B00303;delta=0.0279480657895;pvalue=0.605503787241;tad_sep=-0.01307225\n+chr3L\tHiCExplorer\tboundary\t1532500\t1537500\t-0.08711525\t.\t.\tID=B00317;delta=0.0325782763158;pvalue=0.900898397027;tad_sep=-0.08711525\n+chr3L\tHiCExplorer\tboundary\t1577500\t1582500\t-0.08235875\t.\t.\tID=B00326;delta=0.0138771973684;pvalue=0.819230752873;tad_sep=-0.08235875\n+chr3L\tHiCExplorer\tboundary\t1637500\t1642500\t-0.0628755\t.\t.\tID=B00338;delta=0.0229921710526;pvalue=0.763101258064;tad_sep=-0.0628755\n+chr3L\tHiCExplorer\tboundary\t1667500\t1672500\t-0.037945\t.\t.\tID=B00344;delta=0.0121138026316;pvalue=0.876302477922;tad_sep=-0.037945\n+chr3L\tHiCExplorer\tboundary\t1732500\t1737500\t-0.050313\t.\t.\tID=B00357;delta=0.0373916184211;pvalue=0.699787217442;tad_sep=-0.050313\n+chr3L\tHiCExplorer\tboundary\t1812500\t1817500\t-0.01723525\t.\t.\tID=B00373;delta=0.0390851973684;pvalue=0.524726986549;tad_sep=-0.01723525\n+chr3L\tHiCExplorer\tboundary\t1847500\t1852500\t-0.0259975\t.\t.\tID=B00380;delta=0.0458929868421;pvalue=0.543337134063;tad_sep=-0.0259975\n+chr3L\tHiCExplorer\tboundary\t1922500\t1927500\t8.325e-05\t.\t.\tID=B00395;delta=0.0419640921053;pvalue=0.718745147352;tad_sep=8.325e-05\n+chr3L\tHiCExplorer\tboundary\t2152500\t2157500\t-0.0401965\t.\t.\tID=B00441;delta=0.0494363815789;pvalue=0.876302477922;tad_sep=-0.0401965\n+chr3L\tHiCExplorer\tboundary\t2257500\t2262500\t-0.07518575\t.\t.\tID=B00462;delta=0.0447468026316;pvalue=0.522884086855;tad_sep=-0.07518575\n+chr3L\tHiCExplorer\tboundary\t2387500\t2392500\t-0.072071\t.\t.\tID=B00488;delta=0.0427154736842;pvalue=0.600572469118;tad_sep=-0.072071\n+chr3L\tHiCExplorer\tboundary\t2457500\t2462500\t-0.09132325\t.\t.\tID=B00502;delta=0.0525483815789;pvalue=0.387641292676;tad_sep=-0.09132325\n+chr3L\tHiCExplorer\tboundary\t2557500\t2562500\t-0.09179675\t.\t.\tID=B00522;delta=0.0580647763158;pvalue=0.293724987027;tad_sep=-0.09179675\n+chr3L\tHiCExplorer\tboundary\t2597500\t'..b'ndary\t24882500\t24887500\t-0.09323725\t.\t.\tID=B23218;delta=0.0242850657895;pvalue=0.674283084976;tad_sep=-0.09323725\n+chr3R\tHiCExplorer\tboundary\t24992500\t24997500\t-0.0589785\t.\t.\tID=B23240;delta=0.0611537631579;pvalue=0.597622419247;tad_sep=-0.0589785\n+chr3R\tHiCExplorer\tboundary\t25087500\t25092500\t0.03674225\t.\t.\tID=B23259;delta=0.0342633947368;pvalue=0.98306528394;tad_sep=0.03674225\n+chr3R\tHiCExplorer\tboundary\t25162500\t25167500\t-0.0462465\t.\t.\tID=B23274;delta=0.0399657631579;pvalue=0.294701990791;tad_sep=-0.0462465\n+chr3R\tHiCExplorer\tboundary\t25327500\t25332500\t-0.08303325\t.\t.\tID=B23307;delta=0.0424824078947;pvalue=0.515089010427;tad_sep=-0.08303325\n+chr3R\tHiCExplorer\tboundary\t25402500\t25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diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_domains.bed Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,1403 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diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_score.bedgraph Sat Dec 30 09:19:19 2017 -0500

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_tad_score.bm Sat Dec 30 09:19:19 2017 -0500

diff -r 000000000000 -r 369f6cb43a86 test-data/find_TADs/multiNone_zscore_matrix.h5

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicBuildMatrix_result1.bam

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicCorrectMatrix_result1.npz.h5

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

diff -r 000000000000 -r 369f6cb43a86 test-data/hicCorrelate_heatmap_result1.png

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicCorrelate_scatter_result1.png

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicFindTADs_TAD_score.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindTADs_TAD_score.tabular Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,25261 @@\n+#{"numberOfProcessors":1,"minDepth":20000,"matrix":"matrix.npz.h5","outFileName":"./tadScoreFile.tabular","binsize":5000,"step":100000,"command":"TAD_score","maxDepth":60000,"zscore_matrix":"./tadScoreFile.tabular_zscore_matrix.h5"}\n+chr2RHet\t0\t5000\t0.000000\n+chr2RHet\t5000\t10000\t-0.095120\n+chr2RHet\t10000\t15000\t-0.086382\n+chr2RHet\t15000\t20000\t-0.080500\n+chr2RHet\t20000\t25000\t-0.075802\n+chr2RHet\t25000\t30000\t0.847009\n+chr2RHet\t30000\t35000\t-0.075802\n+chr2RHet\t35000\t40000\t-0.075802\n+chr2RHet\t40000\t45000\t-0.075802\n+chr2RHet\t45000\t50000\t-0.075802\n+chr2RHet\t50000\t55000\t-0.075802\n+chr2RHet\t55000\t60000\t-0.075802\n+chr2RHet\t60000\t65000\t-0.075802\n+chr2RHet\t65000\t70000\t-0.075802\n+chr2RHet\t70000\t75000\t-0.075802\n+chr2RHet\t75000\t80000\t-0.075802\n+chr2RHet\t80000\t85000\t0.580227\n+chr2RHet\t85000\t90000\t0.580227\n+chr2RHet\t90000\t95000\t0.580227\n+chr2RHet\t95000\t100000\t0.339230\n+chr2RHet\t100000\t105000\t0.339230\n+chr2RHet\t105000\t110000\t-0.075802\n+chr2RHet\t110000\t115000\t-0.075802\n+chr2RHet\t115000\t120000\t-0.075802\n+chr2RHet\t120000\t125000\t1.054400\n+chr2RHet\t125000\t130000\t1.054400\n+chr2RHet\t130000\t135000\t-0.075802\n+chr2RHet\t135000\t140000\t-0.075802\n+chr2RHet\t140000\t145000\t0.339230\n+chr2RHet\t145000\t150000\t0.339230\n+chr2RHet\t150000\t155000\t-0.075802\n+chr2RHet\t155000\t160000\t-0.075802\n+chr2RHet\t160000\t165000\t-0.075802\n+chr2RHet\t165000\t170000\t-0.075802\n+chr2RHet\t170000\t175000\t-0.075802\n+chr2RHet\t175000\t180000\t-0.075802\n+chr2RHet\t180000\t185000\t-0.075802\n+chr2RHet\t185000\t190000\t-0.075802\n+chr2RHet\t190000\t195000\t-0.075802\n+chr2RHet\t195000\t200000\t0.328485\n+chr2RHet\t200000\t205000\t1.712156\n+chr2RHet\t205000\t210000\t1.712156\n+chr2RHet\t210000\t215000\t1.712156\n+chr2RHet\t215000\t220000\t1.056126\n+chr2RHet\t220000\t225000\t-0.075802\n+chr2RHet\t225000\t230000\t-0.075802\n+chr2RHet\t230000\t235000\t-0.075802\n+chr2RHet\t235000\t240000\t-0.075802\n+chr2RHet\t240000\t245000\t-0.075802\n+chr2RHet\t245000\t250000\t-0.075802\n+chr2RHet\t250000\t255000\t-0.075802\n+chr2RHet\t255000\t260000\t-0.075802\n+chr2RHet\t260000\t265000\t-0.075802\n+chr2RHet\t265000\t270000\t-0.075802\n+chr2RHet\t270000\t275000\t-0.075802\n+chr2RHet\t275000\t280000\t-0.075802\n+chr2RHet\t280000\t285000\t-0.075802\n+chr2RHet\t285000\t290000\t-0.075802\n+chr2RHet\t290000\t295000\t-0.075802\n+chr2RHet\t295000\t300000\t-0.075802\n+chr2RHet\t300000\t305000\t-0.075802\n+chr2RHet\t305000\t310000\t-0.075802\n+chr2RHet\t310000\t315000\t-0.075802\n+chr2RHet\t315000\t320000\t-0.075802\n+chr2RHet\t320000\t325000\t-0.075802\n+chr2RHet\t325000\t330000\t-0.075802\n+chr2RHet\t330000\t335000\t-0.075802\n+chr2RHet\t335000\t340000\t-0.075802\n+chr2RHet\t340000\t345000\t-0.075802\n+chr2RHet\t345000\t350000\t-0.075802\n+chr2RHet\t350000\t355000\t-0.075802\n+chr2RHet\t355000\t360000\t-0.075802\n+chr2RHet\t360000\t365000\t-0.075802\n+chr2RHet\t365000\t370000\t-0.075802\n+chr2RHet\t370000\t375000\t-0.075802\n+chr2RHet\t375000\t380000\t1.056126\n+chr2RHet\t380000\t385000\t1.056126\n+chr2RHet\t385000\t390000\t1.056126\n+chr2RHet\t390000\t395000\t1.056126\n+chr2RHet\t395000\t400000\t-0.075802\n+chr2RHet\t400000\t405000\t-0.075802\n+chr2RHet\t405000\t410000\t-0.075802\n+chr2RHet\t410000\t415000\t-0.075802\n+chr2RHet\t415000\t420000\t-0.075802\n+chr2RHet\t420000\t425000\t-0.075802\n+chr2RHet\t425000\t430000\t-0.075802\n+chr2RHet\t430000\t435000\t-0.075802\n+chr2RHet\t435000\t440000\t-0.075802\n+chr2RHet\t440000\t445000\t-0.075802\n+chr2RHet\t445000\t450000\t-0.075802\n+chr2RHet\t450000\t455000\t-0.075802\n+chr2RHet\t455000\t460000\t-0.075802\n+chr2RHet\t460000\t465000\t-0.075802\n+chr2RHet\t465000\t470000\t-0.075802\n+chr2RHet\t470000\t475000\t-0.075802\n+chr2RHet\t475000\t480000\t-0.075802\n+chr2RHet\t480000\t485000\t-0.075802\n+chr2RHet\t485000\t490000\t-0.075802\n+chr2RHet\t490000\t495000\t-0.075802\n+chr2RHet\t495000\t500000\t-0.075802\n+chr2RHet\t500000\t505000\t-0.075802\n+chr2RHet\t505000\t510000\t-0.075802\n+chr2RHet\t510000\t515000\t-0.075802\n+chr2RHet\t515000\t520000\t-0.075802\n+chr2RHet\t520000\t525000\t-0.075802\n+chr2RHet\t525000\t530000\t-0.075802\n+chr2RHet\t530000\t535000\t-0.075802\n+chr2RHet\t535000\t540000\t-0.075802\n+chr2RHet\t540000\t545000\t-0.075802\n+chr2RHet\t545000\t550000\t-0.075802\n+chr2RHet\t550000\t555000\t0.848419\n+chr2RHet\t555000\t560000\t1.504449\n+chr'..b'\n+chr3R\t27375000\t27380000\t-0.202334\n+chr3R\t27380000\t27385000\t-0.202334\n+chr3R\t27385000\t27390000\t-0.202334\n+chr3R\t27390000\t27395000\t-0.202334\n+chr3R\t27395000\t27400000\t0.199516\n+chr3R\t27400000\t27405000\t0.726185\n+chr3R\t27405000\t27410000\t1.190531\n+chr3R\t27410000\t27415000\t0.833625\n+chr3R\t27415000\t27420000\t-0.202334\n+chr3R\t27420000\t27425000\t-0.202334\n+chr3R\t27425000\t27430000\t0.368686\n+chr3R\t27430000\t27435000\t0.691346\n+chr3R\t27435000\t27440000\t0.691346\n+chr3R\t27440000\t27445000\t0.430560\n+chr3R\t27445000\t27450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diff -r 000000000000 -r 369f6cb43a86 test-data/hicFindTADs_find_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicFindTADs_find_score.bedgraph Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,25245 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Binary file test-data/hicMergeMatrixBins_result1.npz.h5 has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/hicPlotDistVsCounts_result1.png

Binary file test-data/hicPlotDistVsCounts_result1.png has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/hicPlotDistVsCounts_result2.png

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicPlotTADs_result1.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicPlotTADs_result1.svg Sat Dec 30 09:19:19 2017 -0500

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diff -r 000000000000 -r 369f6cb43a86 test-data/hicSumMatrices_result1.npz.h5

Binary file test-data/hicSumMatrices_result1.npz.h5 has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/li_32-33mb_interactions.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 369f6cb43a86 test-data/li_32mb_interactions.bedgraph
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pca1.bedgraph Sat Dec 30 09:19:19 2017 -0500

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diff -r 000000000000 -r 369f6cb43a86 test-data/pca1.bw

Binary file test-data/pca1.bw has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/pca2.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pca2.bedgraph Sat Dec 30 09:19:19 2017 -0500

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diff -r 000000000000 -r 369f6cb43a86 test-data/pearson_small_50kb.cool

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diff -r 000000000000 -r 369f6cb43a86 test-data/pearson_small_50kb.h5

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diff -r 000000000000 -r 369f6cb43a86 test-data/small_matrix_50kb_pearson_pca1_plot.png

Binary file test-data/small_matrix_50kb_pearson_pca1_plot.png has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_matrix_50kb_pearson_pca1_plot.svg
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diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_R1_unsorted.bam

Binary file test-data/small_test_R1_unsorted.bam has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_R1_unsorted.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_R2_unsorted.bam

Binary file test-data/small_test_R2_unsorted.bam has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_R2_unsorted.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/small_test_R2_unsorted.sam Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,1000 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diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_matrix.h5

Binary file test-data/small_test_matrix.h5 has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_matrix_2.h5

Binary file test-data/small_test_matrix_2.h5 has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_matrix_50kb_res.h5

Binary file test-data/small_test_matrix_50kb_res.h5 has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_matrix_result.bam

Binary file test-data/small_test_matrix_result.bam has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/small_test_matrix_result_sorted.bam

Binary file test-data/small_test_matrix_result_sorted.bam has changed

diff -r 000000000000 -r 369f6cb43a86 test-data/tad_classification.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tad_classification.bed Sat Dec 30 09:19:19 2017 -0500

b'@@ -0,0 +1,2685 @@\n+chr2L\t73103\t94543\tactive\t2\t.\t73103\t94543\t255,255,153\n+chr2L\t94543\t108120\tactive\t4\t.\t94543\t108120\t255,255,153\n+chr2L\t108120\t132269\tactive\t2\t.\t108120\t132269\t255,255,153\n+chr2L\t132269\t143461\tactive\t2\t.\t132269\t143461\t255,255,153\n+chr2L\t143461\t159101\tactive\t2\t.\t143461\t159101\t255,255,153\n+chr2L\t159101\t181297\tinactive\t1\t.\t159101\t181297\t0,0,0\n+chr2L\t181297\t207416\tactive\t4\t.\t181297\t207416\t255,255,153\n+chr2L\t207416\t248687\tactive\t4\t.\t207416\t248687\t255,255,153\n+chr2L\t248687\t271451\tinactive\t1\t.\t248687\t271451\t0,0,0\n+chr2L\t271451\t283072\tactive\t4\t.\t271451\t283072\t255,255,153\n+chr2L\t283072\t294919\tactive\t2\t.\t283072\t294919\t255,255,153\n+chr2L\t294919\t306028\tactive\t4\t.\t294919\t306028\t255,255,153\n+chr2L\t306028\t357775\tinactive\t1\t.\t306028\t357775\t0,0,0\n+chr2L\t357775\t403068\tinactive\t1\t.\t357775\t403068\t0,0,0\n+chr2L\t403068\t421370\tactive\t4\t.\t403068\t421370\t255,255,153\n+chr2L\t421370\t472506\tactive\t2\t.\t421370\t472506\t255,255,153\n+chr2L\t472506\t490303\tactive\t2\t.\t472506\t490303\t255,255,153\n+chr2L\t490303\t541886\tactive\t2\t.\t490303\t541886\t255,255,153\n+chr2L\t541886\t553339\tactive\t2\t.\t541886\t553339\t255,255,153\n+chr2L\t553339\t559789\tactive\t4\t.\t553339\t559789\t255,255,153\n+chr2L\t559789\t574511\tactive\t4\t.\t559789\t574511\t255,255,153\n+chr2L\t574511\t602435\tPcG\t0\t.\t574511\t602435\t56,108,176\n+chr2L\t602435\t810330\tinactive\t1\t.\t602435\t810330\t0,0,0\n+chr2L\t810330\t825970\tactive\t4\t.\t810330\t825970\t255,255,153\n+chr2L\t825970\t853278\tactive\t2\t.\t825970\t853278\t255,255,153\n+chr2L\t853278\t871106\tactive\t2\t.\t853278\t871106\t255,255,153\n+chr2L\t871106\t887664\tactive\t2\t.\t871106\t887664\t255,255,153\n+chr2L\t887664\t1006986\tinactive\t1\t.\t887664\t1006986\t0,0,0\n+chr2L\t1006986\t1077753\tinactive\t1\t.\t1006986\t1077753\t0,0,0\n+chr2L\t1077753\t1102940\tinactive\t1\t.\t1077753\t1102940\t0,0,0\n+chr2L\t1102940\t1108427\tactive\t4\t.\t1102940\t1108427\t255,255,153\n+chr2L\t1108427\t1142854\tactive\t2\t.\t1108427\t1142854\t255,255,153\n+chr2L\t1142854\t1157702\tactive\t4\t.\t1142854\t1157702\t255,255,153\n+chr2L\t1157702\t1185674\tactive\t4\t.\t1157702\t1185674\t255,255,153\n+chr2L\t1185674\t1246112\tinactive\t1\t.\t1185674\t1246112\t0,0,0\n+chr2L\t1246112\t1348267\tinactive\t1\t.\t1246112\t1348267\t0,0,0\n+chr2L\t1348267\t1492300\tinactive\t1\t.\t1348267\t1492300\t0,0,0\n+chr2L\t1492300\t1504156\tinactive\t1\t.\t1492300\t1504156\t0,0,0\n+chr2L\t1504156\t1614536\tinactive\t1\t.\t1504156\t1614536\t0,0,0\n+chr2L\t1614536\t1705229\tPcG\t0\t.\t1614536\t1705229\t56,108,176\n+chr2L\t1705229\t1728747\tactive\t2\t.\t1705229\t1728747\t255,255,153\n+chr2L\t1728747\t1818391\tinactive\t1\t.\t1728747\t1818391\t0,0,0\n+chr2L\t1818391\t1884683\tinactive\t1\t.\t1818391\t1884683\t0,0,0\n+chr2L\t1884683\t1909751\tinactive\t1\t.\t1884683\t1909751\t0,0,0\n+chr2L\t1909751\t1937585\tactive\t2\t.\t1909751\t1937585\t255,255,153\n+chr2L\t1937585\t1974067\tPcG\t0\t.\t1937585\t1974067\t56,108,176\n+chr2L\t1974067\t1987851\tactive\t4\t.\t1974067\t1987851\t255,255,153\n+chr2L\t1987851\t2037530\tinactive\t1\t.\t1987851\t2037530\t0,0,0\n+chr2L\t2037530\t2130843\tinactive\t1\t.\t2037530\t2130843\t0,0,0\n+chr2L\t2130843\t2151583\tactive\t4\t.\t2130843\t2151583\t255,255,153\n+chr2L\t2151583\t2193334\tactive\t2\t.\t2151583\t2193334\t255,255,153\n+chr2L\t2193334\t2216423\tactive\t2\t.\t2193334\t2216423\t255,255,153\n+chr2L\t2216423\t2221910\tactive\t4\t.\t2216423\t2221910\t255,255,153\n+chr2L\t2221910\t2237044\tactive\t4\t.\t2221910\t2237044\t255,255,153\n+chr2L\t2237044\t2362172\tinactive\t1\t.\t2237044\t2362172\t0,0,0\n+chr2L\t2362172\t2383056\tactive\t4\t.\t2362172\t2383056\t255,255,153\n+chr2L\t2383056\t2492696\tinactive\t1\t.\t2383056\t2492696\t0,0,0\n+chr2L\t2492696\t2561589\tinactive\t1\t.\t2492696\t2561589\t0,0,0\n+chr2L\t2561589\t2591551\tactive\t2\t.\t2561589\t2591551\t255,255,153\n+chr2L\t2591551\t2724465\tinactive\t1\t.\t2591551\t2724465\t0,0,0\n+chr2L\t2724465\t2740126\tactive\t2\t.\t2724465\t2740126\t255,255,153\n+chr2L\t2740126\t2750826\tactive\t4\t.\t2740126\t2750826\t255,255,153\n+chr2L\t2750826\t2770137\tactive\t4\t.\t2750826\t2770137\t255,255,153\n+chr2L\t2770137\t2809031\tactive\t2\t.\t2770137\t2809031\t255,255,153\n+chr2L\t2809031\t2855746\tinactive\t1\t.\t2809031\t2855746\t0,0,0\n+chr2L\t2855746\t2874843\tactive\t2\t.\t2855746\t2874843\t255,255,153\n+chr2L\t2874843\t2885455\tactive\t4\t.\t2874843\t2885455\t255,255,153\n+chr2L\t2885455\t2969305\tactive\t2\t.\t2885455\t2969'..b'9171063\t19201498\t255,255,153\n+chrX\t19201498\t19220554\tactive\t2\t.\t19201498\t19220554\t255,255,153\n+chrX\t19220554\t19242911\tinactive\t1\t.\t19220554\t19242911\t0,0,0\n+chrX\t19242911\t19366620\tinactive\t1\t.\t19242911\t19366620\t0,0,0\n+chrX\t19366620\t19374360\tactive\t4\t.\t19366620\t19374360\t255,255,153\n+chrX\t19374360\t19389270\tactive\t4\t.\t19374360\t19389270\t255,255,153\n+chrX\t19389270\t19399952\tactive\t2\t.\t19389270\t19399952\t255,255,153\n+chrX\t19399952\t19416481\tactive\t4\t.\t19399952\t19416481\t255,255,153\n+chrX\t19416481\t19456185\tinactive\t1\t.\t19416481\t19456185\t0,0,0\n+chrX\t19456185\t19473065\tactive\t4\t.\t19456185\t19473065\t255,255,153\n+chrX\t19473065\t19491987\tinactive\t1\t.\t19473065\t19491987\t0,0,0\n+chrX\t19491987\t19507538\tactive\t2\t.\t19491987\t19507538\t255,255,153\n+chrX\t19507538\t19531934\tactive\t4\t.\t19507538\t19531934\t255,255,153\n+chrX\t19531934\t19557899\tactive\t4\t.\t19531934\t19557899\t255,255,153\n+chrX\t19557899\t19577569\tactive\t4\t.\t19557899\t19577569\t255,255,153\n+chrX\t19577569\t19607671\tactive\t4\t.\t19577569\t19607671\t255,255,153\n+chrX\t19607671\t19625150\tinactive\t1\t.\t19607671\t19625150\t0,0,0\n+chrX\t19625150\t19639107\tactive\t2\t.\t19625150\t19639107\t255,255,153\n+chrX\t19639107\t19644907\tactive\t4\t.\t19639107\t19644907\t255,255,153\n+chrX\t19644907\t19657054\tactive\t2\t.\t19644907\t19657054\t255,255,153\n+chrX\t19657054\t19686912\tinactive\t1\t.\t19657054\t19686912\t0,0,0\n+chrX\t19686912\t19745861\tinactive\t1\t.\t19686912\t19745861\t0,0,0\n+chrX\t19745861\t19760530\tactive\t4\t.\t19745861\t19760530\t255,255,153\n+chrX\t19760530\t19815382\tactive\t2\t.\t19760530\t19815382\t255,255,153\n+chrX\t19815382\t19987457\tinactive\t1\t.\t19815382\t19987457\t0,0,0\n+chrX\t19987457\t20054086\tinactive\t1\t.\t19987457\t20054086\t0,0,0\n+chrX\t20054086\t20068910\tactive\t2\t.\t20054086\t20068910\t255,255,153\n+chrX\t20068910\t20125761\tinactive\t1\t.\t20068910\t20125761\t0,0,0\n+chrX\t20125761\t20262048\tinactive\t1\t.\t20125761\t20262048\t0,0,0\n+chrX\t20262048\t20294608\tactive\t4\t.\t20262048\t20294608\t255,255,153\n+chrX\t20294608\t20305771\tactive\t4\t.\t20294608\t20305771\t255,255,153\n+chrX\t20305771\t20339275\tinactive\t1\t.\t20305771\t20339275\t0,0,0\n+chrX\t20339275\t20382809\tactive\t2\t.\t20339275\t20382809\t255,255,153\n+chrX\t20382809\t20395830\tactive\t4\t.\t20382809\t20395830\t255,255,153\n+chrX\t20395830\t20508892\tinactive\t1\t.\t20395830\t20508892\t0,0,0\n+chrX\t20508892\t20526971\tinactive\t1\t.\t20508892\t20526971\t0,0,0\n+chrX\t20526971\t20631727\tinactive\t1\t.\t20526971\t20631727\t0,0,0\n+chrX\t20631727\t20894364\tinactive\t1\t.\t20631727\t20894364\t0,0,0\n+chrX\t20894364\t20907117\tactive\t4\t.\t20894364\t20907117\t255,255,153\n+chrX\t20907117\t20916940\tactive\t4\t.\t20907117\t20916940\t255,255,153\n+chrX\t20916940\t20931445\tactive\t2\t.\t20916940\t20931445\t255,255,153\n+chrX\t20931445\t20944384\tactive\t2\t.\t20931445\t20944384\t255,255,153\n+chrX\t20944384\t20996348\tinactive\t1\t.\t20944384\t20996348\t0,0,0\n+chrX\t20996348\t21012072\tinactive\t1\t.\t20996348\t21012072\t0,0,0\n+chrX\t21012072\t21178100\tinactive\t1\t.\t21012072\t21178100\t0,0,0\n+chrX\t21178100\t21186628\tinactive\t1\t.\t21178100\t21186628\t0,0,0\n+chrX\t21186628\t21194946\tactive\t4\t.\t21186628\t21194946\t255,255,153\n+chrX\t21194946\t21220857\tactive\t4\t.\t21194946\t21220857\t255,255,153\n+chrX\t21220857\t21240098\tactive\t4\t.\t21220857\t21240098\t255,255,153\n+chrX\t21240098\t21271964\tinactive\t1\t.\t21240098\t21271964\t0,0,0\n+chrX\t21271964\t21343699\tinactive\t1\t.\t21271964\t21343699\t0,0,0\n+chrX\t21343699\t21656357\tinactive\t1\t.\t21343699\t21656357\t0,0,0\n+chrX\t21656357\t21857607\tHP1\t3\t.\t21656357\t21857607\t51,160,44\n+chrX\t21857607\t21873688\tactive\t4\t.\t21857607\t21873688\t255,255,153\n+chrX\t21873688\t21889804\tactive\t2\t.\t21873688\t21889804\t255,255,153\n+chrX\t21889804\t21907001\tactive\t4\t.\t21889804\t21907001\t255,255,153\n+chrX\t21907001\t21931844\tinactive\t1\t.\t21907001\t21931844\t0,0,0\n+chrX\t21931844\t21954371\tactive\t2\t.\t21931844\t21954371\t255,255,153\n+chrX\t21954371\t22120033\tinactive\t1\t.\t21954371\t22120033\t0,0,0\n+chrX\t22120033\t22274227\tinactive\t1\t.\t22120033\t22274227\t0,0,0\n+chrX\t22274227\t22287785\tinactive\t1\t.\t22274227\t22287785\t0,0,0\n+chrX\t22287785\t22349277\tinactive\t1\t.\t22287785\t22349277\t0,0,0\n+chrX\t22349277\t22380885\tinactive\t1\t.\t22349277\t22380885\t0,0,0\n+chrX\t22380885\t22421267\tinactive\t1\t.\t22380885\t22421267\t0,0,0\n'

diff -r 000000000000 -r 369f6cb43a86 test-data/tad_score.gz

Binary file test-data/tad_score.gz has changed