Galaxy |

Changeset 2:2bbe234ca6ce (2017-11-02)

Previous changeset 1:2fd2e6382d20 (2017-04-03) Next changeset 3:fd99ba440633 (2017-11-27)

Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251

modified:
hicSumMatrices.xml
macros.xml

removed:
_hicExport._xml
hicFindEnrichedContacts.xml
test-data/hicBuildMatrix_result1.h5
test-data/hicPlotDistVsCounts_result1_.png
test-data/hicPlotMatrix_result1.svg
test-data/tadScoreFile.tabular_zscore_matrix.h5

diff -r 2fd2e6382d20 -r 2bbe234ca6ce _hicExport._xml
--- a/_hicExport._xml Mon Apr 03 07:27:50 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,55 +0,0 @@
-<tool id="hicExport" name="hicExport" version="1.0">
-    <description>saves a HiC Matrix in text format</description>
-    <macros>
-        <token name="@BINARY@">hicExport</token>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command><![CDATA[
-        hicExport
-            #if $matrix and $matrix is not None:
-                --matrix $matrix
-            #end if
-            --outputFormat $outputFormat
-            $clearMaskedBins
-            --outFileName $output
-
-    ]]></command>
-    <inputs>
-        <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" />
-        <param label="Output format" name="outputFormat" type="select"
-            help="There are two possibilities: "dekker" and "ren".
-            The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels.
-            The "ren" format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)">
-            <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option>
-            <option value="ren">Ren (chrom, bin_star, bin_end, values)</option>
-        </param>
-        <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix"
-            help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" />
-    </inputs>
-    <outputs>
-        <data format="txt" name="output"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="matrix" value="hicBuildMatrix_result1.npz"/>
-            <param name="outputFormat" value="dekker"/>
-            <output name="output" file="hicExport_result1.txt" ftpye="txt"/>
-        </test>
-        <test>
-            <param name="matrix" value="hicBuildMatrix_result1.npz"/>
-            <param name="outputFormat" value="ren"/>
-            <param name="clearMaskedBins" value="True"/>
-            <output name="output" file="hicExport_result2.txt" ftpye="txt"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-**What it does**
-
-Saves a HiC Matrix in text format
-
-    ]]></help>
-    <expand macro="citations" />
-</tool>
-

diff -r 2fd2e6382d20 -r 2bbe234ca6ce hicSumMatrices.xml
--- a/hicSumMatrices.xml Mon Apr 03 07:27:50 2017 -0400
+++ b/hicSumMatrices.xml Thu Nov 02 11:13:21 2017 -0400

[

@@ -5,24 +5,21 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
+
         #for $counter, $m in enumerate($matrices):
             ln -s '$m' ${counter}.npz.h5 &&
         #end for

-       #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ])
+        #set $m = '" "'.join([ '%s.npz.h5' % $counter for $counter, $matrix in enumerate($matrices) ])
         hicSumMatrices
             --matrices "$m"
             --outFileName ./out.npz.h5
-
]]>
     </command>
     <inputs>
-
         <param argument="--matrices" type="data" format="h5" multiple="True"
             label="Matrices to combine" help="Needs to have the same shape"/>
-
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>

diff -r 2fd2e6382d20 -r 2bbe234ca6ce macros.xml
--- a/macros.xml Mon Apr 03 07:27:50 2017 -0400
+++ b/macros.xml Thu Nov 02 11:13:21 2017 -0400

@@ -1,24 +1,11 @@
<macros>
-    <xml name="stdio">
-        <stdio>
-            <exit_code range="1:" />
-            <exit_code range=":-1" />
-            <regex match="Error:" />
-            <regex match="Exception:" />
-            <regex match="EXception:" />
-            <regex match="Traceback" />
-        </stdio>
-    </xml>
-
-    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.7.2</token>
+    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
+    <token name="@WRAPPER_VERSION@">1.8</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.7.13">python</requirement>
             <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
             <yield />
         </requirements>
-        <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
     </xml>

@@ -325,7 +312,7 @@

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _help site: https://github.com/fidelram/deepTools/wiki/
+.. _help site: https://hicexplorer.readthedocs.org

     </token>

@@ -537,6 +524,33 @@
         </data>
     </xml>

-
+    <xml name="track_input_h5_macro">
+        <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/>
+    </xml>
+    <xml name="track_input_bed_macro">
+        <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
+    </xml>
+    <xml name="track_input_bedgraph_macro">
+        <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
+    </xml>
+    <xml name="track_input_bigwig_macro">
+        <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
+    </xml>
+    <xml name="track_input_bedgraph_matrix_macro">
+        <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
+    </xml>
+    <xml name="track_input_tabular_macro">
+        <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
+    </xml>
+    <xml name="plot_title">
+        <param name="title" type="text" optional="true" label="Plot title"/>
+    </xml>

+    <xml name="spacer_macro">
+        <param name="spacer_width" type="float" value="" optional="True"
+                label="Include spacer at the end of the track." help="Width of the spacer." />
+    </xml>
+    <xml name="fontsize_macro">
+                    <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+    </xml>
</macros>

diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/bedgraph_chrx_2e6_5e6.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedgraph_chrx_2e6_5e6.bg Thu Nov 02 11:13:21 2017 -0400

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diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/bigwig_chrx_2e6_5e6.bw

Binary file test-data/bigwig_chrx_2e6_5e6.bw has changed

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

@@ -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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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 2fd2e6382d20 -r 2bbe234ca6ce test-data/find_TADs/multiBonferroni_zscore_matrix.h5

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

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

@@ -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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/find_TADs/multiFDR_zscore_matrix.h5

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

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

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 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

b'@@ -0,0 +1,1403 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diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

diff -r 2fd2e6382d20 -r 2bbe234ca6ce 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 Thu Nov 02 11:13:21 2017 -0400

diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/find_TADs/multiNone_zscore_matrix.h5

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

diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/hicBuildMatrix_result1.h5

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diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/hicMergeMatrixBins_result1.npz.h5

Binary file test-data/hicMergeMatrixBins_result1.npz.h5 has changed

diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/hicPlotDistVsCounts_result1_.png

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diff -r 2fd2e6382d20 -r 2bbe234ca6ce test-data/hicPlotMatrix_result1.svg
--- a/test-data/hicPlotMatrix_result1.svg Mon Apr 03 07:27:50 2017 -0400
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