Galaxy |

Changeset 2:ecf11dda45f7 (2017-11-02)

Previous changeset 1:1e0d8c6b3483 (2017-04-03) Next changeset 3:33064489fb8a (2017-11-27)

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

modified:
hicCorrectMatrix.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 1e0d8c6b3483 -r ecf11dda45f7 _hicExport._xml
--- a/_hicExport._xml Mon Apr 03 07:06:43 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 1e0d8c6b3483 -r ecf11dda45f7 hicCorrectMatrix.xml
--- a/hicCorrectMatrix.xml Mon Apr 03 07:06:43 2017 -0400
+++ b/hicCorrectMatrix.xml Thu Nov 02 11:10:27 2017 -0400

[

@@ -5,8 +5,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
+
         ln -s '$matrix' temp_matrix.npz.h5 &&

         hicCorrectMatrix
@@ -50,7 +50,7 @@
                     --xMax $mode.xMax
                 #end if
                 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
-                    --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
+                    --filterThreshold '$mode.filterThreshold_low' '$mode.filterThreshold_large'
                 #end if
             #else:
                 --plotName diagnostic_plot.png
@@ -101,10 +101,12 @@
             </when>
         </conditional>

-        <repeat name="chromosomes" min="1"
+        <repeat name="chromosomes" min="0"
             title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
                     The order of the given chromosomes will be kept for the resulting corrected matrix">
-            <param name="chromosome" type="text" value="" />
+            <param name="chromosome" type="text" value="" >
+                <validator type="empty_field" />
+            </param>
         </repeat>

     </inputs>
@@ -118,7 +120,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
+            <param name="matrix" value="small_test_matrix.h5" ftype="h5"/>
             <param name="mode_selector" value="correct"/>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra"/>
@@ -129,7 +131,7 @@
             <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/>
+            <param name="matrix" ftype="h5" value="small_test_matrix.h5"/>
             <param name="mode_selector" value="diagnostic_plot"/>
             <repeat name="chromosomes">
                 <param name="chromosome" value="chrUextra"/>
@@ -144,18 +146,16 @@

**What it does**

-Runs Dekker's iterative correction over a hic matrix.
+Runs Dekker's iterative correction over a Hi-C matrix.

+correct:         Run the iterative correction.

-    correct        Run the iterative correction.
-    diagnostic_plot
-                   Plots a histogram of the coverage per bin together with the
-                   modified z-score based on the median absolute deviation
-                   method (see Boris Iglewicz and David Hoaglin 1993, Volume
-                   16: How to Detect and Handle Outliers The ASQC Basic
-                   References in Quality Control: Statistical Techniques,
-                   Edward F. Mykytka, Ph.D., Editor.
-
+diagnostic_plot:  Plots a histogram of the coverage per bin together with the
+modified z-score based on the median absolute deviation
+method (see Boris Iglewicz and David Hoaglin 1993, Volume
+16: How to Detect and Handle Outliers The ASQC Basic
+References in Quality Control: Statistical Techniques,
+Edward F. Mykytka, Ph.D., Editor.

]]></help>
     <expand macro="citations" />

diff -r 1e0d8c6b3483 -r ecf11dda45f7 macros.xml
--- a/macros.xml Mon Apr 03 07:06:43 2017 -0400
+++ b/macros.xml Thu Nov 02 11:10:27 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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

b'@@ -0,0 +1,11308 @@\n+chrX\t2000700\t2000750\t1\n+chrX\t2000750\t2000800\t2\n+chrX\t2000800\t2001000\t0\n+chrX\t2001000\t2001100\t1\n+chrX\t2001100\t2001650\t0\n+chrX\t2001650\t2001700\t1\n+chrX\t2001700\t2001750\t2\n+chrX\t2001750\t2001800\t1\n+chrX\t2001800\t2003300\t0\n+chrX\t2003300\t2003350\t5\n+chrX\t2003350\t2003400\t6\n+chrX\t2003400\t2003450\t1\n+chrX\t2003450\t2003500\t0\n+chrX\t2003500\t2003600\t8\n+chrX\t2003600\t2003650\t2\n+chrX\t2003650\t2003750\t0\n+chrX\t2003750\t2003800\t5\n+chrX\t2003800\t2003850\t9\n+chrX\t2003850\t2003900\t8\n+chrX\t2003900\t2003950\t10\n+chrX\t2003950\t2004000\t8\n+chrX\t2004000\t2004050\t7\n+chrX\t2004050\t2004100\t5\n+chrX\t2004100\t2004150\t6\n+chrX\t2004150\t2004200\t7\n+chrX\t2004200\t2004250\t3\n+chrX\t2004250\t2004300\t4\n+chrX\t2004300\t2004400\t8\n+chrX\t2004400\t2004450\t4\n+chrX\t2004450\t2004500\t2\n+chrX\t2004500\t2004550\t3\n+chrX\t2004550\t2004600\t4\n+chrX\t2004600\t2004650\t5\n+chrX\t2004650\t2004700\t4\n+chrX\t2004700\t2004750\t0\n+chrX\t2004750\t2004800\t1\n+chrX\t2004800\t2004850\t3\n+chrX\t2004850\t2004900\t1\n+chrX\t2004900\t2004950\t0\n+chrX\t2004950\t2005000\t1\n+chrX\t2005000\t2005050\t3\n+chrX\t2005050\t2005200\t2\n+chrX\t2005200\t2005250\t0\n+chrX\t2005250\t2005300\t2\n+chrX\t2005300\t2005350\t3\n+chrX\t2005350\t2005400\t5\n+chrX\t2005400\t2005450\t3\n+chrX\t2005450\t2005500\t5\n+chrX\t2005500\t2005550\t7\n+chrX\t2005550\t2005600\t4\n+chrX\t2005600\t2005650\t1\n+chrX\t2005650\t2005700\t2\n+chrX\t2005700\t2005750\t3\n+chrX\t2005750\t2005800\t4\n+chrX\t2005800\t2005850\t6\n+chrX\t2005850\t2005900\t3\n+chrX\t2005900\t2005950\t4\n+chrX\t2005950\t2006000\t2\n+chrX\t2006000\t2006100\t0\n+chrX\t2006100\t2006200\t1\n+chrX\t2006200\t2006250\t4\n+chrX\t2006250\t2006300\t6\n+chrX\t2006300\t2006350\t2\n+chrX\t2006350\t2006400\t1\n+chrX\t2006400\t2006450\t0\n+chrX\t2006450\t2006500\t1\n+chrX\t2006500\t2006550\t0\n+chrX\t2006550\t2006750\t2\n+chrX\t2006750\t2006800\t3\n+chrX\t2006800\t2006850\t2\n+chrX\t2006850\t2006950\t1\n+chrX\t2006950\t2007000\t4\n+chrX\t2007000\t2007050\t3\n+chrX\t2007050\t2007100\t1\n+chrX\t2007100\t2007200\t0\n+chrX\t2007200\t2007450\t1\n+chrX\t2007450\t2007500\t2\n+chrX\t2007500\t2007750\t0\n+chrX\t2007750\t2007850\t1\n+chrX\t2007850\t2008150\t0\n+chrX\t2008150\t2008200\t1\n+chrX\t2008200\t2008500\t0\n+chrX\t2008500\t2008600\t2\n+chrX\t2008600\t2009250\t0\n+chrX\t2009250\t2009300\t1\n+chrX\t2009300\t2009950\t0\n+chrX\t2009950\t2010000\t1\n+chrX\t2010000\t2010050\t2\n+chrX\t2010050\t2010100\t1\n+chrX\t2010100\t2010150\t0\n+chrX\t2010150\t2010200\t2\n+chrX\t2010200\t2010300\t3\n+chrX\t2010300\t2010350\t6\n+chrX\t2010350\t2010400\t7\n+chrX\t2010400\t2010450\t6\n+chrX\t2010450\t2010500\t5\n+chrX\t2010500\t2010550\t3\n+chrX\t2010550\t2010600\t2\n+chrX\t2010600\t2010650\t4\n+chrX\t2010650\t2010750\t1\n+chrX\t2010750\t2010800\t4\n+chrX\t2010800\t2010950\t2\n+chrX\t2010950\t2011050\t3\n+chrX\t2011050\t2011100\t5\n+chrX\t2011100\t2011150\t4\n+chrX\t2011150\t2011200\t3\n+chrX\t2011200\t2011250\t2\n+chrX\t2011250\t2011300\t5\n+chrX\t2011300\t2011350\t7\n+chrX\t2011350\t2011400\t10\n+chrX\t2011400\t2011450\t12\n+chrX\t2011450\t2011550\t8\n+chrX\t2011550\t2011600\t2\n+chrX\t2011600\t2011650\t1\n+chrX\t2011650\t2011700\t0\n+chrX\t2011700\t2011750\t3\n+chrX\t2011750\t2011800\t5\n+chrX\t2011800\t2011850\t1\n+chrX\t2011850\t2011900\t0\n+chrX\t2011900\t2011950\t1\n+chrX\t2011950\t2012050\t3\n+chrX\t2012050\t2012100\t2\n+chrX\t2012100\t2012200\t1\n+chrX\t2012200\t2012250\t0\n+chrX\t2012250\t2012350\t2\n+chrX\t2012350\t2012450\t3\n+chrX\t2012450\t2012500\t6\n+chrX\t2012500\t2012550\t3\n+chrX\t2012550\t2012600\t2\n+chrX\t2012600\t2012650\t4\n+chrX\t2012650\t2012750\t1\n+chrX\t2012750\t2012800\t3\n+chrX\t2012800\t2012850\t5\n+chrX\t2012850\t2012950\t2\n+chrX\t2012950\t2013000\t3\n+chrX\t2013000\t2013050\t5\n+chrX\t2013050\t2013100\t3\n+chrX\t2013100\t2013150\t1\n+chrX\t2013150\t2013200\t6\n+chrX\t2013200\t2013250\t12\n+chrX\t2013250\t2013300\t11\n+chrX\t2013300\t2013350\t3\n+chrX\t2013350\t2013400\t0\n+chrX\t2013400\t2013450\t5\n+chrX\t2013450\t2013500\t6\n+chrX\t2013500\t2013600\t4\n+chrX\t2013600\t2013650\t8\n+chrX\t2013650\t2013700\t5\n+chrX\t2013700\t2013800\t3\n+chrX\t2013800\t2013900\t2\n+chrX\t2013900\t2014000\t3\n+chrX\t2014000\t2014050\t2\n+chrX\t2014050\t2014100\t1\n+chrX\t2014100\t2014150\t3\n+chrX\t2014150\t2014200\t7\n+chrX\t2014200\t2014250\t5\n+chrX\t2014250\t2014300\t4\n+chrX\t2014300\t2014450\t5\n+chrX\t2014450\t2014550\t3\n+chrX\t2014550\t2014650\t5\n+chrX\t2014650\t2014800\t4\n+chrX\t2014800\t2014850\t3\n+chrX\t2014850\t2014900\t0\n+chrX\t2014900\t2014950\t2\n+chrX\t2014950\t2015000\t4\n+chrX\t2015000\t'..b'976600\t4976900\t0\n+chrX\t4976900\t4976950\t3\n+chrX\t4976950\t4977000\t1\n+chrX\t4977000\t4977050\t0\n+chrX\t4977050\t4977150\t1\n+chrX\t4977150\t4977550\t0\n+chrX\t4977550\t4977650\t1\n+chrX\t4977650\t4977800\t0\n+chrX\t4977800\t4977900\t1\n+chrX\t4977900\t4978500\t0\n+chrX\t4978500\t4978550\t2\n+chrX\t4978550\t4978600\t3\n+chrX\t4978600\t4978650\t2\n+chrX\t4978650\t4978700\t0\n+chrX\t4978700\t4978800\t1\n+chrX\t4978800\t4981400\t0\n+chrX\t4981400\t4981600\t1\n+chrX\t4981600\t4983500\t0\n+chrX\t4983500\t4983550\t1\n+chrX\t4983550\t4983850\t0\n+chrX\t4983850\t4983900\t3\n+chrX\t4983900\t4983950\t1\n+chrX\t4983950\t4984650\t0\n+chrX\t4984650\t4984750\t2\n+chrX\t4984750\t4984950\t0\n+chrX\t4984950\t4985050\t1\n+chrX\t4985050\t4990350\t0\n+chrX\t4990350\t4990400\t7\n+chrX\t4990400\t4990450\t18\n+chrX\t4990450\t4990500\t7\n+chrX\t4990500\t4990550\t1\n+chrX\t4990550\t4990600\t2\n+chrX\t4990600\t4990650\t1\n+chrX\t4990650\t4990700\t2\n+chrX\t4990700\t4990750\t4\n+chrX\t4990750\t4990800\t6\n+chrX\t4990800\t4990850\t10\n+chrX\t4990850\t4990900\t12\n+chrX\t4990900\t4990950\t10\n+chrX\t4990950\t4991000\t12\n+chrX\t4991000\t4991050\t6\n+chrX\t4991050\t4991100\t9\n+chrX\t4991100\t4991150\t8\n+chrX\t4991150\t4991200\t14\n+chrX\t4991200\t4991250\t26\n+chrX\t4991250\t4991300\t23\n+chrX\t4991300\t4991350\t10\n+chrX\t4991350\t4991400\t23\n+chrX\t4991400\t4991450\t27\n+chrX\t4991450\t4991500\t10\n+chrX\t4991500\t4991550\t11\n+chrX\t4991550\t4991600\t15\n+chrX\t4991600\t4991700\t13\n+chrX\t4991700\t4991750\t6\n+chrX\t4991750\t4991800\t2\n+chrX\t4991800\t4991850\t5\n+chrX\t4991850\t4991900\t6\n+chrX\t4991900\t4991950\t13\n+chrX\t4991950\t4992000\t6\n+chrX\t4992000\t4992050\t26\n+chrX\t4992050\t4992100\t27\n+chrX\t4992100\t4992150\t5\n+chrX\t4992150\t4992200\t8\n+chrX\t4992200\t4992250\t7\n+chrX\t4992250\t4992300\t2\n+chrX\t4992300\t4992350\t0\n+chrX\t4992350\t4992400\t5\n+chrX\t4992400\t4992450\t6\n+chrX\t4992450\t4992500\t4\n+chrX\t4992500\t4992550\t8\n+chrX\t4992550\t4992750\t4\n+chrX\t4992750\t4992800\t10\n+chrX\t4992800\t4992850\t15\n+chrX\t4992850\t4992900\t7\n+chrX\t4992900\t4992950\t2\n+chrX\t4992950\t4993000\t4\n+chrX\t4993000\t4993050\t5\n+chrX\t4993050\t4993100\t11\n+chrX\t4993100\t4993150\t10\n+chrX\t4993150\t4993200\t6\n+chrX\t4993200\t4993250\t10\n+chrX\t4993250\t4993300\t14\n+chrX\t4993300\t4993350\t13\n+chrX\t4993350\t4993400\t19\n+chrX\t4993400\t4993450\t14\n+chrX\t4993450\t4993500\t7\n+chrX\t4993500\t4993550\t5\n+chrX\t4993550\t4993600\t10\n+chrX\t4993600\t4993650\t18\n+chrX\t4993650\t4993700\t11\n+chrX\t4993700\t4993750\t18\n+chrX\t4993750\t4993800\t15\n+chrX\t4993800\t4993850\t10\n+chrX\t4993850\t4993900\t12\n+chrX\t4993900\t4993950\t11\n+chrX\t4993950\t4994000\t13\n+chrX\t4994000\t4994050\t12\n+chrX\t4994050\t4994100\t14\n+chrX\t4994100\t4994150\t19\n+chrX\t4994150\t4994200\t12\n+chrX\t4994200\t4994250\t1\n+chrX\t4994250\t4994300\t2\n+chrX\t4994300\t4994350\t6\n+chrX\t4994350\t4994400\t15\n+chrX\t4994400\t4994450\t13\n+chrX\t4994450\t4994500\t8\n+chrX\t4994500\t4994550\t10\n+chrX\t4994550\t4994600\t14\n+chrX\t4994600\t4994650\t11\n+chrX\t4994650\t4994700\t13\n+chrX\t4994700\t4994750\t15\n+chrX\t4994750\t4994800\t6\n+chrX\t4994800\t4994850\t5\n+chrX\t4994850\t4994950\t4\n+chrX\t4994950\t4995000\t7\n+chrX\t4995000\t4995050\t5\n+chrX\t4995050\t4995100\t7\n+chrX\t4995100\t4995150\t8\n+chrX\t4995150\t4995200\t10\n+chrX\t4995200\t4995250\t14\n+chrX\t4995250\t4995350\t4\n+chrX\t4995350\t4995400\t3\n+chrX\t4995400\t4995450\t8\n+chrX\t4995450\t4995500\t5\n+chrX\t4995500\t4995550\t16\n+chrX\t4995550\t4995600\t13\n+chrX\t4995600\t4995650\t9\n+chrX\t4995650\t4995700\t19\n+chrX\t4995700\t4995750\t30\n+chrX\t4995750\t4995800\t16\n+chrX\t4995800\t4995850\t18\n+chrX\t4995850\t4995900\t15\n+chrX\t4995900\t4995950\t9\n+chrX\t4995950\t4996000\t11\n+chrX\t4996000\t4996050\t13\n+chrX\t4996050\t4996100\t6\n+chrX\t4996100\t4996150\t4\n+chrX\t4996150\t4996250\t10\n+chrX\t4996250\t4996350\t5\n+chrX\t4996350\t4996400\t14\n+chrX\t4996400\t4996450\t12\n+chrX\t4996450\t4996500\t10\n+chrX\t4996500\t4996550\t12\n+chrX\t4996550\t4996600\t9\n+chrX\t4996600\t4996650\t6\n+chrX\t4996650\t4996750\t5\n+chrX\t4996750\t4996800\t7\n+chrX\t4996800\t4996850\t11\n+chrX\t4996850\t4996950\t13\n+chrX\t4996950\t4997000\t5\n+chrX\t4997000\t4997050\t3\n+chrX\t4997050\t4997100\t8\n+chrX\t4997100\t4997150\t9\n+chrX\t4997150\t4997200\t12\n+chrX\t4997200\t4997250\t11\n+chrX\t4997250\t4997350\t2\n+chrX\t4997350\t4997400\t1\n+chrX\t4997400\t4997450\t4\n+chrX\t4997450\t4997500\t12\n+chrX\t4997500\t4997550\t22\n+chrX\t4997550\t4997600\t12\n+chrX\t4997600\t4997700\t4\n+chrX\t4997700\t4997750\t6\n+chrX\t4997750\t4997900\t3\n'

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/bigwig_chrx_2e6_5e6.bw

Binary file test-data/bigwig_chrx_2e6_5e6.bw has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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\t0.044329\n+chr3R\t27655000\t27660000\t0.221172\t0.157286\t0.039477\t0.057272\n+chr3R\t27660000\t27665000\t0.169178\t0.121746\t0.039477\t0.055596\n+chr3R\t27665000\t27670000\t0.105701\t0.086040\t0.038175\t0.075533\n+chr3R\t27670000\t27675000\t0.056946\t0.097388\t0.030236\t0.070651\n+chr3R\t27675000\t27680000\t0.056946\t0.068141\t0.017238\t0.048082\n+chr3R\t27680000\t27685000\t-0.038675\t0.079148\t0.007562\t0.042964\n+chr3R\t27685000\t27690000\t-0.044280\t0.033373\t0.024916\t0.048539\n+chr3R\t27690000\t27695000\t-0.044280\t0.033373\t0.024916\t0.048539\n+chr3R\t27695000\t27700000\t-0.044280\t0.033373\t0.062620\t0.048539\n+chr3R\t27700000\t27705000\t-0.084029\t-0.053780\t0.048357\t0.028052\n+chr3R\t27705000\t27710000\t-0.084029\t-0.053780\t0.048357\t0.028052\n+chr3R\t27710000\t27715000\t-0.045339\t-0.025686\t0.058030\t0.019198\n+chr3R\t27715000\t27720000\t-0.045339\t-0.025686\t0.076979\t0.019198\n+chr3R\t27720000\t27725000\t-0.045339\t-0.025686\t0.076979\t0.019198\n+chr3R\t27725000\t27730000\t-0.103607\t0.016512\t0.033564\t0.019198\n+chr3R\t27730000\t27735000\t-0.050204\t0.046552\t0.068839\t0.039696\n+chr3R\t27735000\t27740000\t0.046239\t0.185635\t0.092949\t0.064425\n+chr3R\t27740000\t27745000\t0.007548\t0.121674\t0.083277\t0.059309\n+chr3R\t27745000\t27750000\t0.007548\t0.001158\t0.083277\t0.063163\n+chr3R\t27750000\t27755000\t-0.026993\t-0.060469\t0.078472\t0.063299\n+chr3R\t27755000\t27760000\t-0.026993\t-0.017832\t0.078472\t0.067620\n+chr3R\t27760000\t27765000\t-0.001206\t-0.003327\t0.070352\t0.067393\n+chr3R\t27765000\t27770000\t0.037229\t-0.024344\t0.098718\t0.089941\n+chr3R\t27770000\t27775000\t-0.027695\t-0.060863\t0.099720\t0.080688\n+chr3R\t27775000\t27780000\t-0.027695\t-0.060863\t0.164400\t0.086511\n+chr3R\t27780000\t27785000\t-0.027695\t-0.060863\t0.145646\t0.092831\n+chr3R\t27785000\t27790000\t-0.027695\t-0.060863\t0.106650\t0.099734\n+chr3R\t27790000\t27795000\t0.039961\t0.063357\t0.089896\t0.104915\n+chr3R\t27795000\t27800000\t0.021098\t0.084764\t0.107981\t0.120654\n+chr3R\t27800000\t27805000\t-0.037165\t0.094196\t0.100334\t0.117915\n+chr3R\t27805000\t27810000\t-0.027092\t0.130175\t0.075438\t0.125259\n+chr3R\t27810000\t27815000\t0.108330\t0.137264\t0.087805\t0.138864\n+chr3R\t27815000\t27820000\t0.213050\t0.158958\t0.113384\t0.126028\n+chr3R\t27820000\t27825000\t0.278008\t0.153292\t0.121643\t0.135627\n+chr3R\t27825000\t27830000\t0.222549\t0.164302\t0.142172\t0.154614\n+chr3R\t27830000\t27835000\t0.153621\t0.136752\t0.157731\t0.170551\n+chr3R\t27835000\t27840000\t0.189472\t0.176743\t0.191033\t0.149134\n+chr3R\t27840000\t27845000\t0.140679\t0.164483\t0.190586\t0.151061\n+chr3R\t27845000\t27850000\t0.140679\t0.130683\t0.214692\t0.171213\n+chr3R\t27850000\t27855000\t0.223557\t0.140759\t0.273233\t0.176608\n+chr3R\t27855000\t27860000\t0.189488\t0.166013\t0.211109\t0.203789\n+chr3R\t27860000\t27865000\t0.090674\t0.097172\t0.179576\t0.188729\n+chr3R\t27865000\t27870000\t0.060550\t0.141907\t0.227388\t0.233385\n+chr3R\t27870000\t27875000\t-0.035456\t0.017860\t0.044535\t0.107397\n+chr3R\t27875000\t27880000\t-0.107824\t-0.110119\t-0.030346\t0.069037\n+chr3R\t27880000\t27885000\t-0.162785\t-0.151946\t-0.133607\t0.016560\n+chr3R\t27885000\t27890000\t-0.166657\t-0.155451\t-0.136374\t0.048640\n+chr3R\t27890000\t27895000\t-0.171304\t-0.159528\t-0.139673\t0.103330\n+chr3R\t27895000\t27900000\t-0.177135\t-0.164497\t-0.143549\t-0.128057\n+chr3R\t27900000\t27905000\t-0.184873\t-0.170507\t-0.148271\t-0.131426\n+chr3R\t27905000\t27905053\t0.000000\t0.000000\t0.000000\t0.000000\n+chrUextra\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chrUextra\t29000000\t29004656\t0.000000\t0.000000\t0.000000\t0.000000\n+chrM\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chrM\t15000\t19517\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3LHet\t0\t5000\t0.000000\t0.000000\t0.000000\t0.000000\n+chr3LHet\t2555000\t2555491\t0.000000\t0.000000\t0.000000\t0.000000\n'

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_zscore_matrix.h5

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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-0.159737358616\n+chr3L\t7500\t12500\t-0.155082487586\n+chr3L\t12500\t17500\t-0.151168327942\n+chr3L\t17500\t22500\t-0.147873215842\n+chr3L\t22500\t27500\t-0.144772772067\n+chr3L\t27500\t32500\t-0.141868972264\n+chr3L\t32500\t37500\t-0.139208396548\n+chr3L\t37500\t42500\t-0.136695519504\n+chr3L\t42500\t47500\t-0.13435784673\n+chr3L\t47500\t52500\t-0.132198322928\n+chr3L\t52500\t57500\t-0.130138647123\n+chr3L\t57500\t62500\t-0.094024059437\n+chr3L\t62500\t67500\t-0.0764270277659\n+chr3L\t67500\t72500\t-0.0418312780272\n+chr3L\t72500\t77500\t0.0197073538633\n+chr3L\t77500\t82500\t0.0705286553822\n+chr3L\t82500\t87500\t0.0728398203412\n+chr3L\t87500\t92500\t0.0704550755289\n+chr3L\t92500\t97500\t0.0683612984106\n+chr3L\t97500\t102500\t0.0699935523517\n+chr3L\t102500\t107500\t0.0683284920538\n+chr3L\t107500\t112500\t0.0668530433483\n+chr3L\t112500\t117500\t0.0655400239401\n+chr3L\t117500\t122500\t0.0643615010968\n+chr3L\t122500\t127500\t0.00960322899463\n+chr3L\t127500\t132500\t0.0122848570996\n+chr3L\t132500\t137500\t-0.00142777411793\n+chr3L\t137500\t142500\t-0.0603620960568\n+chr3L\t142500\t147500\t-0.0515625340117\n+chr3L\t147500\t152500\t-0.05521871309\n+chr3L\t152500\t157500\t-0.0666038885164\n+chr3L\t157500\t162500\t-0.0700877787653\n+chr3L\t162500\t167500\t-0.103166582026\n+chr3L\t167500\t172500\t-0.103166582026\n+chr3L\t172500\t177500\t-0.103166582026\n+chr3L\t177500\t182500\t-0.0892268305271\n+chr3L\t182500\t187500\t-0.0778912906571\n+chr3L\t187500\t192500\t-0.0547473455607\n+chr3L\t192500\t197500\t-0.0624074978774\n+chr3L\t197500\t202500\t-0.0402670995717\n+chr3L\t202500\t207500\t-0.0180889610265\n+chr3L\t207500\t212500\t-0.0180889610265\n+chr3L\t212500\t217500\t-0.0180889610265\n+chr3L\t217500\t222500\t0.0190634988953\n+chr3L\t222500\t227500\t0.0112223886772\n+chr3L\t227500\t232500\t-0.00338415767042\n+chr3L\t232500\t237500\t0.0186707022549\n+chr3L\t237500\t242500\t0.0157587330805\n+chr3L\t242500\t247500\t0.0157587330805\n+chr3L\t247500\t252500\t-0.00807602631835\n+chr3L\t252500\t257500\t-0.0104750989089\n+chr3L\t257500\t262500\t-0.0266548620056\n+chr3L\t262500\t267500\t-0.0146100294292\n+chr3L\t267500\t272500\t-0.0173923184009\n+chr3L\t272500\t277500\t0.00661604790157\n+chr3L\t277500\t282500\t0.0262671919612\n+chr3L\t282500\t287500\t0.0267167034717\n+chr3L\t287500\t292500\t0.0443137229877\n+chr3L\t292500\t297500\t0.0751279690126\n+chr3L\t297500\t302500\t0.0517535485658\n+chr3L\t302500\t307500\t0.0349828408048\n+chr3L\t307500\t312500\t0.0428087068076\n+chr3L\t312500\t317500\t-0.00566065878864\n+chr3L\t317500\t322500\t-0.00566065878864\n+chr3L\t322500\t327500\t-0.0169961986586\n+chr3L\t327500\t332500\t0.000157299660421\n+chr3L\t332500\t337500\t-0.0308482500837\n+chr3L\t337500\t342500\t-0.0226411965829\n+chr3L\t342500\t347500\t-0.0160718960842\n+chr3L\t347500\t352500\t-0.0300379106017\n+chr3L\t352500\t357500\t-0.0029144271306\n+chr3L\t357500\t362500\t-0.0580815967953\n+chr3L\t362500\t367500\t-0.0423382381668\n+chr3L\t367500\t372500\t-0.0243196018461\n+chr3L\t372500\t377500\t-0.0233236395501\n+chr3L\t377500\t382500\t0.0166536103463\n+chr3L\t382500\t387500\t0.0166536103463\n+chr3L\t387500\t392500\t0.0301338406883\n+chr3L\t392500\t397500\t0.019663316174\n+chr3L\t397500\t402500\t0.0270557022414\n+chr3L\t402500\t407500\t0.0371528801145\n+chr3L\t407500\t412500\t0.0321503361064\n+chr3L\t412500\t417500\t0.0071021124075\n+chr3L\t417500\t422500\t0.015319291476\n+chr3L\t422500\t427500\t0.0494427478616\n+chr3L\t427500\t432500\t0.0173949964846\n+chr3L\t432500\t437500\t0.0233486050163\n+chr3L\t437500\t442500\t0.0109350346776\n+chr3L\t442500\t447500\t0.0152410366959\n+chr3L\t447500\t452500\t-0.00172733084048\n+chr3L\t452500\t457500\t-0.00621496545075\n+chr3L\t457500\t462500\t-0.0121685739825\n+chr3L\t462500\t467500\t-0.00424252683144\n+chr3L\t467500\t472500\t0.000837611009745\n+chr3L\t472500\t477500\t-0.020134598244\n+chr3L\t477500\t482500\t-0.0582660019386\n+chr3L\t482500\t487500\t-0.0716979304628\n+chr3L\t487500\t492500\t-0.046010910774\n+chr3L\t492500\t497500\t-0.0233382831898\n+chr3L\t497500\t502500\t-0.00838723736395\n+chr3L\t502500\t507500\t-0.064184454726\n+chr3L\t507500\t512500\t-0.0674580254141\n+chr3L\t512500\t517500\t-0.0674580254141\n+chr3L\t517500\t522500\t-0.0992'..b'7432500\t-0.0366556086444\n+chr3R\t27432500\t27437500\t-0.0366556086444\n+chr3R\t27437500\t27442500\t-0.0474877411784\n+chr3R\t27442500\t27447500\t-0.0551103667922\n+chr3R\t27447500\t27452500\t-0.0573623591363\n+chr3R\t27452500\t27457500\t-0.0233204047703\n+chr3R\t27457500\t27462500\t-0.00202637276643\n+chr3R\t27462500\t27467500\t0.0250198151374\n+chr3R\t27467500\t27472500\t0.0363309617631\n+chr3R\t27472500\t27477500\t0.0363309617631\n+chr3R\t27477500\t27482500\t0.0363309617631\n+chr3R\t27482500\t27487500\t0.0672663093487\n+chr3R\t27487500\t27492500\t0.0672663093487\n+chr3R\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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_zscore_matrix.h5

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 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\t25407500\t-0.00546225\t.\t.\tID=B23322;delta=0.0185628552632;pvalue=0.846835522646;tad_sep=-0.00546225\n+chr3R\tHiCExplorer\tboundary\t25567500\t25572500\t-0.04654075\t.\t.\tID=B23355;delta=0.0566089736842;pvalue=0.576192906383;tad_sep=-0.04654075\n+chr3R\tHiCExplorer\tboundary\t25577500\t25582500\t-0.01871575\t.\t.\tID=B23357;delta=0.0281310394737;pvalue=0.314699364851;tad_sep=-0.01871575\n+chr3R\tHiCExplorer\tboundary\t25727500\t25732500\t-0.00858875\t.\t.\tID=B23387;delta=0.0986943815789;pvalue=0.112031426493;tad_sep=-0.00858875\n+chr3R\tHiCExplorer\tboundary\t25877500\t25882500\t-0.10581625\t.\t.\tID=B23417;delta=0.0288810657895;pvalue=0.48806712443;tad_sep=-0.10581625\n+chr3R\tHiCExplorer\tboundary\t25987500\t25992500\t-0.090403\t.\t.\tID=B23439;delta=0.0182022894737;pvalue=0.952043612098;tad_sep=-0.090403\n+chr3R\tHiCExplorer\tboundary\t26047500\t26052500\t-0.0935315\t.\t.\tID=B23451;delta=0.0351577631579;pvalue=0.420309304718;tad_sep=-0.0935315\n+chr3R\tHiCExplorer\tboundary\t26177500\t26182500\t-0.11469275\t.\t.\tID=B23477;delta=0.0468813947368;pvalue=0.407773352255;tad_sep=-0.11469275\n+chr3R\tHiCExplorer\tboundary\t26272500\t26277500\t-0.1002735\t.\t.\tID=B23496;delta=0.0265311973684;pvalue=0.866273462912;tad_sep=-0.1002735\n+chr3R\tHiCExplorer\tboundary\t26327500\t26332500\t-0.092304\t.\t.\tID=B23507;delta=0.0340349736842;pvalue=0.801678295331;tad_sep=-0.092304\n+chr3R\tHiCExplorer\tboundary\t26487500\t26492500\t0.0627965\t.\t.\tID=B23539;delta=0.0261305394737;pvalue=0.917163037297;tad_sep=0.0627965\n+chr3R\tHiCExplorer\tboundary\t26562500\t26567500\t-0.01974475\t.\t.\tID=B23554;delta=0.0717252631579;pvalue=0.774996850942;tad_sep=-0.01974475\n+chr3R\tHiCExplorer\tboundary\t26637500\t26642500\t-0.07430725\t.\t.\tID=B23569;delta=0.0364784868421;pvalue=0.687771555077;tad_sep=-0.07430725\n+chr3R\tHiCExplorer\tboundary\t26712500\t26717500\t-0.049789\t.\t.\tID=B23584;delta=0.0413630789474;pvalue=0.926151939522;tad_sep=-0.049789\n+chr3R\tHiCExplorer\tboundary\t26867500\t26872500\t-0.0249905\t.\t.\tID=B23615;delta=0.0878640789474;pvalue=0.360644376149;tad_sep=-0.0249905\n+chr3R\tHiCExplorer\tboundary\t27042500\t27047500\t-0.074189\t.\t.\tID=B23650;delta=0.0714735131579;pvalue=0.596640534697;tad_sep=-0.074189\n+chr3R\tHiCExplorer\tboundary\t27152500\t27157500\t-0.00609925\t.\t.\tID=B23672;delta=0.0508306842105;pvalue=0.667062852012;tad_sep=-0.00609925\n+chr3R\tHiCExplorer\tboundary\t27182500\t27187500\t-0.01281025\t.\t.\tID=B23678;delta=0.0210053815789;pvalue=0.481433141582;tad_sep=-0.01281025\n+chr3R\tHiCExplorer\tboundary\t27247500\t27252500\t-0.04990275\t.\t.\tID=B23691;delta=0.0377629210526;pvalue=0.746434392485;tad_sep=-0.04990275\n+chr3R\tHiCExplorer\tboundary\t27382500\t27387500\t-0.041305\t.\t.\tID=B23718;delta=0.0604152368421;pvalue=0.443941047643;tad_sep=-0.041305\n+chr3R\tHiCExplorer\tboundary\t27417500\t27422500\t-0.0499295\t.\t.\tID=B23725;delta=0.040293;pvalue=0.772288553997;tad_sep=-0.0499295\n+chr3R\tHiCExplorer\tboundary\t27567500\t27572500\t-0.08094325\t.\t.\tID=B23755;delta=0.0899101052632;pvalue=0.377997904893;tad_sep=-0.08094325\n+chr3R\tHiCExplorer\tboundary\t27697500\t27702500\t-0.01535\t.\t.\tID=B23781;delta=0.0567128421053;pvalue=0.546627372724;tad_sep=-0.01535\n+chr3R\tHiCExplorer\tboundary\t27747500\t27752500\t0.01357725\t.\t.\tID=B23791;delta=0.0162098684211;pvalue=0.746434392485;tad_sep=0.01357725\n+chr3R\tHiCExplorer\tboundary\t27767500\t27772500\t0.0229625\t.\t.\tID=B23795;delta=0.0310075921053;pvalue=0.767420623706;tad_sep=0.0229625\n'

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

b'@@ -0,0 +1,1403 @@\n+chr3L\t165000\t260000\tID_0.01_1\t-0.10316675\t.\t165000\t260000\t31,120,180\n+chr3L\t260000\t335000\tID_0.01_2\t-0.026655\t.\t260000\t335000\t51,160,44\n+chr3L\t335000\t360000\tID_0.01_3\t-0.030848\t.\t335000\t360000\t31,120,180\n+chr3L\t360000\t485000\tID_0.01_4\t-0.0580815\t.\t360000\t485000\t51,160,44\n+chr3L\t485000\t525000\tID_0.01_5\t-0.07169775\t.\t485000\t525000\t31,120,180\n+chr3L\t525000\t680000\tID_0.01_6\t-0.1060405\t.\t525000\t680000\t51,160,44\n+chr3L\t680000\t705000\tID_0.01_7\t-0.0148855\t.\t680000\t705000\t31,120,180\n+chr3L\t705000\t740000\tID_0.01_8\t0.002784\t.\t705000\t740000\t51,160,44\n+chr3L\t740000\t870000\tID_0.01_9\t0.00949975\t.\t740000\t870000\t31,120,180\n+chr3L\t870000\t1010000\tID_0.01_10\t-0.09546975\t.\t870000\t1010000\t51,160,44\n+chr3L\t1010000\t1040000\tID_0.01_11\t-0.05182175\t.\t1010000\t1040000\t31,120,180\n+chr3L\t1040000\t1110000\tID_0.01_12\t-0.05874875\t.\t1040000\t1110000\t51,160,44\n+chr3L\t1110000\t1210000\tID_0.01_13\t-0.048349\t.\t1110000\t1210000\t31,120,180\n+chr3L\t1210000\t1245000\tID_0.01_14\t-0.0567565\t.\t1210000\t1245000\t51,160,44\n+chr3L\t1245000\t1300000\tID_0.01_15\t-0.0641435\t.\t1245000\t1300000\t31,120,180\n+chr3L\t1300000\t1465000\tID_0.01_16\t-0.091379\t.\t1300000\t1465000\t51,160,44\n+chr3L\t1465000\t1535000\tID_0.01_17\t-0.01307225\t.\t1465000\t1535000\t31,120,180\n+chr3L\t1535000\t1580000\tID_0.01_18\t-0.08711525\t.\t1535000\t1580000\t51,160,44\n+chr3L\t1580000\t1640000\tID_0.01_19\t-0.08235875\t.\t1580000\t1640000\t31,120,180\n+chr3L\t1640000\t1670000\tID_0.01_20\t-0.0628755\t.\t1640000\t1670000\t51,160,44\n+chr3L\t1670000\t1735000\tID_0.01_21\t-0.037945\t.\t1670000\t1735000\t31,120,180\n+chr3L\t1735000\t1815000\tID_0.01_22\t-0.050313\t.\t1735000\t1815000\t51,160,44\n+chr3L\t1815000\t1850000\tID_0.01_23\t-0.01723525\t.\t1815000\t1850000\t31,120,180\n+chr3L\t1850000\t1925000\tID_0.01_24\t-0.0259975\t.\t1850000\t1925000\t51,160,44\n+chr3L\t1925000\t2155000\tID_0.01_25\t8.325e-05\t.\t1925000\t2155000\t31,120,180\n+chr3L\t2155000\t2260000\tID_0.01_26\t-0.0401965\t.\t2155000\t2260000\t51,160,44\n+chr3L\t2260000\t2390000\tID_0.01_27\t-0.07518575\t.\t2260000\t2390000\t31,120,180\n+chr3L\t2390000\t2460000\tID_0.01_28\t-0.072071\t.\t2390000\t2460000\t51,160,44\n+chr3L\t2460000\t2560000\tID_0.01_29\t-0.09132325\t.\t2460000\t2560000\t31,120,180\n+chr3L\t2560000\t2600000\tID_0.01_30\t-0.09179675\t.\t2560000\t2600000\t51,160,44\n+chr3L\t2600000\t2740000\tID_0.01_31\t-0.0934855\t.\t2600000\t2740000\t31,120,180\n+chr3L\t2740000\t2885000\tID_0.01_32\t-0.08927875\t.\t2740000\t2885000\t51,160,44\n+chr3L\t2885000\t2945000\tID_0.01_33\t-0.08972575\t.\t2885000\t2945000\t31,120,180\n+chr3L\t2945000\t2960000\tID_0.01_34\t0.029899\t.\t2945000\t2960000\t51,160,44\n+chr3L\t2960000\t3045000\tID_0.01_35\t0.0356865\t.\t2960000\t3045000\t31,120,180\n+chr3L\t3045000\t3135000\tID_0.01_36\t-0.00466875\t.\t3045000\t3135000\t51,160,44\n+chr3L\t3135000\t3220000\tID_0.01_37\t0.055702\t.\t3135000\t3220000\t31,120,180\n+chr3L\t3220000\t3255000\tID_0.01_38\t-0.059463\t.\t3220000\t3255000\t51,160,44\n+chr3L\t3255000\t3315000\tID_0.01_39\t-0.045796\t.\t3255000\t3315000\t31,120,180\n+chr3L\t3315000\t3345000\tID_0.01_40\t-0.05499875\t.\t3315000\t3345000\t51,160,44\n+chr3L\t3345000\t3475000\tID_0.01_41\t-0.04234075\t.\t3345000\t3475000\t31,120,180\n+chr3L\t3475000\t3515000\tID_0.01_42\t-0.05097675\t.\t3475000\t3515000\t51,160,44\n+chr3L\t3515000\t3545000\tID_0.01_43\t-0.012488\t.\t3515000\t3545000\t31,120,180\n+chr3L\t3545000\t3615000\tID_0.01_44\t0.02457925\t.\t3545000\t3615000\t51,160,44\n+chr3L\t3615000\t3670000\tID_0.01_45\t0.019683\t.\t3615000\t3670000\t31,120,180\n+chr3L\t3670000\t3765000\tID_0.01_46\t0.09945325\t.\t3670000\t3765000\t51,160,44\n+chr3L\t3765000\t3785000\tID_0.01_47\t-0.047454\t.\t3765000\t3785000\t31,120,180\n+chr3L\t3785000\t3825000\tID_0.01_48\t-0.041084\t.\t3785000\t3825000\t51,160,44\n+chr3L\t3825000\t3900000\tID_0.01_49\t-0.06101175\t.\t3825000\t3900000\t31,120,180\n+chr3L\t3900000\t4000000\tID_0.01_50\t-0.0684535\t.\t3900000\t4000000\t51,160,44\n+chr3L\t4000000\t4120000\tID_0.01_51\t-0.03007875\t.\t4000000\t4120000\t31,120,180\n+chr3L\t4120000\t4165000\tID_0.01_52\t-0.0807515\t.\t4120000\t4165000\t51,160,44\n+chr3L\t4165000\t4200000\tID_0.01_53\t-0.088488\t.\t4165000\t4200000\t31,120,180\n+chr3L\t4200000\t4220000\tID_0.01_54\t-0.098724\t.\t4200000\t4220000\t51,160,44\n+chr3L\t4220000\t4270000\tID_0.01_55\t-0.088911\t.\t4220000\t4270000\t'..b'0\t31,120,180\n+chr3R\t22605000\t22695000\tID_0.01_1354\t-0.011252\t.\t22605000\t22695000\t51,160,44\n+chr3R\t22695000\t22780000\tID_0.01_1355\t-0.089033\t.\t22695000\t22780000\t31,120,180\n+chr3R\t22780000\t22885000\tID_0.01_1356\t-0.04050025\t.\t22780000\t22885000\t51,160,44\n+chr3R\t22885000\t22985000\tID_0.01_1357\t-0.05683475\t.\t22885000\t22985000\t31,120,180\n+chr3R\t22985000\t23110000\tID_0.01_1358\t-0.0237815\t.\t22985000\t23110000\t51,160,44\n+chr3R\t23110000\t23185000\tID_0.01_1359\t-0.100625\t.\t23110000\t23185000\t31,120,180\n+chr3R\t23185000\t23195000\tID_0.01_1360\t-0.00294725\t.\t23185000\t23195000\t51,160,44\n+chr3R\t23195000\t23415000\tID_0.01_1361\t-0.00275775\t.\t23195000\t23415000\t31,120,180\n+chr3R\t23415000\t23560000\tID_0.01_1362\t-0.090027\t.\t23415000\t23560000\t51,160,44\n+chr3R\t23560000\t23770000\tID_0.01_1363\t-0.104602\t.\t23560000\t23770000\t31,120,180\n+chr3R\t23770000\t23815000\tID_0.01_1364\t-0.1119105\t.\t23770000\t23815000\t51,160,44\n+chr3R\t23815000\t23920000\tID_0.01_1365\t-0.0660765\t.\t23815000\t23920000\t31,120,180\n+chr3R\t23920000\t24030000\tID_0.01_1366\t-0.04218475\t.\t23920000\t24030000\t51,160,44\n+chr3R\t24030000\t24160000\tID_0.01_1367\t-0.05579575\t.\t24030000\t24160000\t31,120,180\n+chr3R\t24160000\t24205000\tID_0.01_1368\t-0.01546725\t.\t24160000\t24205000\t51,160,44\n+chr3R\t24205000\t24345000\tID_0.01_1369\t-0.0326015\t.\t24205000\t24345000\t31,120,180\n+chr3R\t24345000\t24375000\tID_0.01_1370\t-0.0623065\t.\t24345000\t24375000\t51,160,44\n+chr3R\t24375000\t24450000\tID_0.01_1371\t-0.0749395\t.\t24375000\t24450000\t31,120,180\n+chr3R\t24450000\t24625000\tID_0.01_1372\t-0.09836075\t.\t24450000\t24625000\t51,160,44\n+chr3R\t24625000\t24745000\tID_0.01_1373\t-0.03171375\t.\t24625000\t24745000\t31,120,180\n+chr3R\t24745000\t24885000\tID_0.01_1374\t-0.08589625\t.\t24745000\t24885000\t51,160,44\n+chr3R\t24885000\t24995000\tID_0.01_1375\t-0.09323725\t.\t24885000\t24995000\t31,120,180\n+chr3R\t24995000\t25090000\tID_0.01_1376\t-0.0589785\t.\t24995000\t25090000\t51,160,44\n+chr3R\t25090000\t25165000\tID_0.01_1377\t0.03674225\t.\t25090000\t25165000\t31,120,180\n+chr3R\t25165000\t25330000\tID_0.01_1378\t-0.0462465\t.\t25165000\t25330000\t51,160,44\n+chr3R\t25330000\t25405000\tID_0.01_1379\t-0.08303325\t.\t25330000\t25405000\t31,120,180\n+chr3R\t25405000\t25570000\tID_0.01_1380\t-0.00546225\t.\t25405000\t25570000\t51,160,44\n+chr3R\t25570000\t25580000\tID_0.01_1381\t-0.04654075\t.\t25570000\t25580000\t31,120,180\n+chr3R\t25580000\t25730000\tID_0.01_1382\t-0.01871575\t.\t25580000\t25730000\t51,160,44\n+chr3R\t25730000\t25880000\tID_0.01_1383\t-0.00858875\t.\t25730000\t25880000\t31,120,180\n+chr3R\t25880000\t25990000\tID_0.01_1384\t-0.10581625\t.\t25880000\t25990000\t51,160,44\n+chr3R\t25990000\t26050000\tID_0.01_1385\t-0.090403\t.\t25990000\t26050000\t31,120,180\n+chr3R\t26050000\t26180000\tID_0.01_1386\t-0.0935315\t.\t26050000\t26180000\t51,160,44\n+chr3R\t26180000\t26275000\tID_0.01_1387\t-0.11469275\t.\t26180000\t26275000\t31,120,180\n+chr3R\t26275000\t26330000\tID_0.01_1388\t-0.1002735\t.\t26275000\t26330000\t51,160,44\n+chr3R\t26330000\t26490000\tID_0.01_1389\t-0.092304\t.\t26330000\t26490000\t31,120,180\n+chr3R\t26490000\t26565000\tID_0.01_1390\t0.0627965\t.\t26490000\t26565000\t51,160,44\n+chr3R\t26565000\t26640000\tID_0.01_1391\t-0.01974475\t.\t26565000\t26640000\t31,120,180\n+chr3R\t26640000\t26715000\tID_0.01_1392\t-0.07430725\t.\t26640000\t26715000\t51,160,44\n+chr3R\t26715000\t26870000\tID_0.01_1393\t-0.049789\t.\t26715000\t26870000\t31,120,180\n+chr3R\t26870000\t27045000\tID_0.01_1394\t-0.0249905\t.\t26870000\t27045000\t51,160,44\n+chr3R\t27045000\t27155000\tID_0.01_1395\t-0.074189\t.\t27045000\t27155000\t31,120,180\n+chr3R\t27155000\t27185000\tID_0.01_1396\t-0.00609925\t.\t27155000\t27185000\t51,160,44\n+chr3R\t27185000\t27250000\tID_0.01_1397\t-0.01281025\t.\t27185000\t27250000\t31,120,180\n+chr3R\t27250000\t27385000\tID_0.01_1398\t-0.04990275\t.\t27250000\t27385000\t51,160,44\n+chr3R\t27385000\t27420000\tID_0.01_1399\t-0.041305\t.\t27385000\t27420000\t31,120,180\n+chr3R\t27420000\t27570000\tID_0.01_1400\t-0.0499295\t.\t27420000\t27570000\t51,160,44\n+chr3R\t27570000\t27700000\tID_0.01_1401\t-0.08094325\t.\t27570000\t27700000\t31,120,180\n+chr3R\t27700000\t27750000\tID_0.01_1402\t-0.01535\t.\t27700000\t27750000\t51,160,44\n+chr3R\t27750000\t27770000\tID_0.01_1403\t0.01357725\t.\t27750000\t27770000\t31,120,180\n'

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

diff -r 1e0d8c6b3483 -r ecf11dda45f7 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 11:10:27 2017 -0400

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_zscore_matrix.h5

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/hicBuildMatrix_result1.h5

Binary file test-data/hicBuildMatrix_result1.h5 has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/hicMergeMatrixBins_result1.npz.h5

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

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/hicPlotDistVsCounts_result1_.png

Binary file test-data/hicPlotDistVsCounts_result1_.png has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/hicPlotMatrix_result1.svg
--- a/test-data/hicPlotMatrix_result1.svg Mon Apr 03 07:06:43 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,591 +0,0 @@\n-<?xml version="1.0" encoding="utf-8" standalone="no"?>\n-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"\n- "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">\n-\n-<svg height="432pt" version="1.1" viewBox="0 0 504 432" width="504pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">\n- <defs>\n- <style type="text/css">\n-*{stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:100000;}\n- </style>\n- </defs>\n- <g id="figure_1">\n- <g id="patch_1">\n- <path d="M 0 432 \n-L 504 432 \n-L 504 0 \n-L 0 0 \n-z\n-" style="fill:#ffffff;"/>\n- </g>\n- <g id="axes_1">\n- <g id="patch_2">\n- <path d="M 65.52 381.6 \n-L 368.27122 381.6 \n-L 368.27122 21.6 \n-L 65.52 21.6 \n-z\n-" style="fill:#ffffff;"/>\n- </g>\n- <image height="360.0" id="imageecf3b4cfd0" width="302.0" x="66.0" xlink:href="data:image/png;base64,\n-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'..b' \n- <g transform="translate(386.32 302.409660814)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-35"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_8">\n- <g id="line2d_20">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="263.566910348"/>\n- </g>\n- </g>\n- <g id="text_14">\n- \n- <g transform="translate(386.32 266.878160348)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-31"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_9">\n- <g id="line2d_21">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="228.035409882"/>\n- </g>\n- </g>\n- <g id="text_15">\n- \n- <g transform="translate(386.32 231.346659882)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-32"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_10">\n- <g id="line2d_22">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="181.065321162"/>\n- </g>\n- </g>\n- <g id="text_16">\n- \n- <g transform="translate(386.32 184.376571162)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-35"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_11">\n- <g id="line2d_23">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="145.533820696"/>\n- </g>\n- </g>\n- <g id="text_17">\n- \n- <g transform="translate(386.32 148.845070696)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-31"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- <use x="127.24609375" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_12">\n- <g id="line2d_24">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="110.00232023"/>\n- </g>\n- </g>\n- <g id="text_18">\n- \n- <g transform="translate(386.32 113.31357023)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-32"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- <use x="127.24609375" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_13">\n- <g id="line2d_25">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="63.0322315098"/>\n- </g>\n- </g>\n- <g id="text_19">\n- \n- <g transform="translate(386.32 66.3434815098)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-35"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- <use x="127.24609375" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- <g id="ytick_14">\n- <g id="line2d_26">\n- <g>\n- <use style="stroke:#000000;stroke-width:0.5;" x="382.32" xlink:href="#m2c7b8366e1" y="27.5007310436"/>\n- </g>\n- </g>\n- <g id="text_20">\n- \n- <g transform="translate(386.32 30.8119810436)scale(0.12 -0.12)">\n- <use xlink:href="#BitstreamVeraSans-Roman-31"/>\n- <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- <use x="127.24609375" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- <use x="190.869140625" xlink:href="#BitstreamVeraSans-Roman-30"/>\n- </g>\n- </g>\n- </g>\n- </g>\n- </g>\n- </g>\n- <defs>\n- <clipPath id="p858d1c6223">\n- <rect height="360.0" width="7.5687804878" x="374.751219512" y="21.6"/>\n- </clipPath>\n- </defs>\n-</svg>\n'

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/master_TADs_plot.png

Binary file test-data/master_TADs_plot.png has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/master_matrix_plot.png

Binary file test-data/master_matrix_plot.png has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/small_test_matrix.h5

Binary file test-data/small_test_matrix.h5 has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/small_test_matrix_result.bam

Binary file test-data/small_test_matrix_result.bam has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/small_test_matrix_result_sorted.bam

Binary file test-data/small_test_matrix_result_sorted.bam has changed

diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/tadScoreFile.tabular_zscore_matrix.h5

Binary file test-data/tadScoreFile.tabular_zscore_matrix.h5 has changed