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Changeset 0:1c2e79e9311a (2020-01-23)

Next changeset 1:68648299ffc4 (2020-03-10)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"

diff -r 000000000000 -r 1c2e79e9311a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jan 23 16:04:57 2020 -0500

[

b'@@ -0,0 +1,175 @@\n+<macros>\n+ <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n+ <token name="@WRAPPER_VERSION@">1</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">schicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+ <xml name=\'matrix_mcooler_macro\'>\n+ <param name=\'matrix_mcooler\' type="data" format="mcool"\n+ label="Matrix to compute on"/>\n+ </xml>\n+ <xml name=\'matrix_cooler_multiple_macro\'>\n+ <param name=\'matrix_cooler_multiple\' type="data" format="cool"\n+ label="Matricies to compute on" multiple="true"/>\n+ </xml>\n+ <token name="@ESCAPE_IDENTIFIER_FASTQ@"><![CDATA[re.sub(\'[^\\s\\w\\.]\', \'_\', str($fastq.element_identifier))]]></token>\n+ <token name="@ESCAPE_IDENTIFIER_MCOOL@"><![CDATA[re.sub(\'[^\\s\\w\\.]\', \'_\', str($matrix_mcooler.element_identifier))]]></token>\n+ <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub(\'[^\\s\\w\\-\\.]\', \'_\', str($m.element_identifier))]]></token>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">https://github.com/joachimwolff/scHiCExplorer</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option va'..b'lue="Oranges_r">Oranges reversed</option>\n+ <option value="Greens_r">Greens reversed</option>\n+ <option value="Blues_r">Blues reversed</option>\n+ <option value="Greys_r">Greys reversed</option>\n+ <option value="Purples_r">Purples reversed</option>\n+ <option value="Paired_r">Paired reversed</option>\n+ <option value="Pastel1_r">Pastel1 reversed</option>\n+ <option value="Pastel2_r">Pastel2 reversed</option>\n+ <option value="spring_r">spring reversed</option>\n+ <option value="summer_r">summer reversed</option>\n+ <option value="autumn_r">autumn reversed</option>\n+ <option value="winter_r">winter reversed</option>\n+ <option value="hot_r">hot reversed</option>\n+ <option value="coolwarm_r">coolwarm reversed</option>\n+ <option value="cool_r">cool reversed</option>\n+ <option value="seismic_r">seismic reversed</option>\n+ <option value="terrain_r">terrain reversed</option>\n+ <option value="ocean_r">ocean reversed</option>\n+ <option value="rainbow_r">rainbow reversed</option>\n+ <option value="bone_r">bone reversed</option>\n+ <option value="flag_r">flag reversed</option>\n+ <option value="prism_r">prism reversed</option>\n+ <option value="cubehelix_r">cubehelix reversed</option>\n+ <option value="binary_r">binary reversed</option>\n+ <option value="pink_r">pink reversed</option>\n+ <option value="gray_r">gray reversed</option>\n+ <option value="copper_r">copper reversed</option>\n+ <option value="BrBG_r">BrBG reversed</option>\n+ <option value="BuGn_r">BuGn reversed</option>\n+ <option value="BuPu_r">BuPu reversed</option>\n+ <option value="GnBu_r">GnBu reversed</option>\n+ <option value="OrRd_r">OrRd reversed</option>\n+ <option value="PiYG_r">PiYG reversed</option>\n+ <option value="PRGn_r">PRGn reversed</option>\n+ <option value="PuOr_r">PuOr reversed</option>\n+ <option value="PuRd_r">PuRd reversed</option>\n+ <option value="PuBu_r">PuBu reversed</option>\n+ <option value="RdBu_r">RdBu reversed</option>\n+ <option value="RdGy_r">RdGy reversed</option>\n+ <option value="RdPu_r">RdPu reversed</option>\n+ <option value="YlGn_r">YlGn reversed</option>\n+ <option value="PuBuGn_r">PuBuGn reversed</option>\n+ <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>\n+ <option value="RdYlGn_r">RdYlGn reversed</option>\n+ <option value="YlGnBu_r">YlGnBu reversed</option>\n+ <option value="YlOrBr_r">YlOrBr reversed</option>\n+ <option value="YlOrRd_r">YlOrRd reversed</option>\n+ <option value="gist_gray_r">gist_gray reversed</option>\n+ <option value="gist_stern_r">gist_stern reversed</option>\n+ <option value="gist_earth_r">gist_earth reversed</option>\n+ <option value="gist_yarg_r">gist_yarg reversed</option>\n+ <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ <option value="plasma_r">plasma reversed</option>\n+ </param>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 1c2e79e9311a scHicClusterMinHash.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicClusterMinHash.xml Thu Jan 23 16:04:57 2020 -0500

[

@@ -0,0 +1,106 @@
+<tool id="schicexplorer_schicclusterminhash" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>clusters single-cell Hi-C interaction matrices with MinHash dimension reduction</description>
+    <macros>
+        <token name="@BINARY@">scHicClusterMinHash</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix '$matrix_mcooler'
+
+        --numberOfClusters $numberOfClusters
+
+        --clusterMethod $clusterMethod_selector
+        --numberOfHashFunctions $numberOfHashFunctions
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+
+        #if $exactModeMinhash:
+            $exactModeMinhash
+        #end if
+
+        --outFileName cluster_list.txt
+
+        --threads @THREADS@
+
+
+
+    ]]></command>
+    <inputs>
+
+        <expand macro="matrix_mcooler_macro"/>
+        <param name="clusterMethod_selector" type="select" label="Cluster method:">
+                <option value="kmeans" selected="True">K-means</option>
+                <option value="spectral" >Spectral clustering</option>
+        </param>
+
+        <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />
+        <param name="numberOfHashFunctions" type="integer" value="800"  label="Number of hash functions" help='How many hash functions the minHash algorithm uses.' />
+
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+        <param name='exactModeMinhash' type='boolean' truevalue='--exactModeMinHash' label='The MinHash algorithm computes additional the exact euclidean distance.'/>
+
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <param name='numberOfHashFunctions' value='800' />
+
+            <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='spectral' />
+            <param name='numberOfClusters' value='3' />
+            <param name='numberOfHashFunctions' value='800' />
+
+            <output name="outFileName" file="scHicClusterMinHash/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <param name='numberOfHashFunctions' value='800' />
+            <param name='exactModeMinhash' value='true' />
+
+            <output name="outFileName" file="scHicClusterMinHash/cluster_kmeans_exact.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='spectral' />
+            <param name='numberOfClusters' value='3' />
+            <param name='numberOfHashFunctions' value='800' />
+            <param name='chromosomes' value='chr1 chr2' />
+
+
+            <output name="outFileName" file="scHicClusterMinHash/cluster_spectral_chromosomes.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+
+
+    </tests>
+    <help><![CDATA[
+
+Clustering with dimension reduction via MinHash
+===============================================
+
+scHicClusterMinHash uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle.
+The clustering is applied on dimension reduced data based on an approximate kNN search with the local sensitive hashing technique MinHash. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * samples.
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results,
+can be faster or less memory demanding.
+
+For more information about scHiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://schicexplorer.readthedocs.io/
+]]></help>
+    <expand macro="citations" />
+
+</tool>

diff -r 000000000000 -r 1c2e79e9311a static/images/clusters_svl_spectral.png

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diff -r 000000000000 -r 1c2e79e9311a static/images/consensus_svl_spectral.png

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diff -r 000000000000 -r 1c2e79e9311a static/images/density.png

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diff -r 000000000000 -r 1c2e79e9311a static/images/read_coverage.png

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diff -r 000000000000 -r 1c2e79e9311a test-data/scHicCluster/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicCluster/cluster_kmeans.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
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+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 1

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicCluster/cluster_kmeans_chromosomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicCluster/cluster_kmeans_chromosomes.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
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+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 0
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+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 0
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+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 1
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 1
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 1

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicCluster/cluster_spectral_knn.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicCluster/cluster_spectral_knn.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 1
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 0
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 0
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+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 0
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+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicCluster/cluster_spectral_pca.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicCluster/cluster_spectral_pca.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,19 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 0
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 0
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 0
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+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 0
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+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 0
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+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterCompartments/cluster_kmeans.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 1
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 1
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 2
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 2
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 0
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 2
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 1
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+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 1
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 1

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
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+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 3
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 4

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/cluster_spectral.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterCompartments/cluster_spectral.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 0
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 0
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 2
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 2
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 1
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 2
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 0
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 1
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 1
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 1
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 1
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 1
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 1
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 1

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/mm9_H3K36me3.bed.gz

Binary file test-data/scHicClusterCompartments/mm9_H3K36me3.bed.gz has changed

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterCompartments/mm9_gene.bed.gz

Binary file test-data/scHicClusterCompartments/mm9_gene.bed.gz has changed

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterMinHash/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterMinHash/cluster_kmeans.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 1
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 1
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 0
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 1
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 1
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterMinHash/cluster_kmeans_exact.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterMinHash/cluster_kmeans_exact.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 1
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 2
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 2
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 2
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 2
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 2
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 2
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 2
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterMinHash/cluster_spectral.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterMinHash/cluster_spectral.txt Thu Jan 23 16:04:57 2020 -0500

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterMinHash/cluster_spectral_chromosomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterMinHash/cluster_spectral_chromosomes.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 0
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 0
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 1
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 1
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 1
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 2

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterSVL/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterSVL/cluster_kmeans.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 1
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 1
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 0
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 1
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 1
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 2
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 0
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 1
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 1
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 0

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicClusterSVL/cluster_spectral.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicClusterSVL/cluster_spectral.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,20 @@
+/Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz 0
+/Diploid_1_CGTACTAG_ACTGCATA_R1fastqgz 2
+/Diploid_1_CGTACTAG_CGTCTAAT_R1fastqgz 2
+/Diploid_1_CGTACTAG_CTAAGCCT_R1fastqgz 2
+/Diploid_1_CGTACTAG_CTCTCTAT_R1fastqgz 0
+/Diploid_1_CGTACTAG_GTAAGGAG_R1fastqgz 2
+/Diploid_1_CGTACTAG_TATCCTCT_R1fastqgz 1
+/Diploid_1_CGTACTAG_TCTCTCCG_R1fastqgz 1
+/Diploid_1_TAAGGCGA_AAGGAGTA_R1fastqgz 2
+/Diploid_1_TAAGGCGA_CGTCTAAT_R1fastqgz 0
+/Diploid_1_TAAGGCGA_CTAAGCCT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_AAGGAGTA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_ACTGCATA_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CGTCTAAT_R1fastqgz 0
+/Diploid_2_AAGAGGCA_CTAAGCCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_CTCTCTAT_R1fastqgz 1
+/Diploid_2_AAGAGGCA_GTAAGGAG_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TATCCTCT_R1fastqgz 2
+/Diploid_2_AAGAGGCA_TCTCTCCG_R1fastqgz 0
+/Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz 1

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicConsensusMatrices/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicConsensusMatrices/cluster_kmeans.txt Thu Jan 23 16:04:57 2020 -0500

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicConsensusMatrices/consensus_matrix.mcool

Binary file test-data/scHicConsensusMatrices/consensus_matrix.mcool has changed

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicDemultiplex/GSE94489_README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicDemultiplex/GSE94489_README.txt Thu Jan 23 16:04:57 2020 -0500

b'@@ -0,0 +1,5933 @@\n+GEO_Sample_ID\tLane\tFive_prime_barcode\tThree_prime_barcode\tName\tNature_Reference_ID\r\n+Diploid_1_6\t3897\tCGTACTAG\tAAGGAGTA\t1CDS1-1\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tACTGCATA\t1CDS1-2\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tCGTCTAAT\t1CDS1-3\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tCTAAGCCT\t1CDS1-4\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tCTCTCTAT\t1CDS1-5\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tGTAAGGAG\t1CDS1-6\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tTATCCTCT\t1CDS1-7\tDiploid_1\r\n+Diploid_1_6\t3897\tCGTACTAG\tTCTCTCCG\t1CDS1-8\tDiploid_1\r\n+Diploid_1_6\t3897\tTAAGGCGA\tAAGGAGTA\t1CDS1-9\tDiploid_1\r\n+Diploid_1_6\t3897\tTAAGGCGA\tCGTCTAAT\t1CDS1-11\tDiploid_1\r\n+Diploid_1_6\t3897\tTAAGGCGA\tCTAAGCCT\t1CDS1-12\tDiploid_1\r\n+Diploid_1_6\t3897\tTAAGGCGA\tCTCTCTAT\t1CDS2-9\tDiploid_6\r\n+Diploid_1_6\t3897\tTAAGGCGA\tGTAAGGAG\t1CDS2-10\tDiploid_6\r\n+Diploid_1_6\t3897\tTAAGGCGA\tTATCCTCT\t1CDS2-11\tDiploid_6\r\n+Diploid_1_6\t3897\tTAAGGCGA\tTCTCTCCG\t1CDS2-12\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tAAGGAGTA\t1CDS2-1\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tACTGCATA\t1CDS2-2\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tCGTCTAAT\t1CDS2-3\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tCTAAGCCT\t1CDS2-4\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tCTCTCTAT\t1CDS2-5\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tGTAAGGAG\t1CDS2-6\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tTATCCTCT\t1CDS2-7\tDiploid_6\r\n+Diploid_1_6\t3897\tTCCTGAGC\tTCTCTCCG\t1CDS2-8\tDiploid_6\r\n+Diploid_11\t3070\tACTCGCTA\tAAGGCTAT\t1CDU-11\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tCCTAGAGT\t1CDU-12\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tCTATTAAG\t1CDU-13\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tGAGCCTTA\t1CDU-14\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tGCGTAAGA\t1CDU-15\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tTCGACTAG\t1CDU-16\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tTTATGCGA\t1CDU-17\tDiploid_11\r\n+Diploid_11\t3070\tACTCGCTA\tTTCTAGCT\t1CDU-18\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tAAGGCTAT\t1CDU-21\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tCCTAGAGT\t1CDU-22\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tCTATTAAG\t1CDU-23\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tGAGCCTTA\t1CDU-24\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tGCGTAAGA\t1CDU-25\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tTCGACTAG\t1CDU-26\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tTTATGCGA\t1CDU-27\tDiploid_11\r\n+Diploid_11\t3070\tACTGAGCG\tTTCTAGCT\t1CDU-28\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tAAGGCTAT\t1CDU-31\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tCCTAGAGT\t1CDU-32\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tCTATTAAG\t1CDU-33\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tGCGTAAGA\t1CDU-35\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tTCGACTAG\t1CDU-36\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tTTATGCGA\t1CDU-37\tDiploid_11\r\n+Diploid_11\t3070\tATGCGCAG\tTTCTAGCT\t1CDU-38\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tAAGGCTAT\t1CDU-41\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tCCTAGAGT\t1CDU-42\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tCTATTAAG\t1CDU-43\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tGAGCCTTA\t1CDU-44\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tTCGACTAG\t1CDU-46\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tTTATGCGA\t1CDU-47\tDiploid_11\r\n+Diploid_11\t3070\tCCTAAGAC\tTTCTAGCT\t1CDU-48\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tCCTAGAGT\t1CDU-52\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tCTATTAAG\t1CDU-53\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tGAGCCTTA\t1CDU-54\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tGCGTAAGA\t1CDU-55\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tTCGACTAG\t1CDU-56\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tTTATGCGA\t1CDU-57\tDiploid_11\r\n+Diploid_11\t3070\tCGATCAGT\tTTCTAGCT\t1CDU-58\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tAAGGCTAT\t1CDU-61\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tCCTAGAGT\t1CDU-62\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tCTATTAAG\t1CDU-63\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tGAGCCTTA\t1CDU-64\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tGCGTAAGA\t1CDU-65\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tTCGACTAG\t1CDU-66\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tTTATGCGA\t1CDU-67\tDiploid_11\r\n+Diploid_11\t3070\tCGGAGCCT\tTTCTAGCT\t1CDU-68\tDiploid_11\r\n+Diploid_11\t3070\tCGTACTAG\tAAGGAGTA\t1CDU-1\tDiploid_11\r\n+Diploid_11\t3070\tCGTACTAG\tACTGCATA\t1CDU-2\tDiploid_11\r\n+Diploid_11\t3070\tCGTACTAG\tCTAAGCCT\t1CDU-4\t'..b'ploid_31\r\n+Diploid_30_31\t5423\tTACGCTGC\tGCGTAAGA\t1CDES_Idx-p6D5\tDiploid_31\r\n+Diploid_30_31\t5423\tTACGCTGC\tCTATTAAG\t1CDES_Idx-p6E5\tDiploid_31\r\n+Diploid_30_31\t5423\tTACGCTGC\tAAGGCTAT\t1CDES_Idx-p6F5\tDiploid_31\r\n+Diploid_30_31\t5423\tTACGCTGC\tGAGCCTTA\t1CDES_Idx-p6G5\tDiploid_31\r\n+Diploid_30_31\t5423\tTACGCTGC\tTTATGCGA\t1CDES_Idx-p6H5\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tTCGACTAG\t1CDES_Idx-p6A6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tTTCTAGCT\t1CDES_Idx-p6B6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tCCTAGAGT\t1CDES_Idx-p6C6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tGCGTAAGA\t1CDES_Idx-p6D6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tCTATTAAG\t1CDES_Idx-p6E6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tAAGGCTAT\t1CDES_Idx-p6F6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tGAGCCTTA\t1CDES_Idx-p6G6\tDiploid_31\r\n+Diploid_30_31\t5423\tATGCGCAG\tTTATGCGA\t1CDES_Idx-p6H6\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tTCGACTAG\t1CDES_Idx-p6A7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tTTCTAGCT\t1CDES_Idx-p6B7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tCCTAGAGT\t1CDES_Idx-p6C7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tGCGTAAGA\t1CDES_Idx-p6D7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tCTATTAAG\t1CDES_Idx-p6E7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tAAGGCTAT\t1CDES_Idx-p6F7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tGAGCCTTA\t1CDES_Idx-p6G7\tDiploid_31\r\n+Diploid_30_31\t5423\tTAGCGCTC\tTTATGCGA\t1CDES_Idx-p6H7\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tTCGACTAG\t1CDES_Idx-p6A8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tTTCTAGCT\t1CDES_Idx-p6B8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tCCTAGAGT\t1CDES_Idx-p6C8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tGCGTAAGA\t1CDES_Idx-p6D8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tCTATTAAG\t1CDES_Idx-p6E8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tAAGGCTAT\t1CDES_Idx-p6F8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tGAGCCTTA\t1CDES_Idx-p6G8\tDiploid_31\r\n+Diploid_30_31\t5423\tACTGAGCG\tTTATGCGA\t1CDES_Idx-p6H8\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tTCGACTAG\t1CDES_Idx-p6A9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tTTCTAGCT\t1CDES_Idx-p6B9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tCCTAGAGT\t1CDES_Idx-p6C9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tGCGTAAGA\t1CDES_Idx-p6D9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tCTATTAAG\t1CDES_Idx-p6E9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tAAGGCTAT\t1CDES_Idx-p6F9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tGAGCCTTA\t1CDES_Idx-p6G9\tDiploid_31\r\n+Diploid_30_31\t5423\tCCTAAGAC\tTTATGCGA\t1CDES_Idx-p6H9\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tTCGACTAG\t1CDES_Idx-p6A10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tTTCTAGCT\t1CDES_Idx-p6B10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tCCTAGAGT\t1CDES_Idx-p6C10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tGCGTAAGA\t1CDES_Idx-p6D10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tCTATTAAG\t1CDES_Idx-p6E10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tAAGGCTAT\t1CDES_Idx-p6F10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tGAGCCTTA\t1CDES_Idx-p6G10\tDiploid_31\r\n+Diploid_30_31\t5423\tCGATCAGT\tTTATGCGA\t1CDES_Idx-p6H10\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tTCGACTAG\t1CDES_Idx-p6A11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tTTCTAGCT\t1CDES_Idx-p6B11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tCCTAGAGT\t1CDES_Idx-p6C11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tGCGTAAGA\t1CDES_Idx-p6D11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tCTATTAAG\t1CDES_Idx-p6E11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tAAGGCTAT\t1CDES_Idx-p6F11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tGAGCCTTA\t1CDES_Idx-p6G11\tDiploid_31\r\n+Diploid_30_31\t5423\tTGCAGCTA\tTTATGCGA\t1CDES_Idx-p6H11\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tTCGACTAG\t1CDES_Idx-p6A12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tTTCTAGCT\t1CDES_Idx-p6B12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tCCTAGAGT\t1CDES_Idx-p6C12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tGCGTAAGA\t1CDES_Idx-p6D12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tCTATTAAG\t1CDES_Idx-p6E12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tAAGGCTAT\t1CDES_Idx-p6F12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tGAGCCTTA\t1CDES_Idx-p6G12\tDiploid_31\r\n+Diploid_30_31\t5423\tTCGACGTC\tTTATGCGA\t1CDES_Idx-p6H12\tDiploid_31\r\n'

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diff -r 000000000000 -r 1c2e79e9311a test-data/scHicDemultiplex/samples.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicDemultiplex/samples.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,45 @@
+SRR5229019 GSM2476401 Diploid_11
+SRR5229021 GSM2476402 Diploid_12
+SRR5229023 GSM2476403 Diploid_13
+SRR5229025 GSM2476404 Diploid_15_16_17_18
+SRR5229027 GSM2476405 Diploid_1_6
+SRR5229029 GSM2476406 Diploid_19
+SRR5229031 GSM2476407 Diploid_20
+SRR5229033 GSM2476408 Diploid_2_14
+SRR5229035 GSM2476409 Diploid_21
+SRR5229037 GSM2476410 Diploid_22
+SRR5229039 GSM2476411 Diploid_23
+SRR5229041 GSM2476412 Diploid_24
+SRR5229043 GSM2476413 Diploid_25
+SRR5229045 GSM2476414 Diploid_26
+SRR5229047 GSM2476415 Diploid_3
+SRR5229049 GSM2476416 Diploid_4
+SRR5229051 GSM2476417 Diploid_5_10
+SRR5229053 GSM2476418 Diploid_7
+SRR5229055 GSM2476419 Diploid_8
+SRR5229057 GSM2476420 Diploid_9
+SRR5229059 GSM2476421 Haploid_10
+SRR5229061 GSM2476422 Haploid_11
+SRR5229063 GSM2476423 Haploid_12
+SRR5229065 GSM2476424 Haploid_13
+SRR5229067 GSM2476425 Haploid_14
+xx GSM2476426 Haploid_15
+SRR5229084 GSM2476427 Haploid_16
+SRR5229086 GSM2476428 Haploid_17
+SRR5229088 GSM2476429 Haploid_18
+SRR5229090 GSM2476430 Haploid_19
+xx GSM2476431 Haploid_1
+SRR5229103 GSM2476432 Haploid_20
+SRR5229105 GSM2476433 Haploid_2
+SRR5229107 GSM2476434 Haploid_3
+SRR5229111 GSM2476435 Haploid_4
+SRR5229113 GSM2476436 Haploid_5
+SRR5229115 GSM2476437 Haploid_6
+SRR5229117 GSM2476438 Haploid_7
+SRR5229119 GSM2476439 Haploid_8
+SRR5229121 GSM2476440 Haploid_9
+xxx GSM2598386 Diploid_27
+SRR5507552 GSM2598387 Diploid_28_29
+SRR5507553 GSM2598388 Diploid_30_31
+SRR5507554 GSM2598389 Diploid_32_33
+SRR5507555 GSM2598390 Diploid_34_35

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicInfo/matrices_info.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicInfo/matrices_info.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,18 @@
+Filename: test_matrix.mcool
+Contains 20 single-cell matrices
+The information stored via cooler.info of the first cell is:
+
+bin-size 1000000
+bin-type fixed
+creation-date 2019-05-16T11:46:31.826214
+format HDF5::Cooler
+format-url https://github.com/mirnylab/cooler
+format-version 3
+generated-by cooler-0.8.3
+genome-assembly unknown
+metadata {}
+nbins 2744
+nchroms 35
+nnz 55498
+storage-mode symmetric-upper
+sum 486056

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diff -r 000000000000 -r 1c2e79e9311a test-data/scHicPlotClusterProfiles/cluster_kmeans.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 1c2e79e9311a test-data/scHicQualityControl/qc_report.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicQualityControl/qc_report.txt Thu Jan 23 16:04:57 2020 -0500

@@ -0,0 +1,6 @@
+# QC report for single-cell Hi-C data generated by scHiCExplorer 1-dev
+scHi-C sample contained 20 cells:
+Number of removed matrices containing bad chromosomes 0
+Number of removed matrices due to low read coverage (< 100000): 8
+Number of removed matrices due to too many zero bins (< 0.001 density, within 30000000 relative genomic distance): 0
+12 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore.
\ No newline at end of file

diff -r 000000000000 -r 1c2e79e9311a test-data/scHicQualityControl/qc_report_chr1_chr2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/scHicQualityControl/qc_report_chr1_chr2.txt Thu Jan 23 16:04:57 2020 -0500

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